http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=Xwjessica RiceWiki - User contributions [en] 2026-05-27T03:08:56Z User contributions MediaWiki 1.30.0 https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181418 Os05g0112000 2014-06-08T15:05:54Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom&lt;ref name=&quot;ref1&quot; /&gt;.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana&lt;ref name=&quot;ref2&quot; /&gt;.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family&lt;ref name=&quot;ref3&quot; /&gt;. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development&lt;ref name=&quot;ref4&quot; /&gt;.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases&lt;ref name=&quot;ref5&quot; /&gt;. In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases&lt;ref name=&quot;ref6&quot; /&gt;.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance&lt;ref name=&quot;ref7&quot; /&gt;.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt;Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt;Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), &quot;green revolution&quot; rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref3&quot;&gt;Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice &quot;green revolution gene&quot; encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref4&quot;&gt;Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref5&quot;&gt;Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref6&quot;&gt;Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, ''Slr1-d'', in rice. Mol Genet Genomics 281: 223-231.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref7&quot;&gt;Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.&lt;/ref&gt;<br /> &lt;/references&gt;<br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181415 Os05g0112000 2014-06-08T15:02:43Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom&lt;ref name=&quot;ref1&quot;&gt;.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana&lt;ref name=&quot;ref2&quot;&gt;.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family&lt;ref name=&quot;ref3&quot;&gt;. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development&lt;ref name=&quot;ref4&quot;&gt;.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases&lt;ref name=&quot;ref5&quot;&gt;. In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases&lt;ref name=&quot;ref6&quot;&gt;.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance&lt;ref name=&quot;ref7&quot;&gt;.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt;Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt;Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), &quot;green revolution&quot; rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref3&quot;&gt;Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice &quot;green revolution gene&quot; encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref4&quot;&gt;Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref5&quot;&gt;Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref6&quot;&gt;Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, ''Slr1-d'', in rice. Mol Genet Genomics 281: 223-231.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref7&quot;&gt;Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.&lt;/ref&gt;<br /> &lt;/references&gt;<br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181394 Os05g0112000 2014-06-08T14:43:51Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.<br /> <br /> [[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]<br /> <br /> '' Phylogenetic analysis of the XB3 family.''<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt;Austin, M.J., Muskett, P., Kahn, K., Feys, B.J., Jones, J.D., and Parker, J.E. (2002). Regulatory role of SGT1 in early R gene-mediated<br /> plant defenses. Science 295, 2077–2080.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt;Liu, G.Z., Pi, L.-Y., Walker, J.C., Ronald, P.C., and Song, W.-Y.(2002b). Biochemical characterization of the kinase domain of the rice<br /> disease resistance receptor-like kinase XA21. J. Biol. Chem. 277, 20264–20269.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref3&quot;&gt;Park CJ, Peng Y, Chen X, Dardick C, Ruan D, et al. (2008) Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21- mediated innate immunity. PLoS Biol 6: e231.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref4&quot;&gt;Jiang Y, Chen X, Ding X, Wang Y, Chen Q, et al. (2012) The XA21 binding protein XB25 is required for maintaining XA21-mediated disease resistance. Plant J. doi: 10.1111/tpj.12076.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref5&quot;&gt;Nodzon LA, Xu WH, Wang Y, Pi LY, Chakrabarty PK, et al. (2004) The ubiquitin ligase XBAT32 regulates lateral root development in Arabidopsis. Plant J 40: 996–1006.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref6&quot;&gt;Goodin MM, Zaitlin D, Naidu RA, Lommel SA (2008) Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol Plant Microbe Interact 21: 1015–1026.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref7&quot;&gt;Xu, W.H., Wang, Y., Liu, G., Chen, X., Tinjuangjun, P., Pi, L.Y., Zhang, Y., and Song, W.Y. (2006). The autophosphorylated Ser686, Thr688<br /> and Ser689 residues within a putative protease cleavage motif in the juxtamembrane domain of XA21 are implicated in the stability control of the rice receptor-like kinase. Plant J. 45, 740–751.&lt;/ref&gt;<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181296 Os05g0112000 2014-06-08T13:51:35Z <p>Xwjessica: /* Evolution */</p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.<br /> <br /> [[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]<br /> <br /> '' Phylogenetic analysis of the XB3 family.''<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181240 Os05g0112000 2014-06-08T13:22:32Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181238 Os05g0112000 2014-06-08T13:20:37Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.[[File: Phylogenetic analysis of the XB3 family.png]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181237 Os05g0112000 2014-06-08T13:19:14Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.[[File:Figure 1. Phylogenetic analysis of the XB3 family]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181236 Os05g0112000 2014-06-08T13:18:50Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.[[File:Figure 1.. Phylogenetic analysis of the XB3 family]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181234 Os05g0112000 2014-06-08T13:18:17Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.[[File:Figure 1..Phylogenetic analysis of the XB3 family.jpg]]<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181232 Os05g0112000 2014-06-08T13:17:18Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome, there are two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development.<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro. ARC1 is positively involved in the self-incompatibility system . It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil. In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis. Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies. Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Figure_1._Phylogenetic_analysis_of_the_XB3_family.png&diff=181222 File:Figure 1. Phylogenetic analysis of the XB3 family.png 2014-06-08T13:13:01Z <p>Xwjessica: uploaded a new version of &amp;quot;File:Figure 1. Phylogenetic analysis of the XB3 family.png&amp;quot;</p> <hr /> <div></div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Figure_1.._Phylogenetic_analysis_of_the_XB3_family_.png&diff=181218 File:Figure 1.. Phylogenetic analysis of the XB3 family .png 2014-06-08T13:11:18Z <p>Xwjessica: The phylogenetic tree was generated by the neighbor-joining method. Accession numbers for the sequences are indicated. The functionally characterized XB3 family members in this study are boxed.</p> <hr /> <div>The phylogenetic tree was generated by the neighbor-joining method. Accession numbers for the sequences are indicated. The functionally characterized XB3 family members in this study are boxed.</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Figure_1._Phylogenetic_analysis_of_the_XB3_family.png&diff=181214 File:Figure 1. Phylogenetic analysis of the XB3 family.png 2014-06-08T13:09:20Z <p>Xwjessica: Blanked the page</p> <hr /> <div></div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Figure_1._Phylogenetic_analysis_of_the_XB3_family.png&diff=181213 File:Figure 1. Phylogenetic analysis of the XB3 family.png 2014-06-08T13:07:21Z <p>Xwjessica: The phylogenetic tree was generated by the neighbor-joining method. Accession numbers for the sequences are indicated. The functionally characterized XB3 family members in this study are boxed.</p> <hr /> <div>The phylogenetic tree was generated by the neighbor-joining method. Accession numbers for the sequences are indicated. The functionally characterized XB3 family members in this study are boxed.</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181190 Os05g0112000 2014-06-08T12:40:26Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome [26], [27], we identified two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development [28].<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases (X. Ding and W.-Y. Song, unpublished data). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro (Gu et al., 1998). ARC1 is positively involved in the self-incompatibility system (Stone et al., 1999). It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil (Stone et al., 2003). In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis (Kim et al., 2000; Lee et al., 2003). Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies (Song et al., 1995; Zhang et al., 1998; Xu et al., 2006). Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> *Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> *Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> *Department of Plant Pathology, University of California, Davis, California <br /> *Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> *Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> *Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181187 Os05g0112000 2014-06-08T12:38:43Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome [26], [27], we identified two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development [28].<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases (X. Ding and W.-Y. Song, unpublished data). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro (Gu et al., 1998). ARC1 is positively involved in the self-incompatibility system (Stone et al., 1999). It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil (Stone et al., 2003). In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis (Kim et al., 2000; Lee et al., 2003). Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies (Song et al., 1995; Zhang et al., 1998; Xu et al., 2006). Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> 1.Department of Plant Pathology, University of Florida, Gainesville, Florida <br /> 2.Department of Agronomy, Louisiana State University, Baton Rouge, Louisiana <br /> 3.Department of Plant Pathology, University of California, Davis, California <br /> 4.Department of Crop Science, North Carolina State University, Raleigh, North Carolina <br /> 5.Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida<br /> 6.Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181178 Os05g0112000 2014-06-08T12:30:04Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome [26], [27], we identified two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development [28].<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases (X. Ding and W.-Y. Song, unpublished data). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro (Gu et al., 1998). ARC1 is positively involved in the self-incompatibility system (Stone et al., 1999). It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil (Stone et al., 2003). In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis (Kim et al., 2000; Lee et al., 2003). Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies (Song et al., 1995; Zhang et al., 1998; Xu et al., 2006). Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> Please input related labs here.<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181177 Os05g0112000 2014-06-08T12:29:21Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> <br /> ===Expression===<br /> XB3 is a member of a highly conserved E3 ubiquitin ligase family. Overexpression of XB3 or other members of this E3 family from rice, Arabidopsis, and citrus induces a cell death response in N. benthamiana.<br /> <br /> ===Evolution===<br /> A total of 58 proteins were identified from diverse plant species ranging from rice and Arabidopsis (annual) to woody citrus (perennial). All of the identified sequences share similar ankyrin-RING structures. Phylogenetic analysis revealed that 34 out of the 58 identified proteins, including XB3, form a large group with two major subclades that differentiate sequences from dicotyledonous and monocotyledonous plants (Figure 1). This group of proteins was apparently more related to XB3, and therefore named the XB3 family. The copy number of the XB3 family members varies among plant species. For instance, rice contains three members, XB3, XBOS31 and XBOS37, whereas Arabidopsis carries only one, XBAT31. In the newly sequenced citrus genome [26], [27], we identified two XB3 family members, XBCT31 and XBCT32. The XB3 family is phylogenetically distinct from XBAT32, an ankyrin-RING protein that has been implicated in lateral root development [28].<br /> <br /> == Knowledge Extension ==<br /> The demonstration of the XA21–XB3 interaction in vivo may be generally important for understanding RLK complexes in rice and in other plants. In a large-scale yeast two-hybrid analysis, nine of 50 randomly chosen rice RLKs interact with four putative E3 ubiquitin ligases (X. Ding and W.-Y. Song, unpublished data). In Brassica napus, the PUB-ARM protein ARC1 interacts with the kinase domain of the S receptor kinase in the yeast two-hybrid system and in vitro (Gu et al., 1998). ARC1 is positively involved in the self-incompatibility system (Stone et al., 1999). It has been proposed that ARC1 promotes the ubiquitination and proteasomal degradation of compatibility factors in the pistil (Stone et al., 2003). In tobacco (Nicotiana tabacum), the Nt PUB4 protein is also a member of the PUB-ARM family. Yeast two-hybrid analysis has linked Nt PUB4 to the kinase domain of the chitinase-related RLK CHRK1 that may be involved in development and cytokinin homeostasis (Kim et al., 2000; Lee et al., 2003). Thus, many plant RLKs may interact with E3 ubiquitin ligases.<br /> When Xb3 is reduced, resistance to Xoo PR6 is compromised in the Xa21 lines. The compromised resistance can be attributed to a decrease in the level of the XA21 protein. The dosage effects have been suggested by several previous studies (Song et al., 1995; Zhang et al., 1998; Xu et al., 2006). Additionally, the heterozygous Xa21 plants generated by a cross between 4021-3 and TP309 are slightly less resistant than the homozygous plant 4021-3. Alternatively, but not mutually exclusive, the reduction of Xb3 may directly contribute to the compromised resistance as well. In this case, the XB3 level is a rate-limiting step for Xa21-mediated resistance.<br /> <br /> ==Labs working on this gene==<br /> Please input related labs here.<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0112000&diff=181152 Os05g0112000 2014-06-08T12:05:00Z <p>Xwjessica: </p> <hr /> <div>Os05g0107700, named as xb3, is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> The receptor kinase XA21 confers resistance to bacterial blight disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv. oryzae (Xoo).The XA21 binding protein 3 (XB3) is capable of inducing cell death when overexpressed in Nicotiana benthamiana. XB3 is a RING finger-containing E3 ubiquitin ligase that has been positively implicated in XA21-mediated resistance. Mutation abolishing the XB3 E3 activity also eliminates its ability to induce cell death. Phylogenetic analysis of XB3-related sequences suggests a family of proteins (XB3 family) with members from diverse plant species. Members of the XB3 family from rice, Arabidopsis and citrus all trigger a similar cell death response in Nicotiana benthamiana, suggesting an evolutionarily conserved role for these proteins in regulating programmed cell death in the plant kingdom.<br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Please input related labs here.<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os05g0112000|<br /> Description = Zinc finger, RING-type domain containing protein|<br /> Version = NM_001060984.1 GI:115461698 GeneID:4337598|<br /> Length = 3751 bp|<br /> Definition = Oryza sativa Japonica Group Os05g0112000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br /> AP = Chromosome 5:617592..621342|<br /> CDS = 618924..619328,619454..619715,620011..620118,620232..620372,620470..620591&lt;br&gt;,620682..620753,620918..620977,621079..621261|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008398:617592..621342<br /> source=RiceChromosome05<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatggcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatga&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATL YDRLSVLHIAAANGRIEVLSMFLDRGAPPDAVNRHKQTPLMLAAMHGKIDCVLKLLQA DANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTTPVADSWGFARFVNVRDDHGA TPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGNLDCIRKLLAW GADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALL EAALMEANREREKKILNGTKYSLPSPSPGDDSADDDACSEVSDTELCCICFDQACTIE VQDCGHQMCAPCTLALCCHNKPNPTTLTPPSPACPFCRGSISRLVVAQTRSACDPDKP SSLQLTRKRSRRSHNLSEGSSSFKGLPSAMGSFSKLGRGSSRMADSDSSNLDKPEHDL &lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2015..2419#1628..1889#1225..1332#971..1111#752..873#590..661#366..425#82..264#attctcactctcggccttccttccacggcagcgccacccactgcgccttcgccggcggcggaggaggagggaggtgcggccatgggtcacggtgtcagctgcgcccgcaccggcgacgagcacgacttcttccgggcggcgcagctcggcgacctcgacgccctggccgccctcctcgccgccgacccttccctcgctcgccgcgccaccctctacgaccgcctctccgtcctccacatcgccgccgccaatggccgcatcgaggtcgctcacctcactgcttcttcttcttcttcttccctcggtctccgggacttgcttgtctcaccctttctctcttgttttctttcttcttcttcttccaggtgctctccatgttcttggatcgcggggcgccgccggacgcggtgaatcggcacaagcaggtgcgagatccccaccaaaatctctcttcttttttgctactgtttttcgaattactagtatctgcttgaaaatatcatattttgattttgaatgaaaaagaaagatctcgtcttgtccttttgttttctcaccttgctttgctcttcttctgcttatgctgcagacgccgctgatgctcgcggccatgcacggcaagatcgactgcgtgctcaagctcctccaggccgacgcaaatgtgagagaaaagaactgcaaaatcagtatactgataatactgtagtaattctgtttgaaaaaatcagtaacagttacgatttcgcaccagatcttgatgttcgactcggtgcacgcgaggacctgcctccaccacgcggcgtactacggccacgtcgactgcctgcaggccatcctcgccgccgcgcagaccacgccggtggccgactcatggtgagatcatcctcatcctgtcgtgtggctttggtacagctatagaatagctctggatgtctctgtgagctcacttgctgctgtcgaagcttggcaggggtttcgcccggttcgtcaacgtcagggacgaccacggcgccactccgctgcatctcgcggccaggcaggggcggccggggtgcgtgcaggtgttgctggagaacggcgccattgtgtcggctttgacaggatcatatgggtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagcttccctggaagcacgtcgcttcatttggctgctcgtagcgggaacttggattgcatcaggaagctgcttgcctggggagctgatcggctccaaagggattcggctgggtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgttgaatttaggtgcttagtagaatccctgcagttcttagacagtagacctcagtctagcaagtagtaacaggtgaactcgctgaccatttgctgaattcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccaggagaattccctattctgttgcgctgaaacggaaccatggagcatgtgcagctttgctgaaccctacatcagcagagcccatggtgtggccatccccacttaagttcatcagtgagcttgaaccagaagctaaggctctcctggaagcagctctgatggaagccaacagggagagggagaagaaaatcctgaatggcacaaagtactccctgccatccccttcgcccggtgatgacagtgccgatgacgatgcatgctcagaggtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacaggtgagcgacacggagctttgctgcatctgcttcgaccaggcttgcaccattgaggtgcaagactgtggacatcaaatgtgtgcaccgtgcacgctggcactgtgctgtcacaacaaacccaatccgacgaccctgacaccgccctcaccggcctgcccattctgccggggcagcatctcacggctggtggtggcccaaacaaggtctgcttgtgatcctgacaagccgtcatccctgcagctcacccggaagcggtcgcgtcgatctcacaacctcagtgagggcagcagcagcttcaaagggctaccttcggccatgggctccttctcaaagcttggccgtggctcgagccgcatggcggacagtgacagcagcaacctggacaagcctgagcacgatctatgaaagcagaacaacgcacggacaatcgccgcatcatcctcaaaacatccgttggtatcagaaacccagatgaaaatccaatggctaatttggagcaactttgatccatggaaagttaaatagatagggactaaataagtagaaccctccactccccattgtctgtgtgcccaccctatttttcggcttgccgggttaagcttagcatatgcataggagctctgaaagaccagagagagagtgagtgagtgagtgagagcaattcatcatcaatcacacagtgagtgttggtgtggttaagggatgcatgcagcagagatgtgaaacggggttcatgttcgtcacctctaaagttagcctgccatggcatgtgagctctgcgccggcctgacccctcctcctctgtgtgatgaatcatgcccccatttttggcccttgtctcgtgttataatggtgcgagttcatgtcctggtgatgctgcagccatcagcagggtggtccattggatcgccatgaattcagcagctgcggtctctgcctatgtgatgacattgtatgtaccgtactccagtgtgtaccggttctttgaactgtggtggcgtgtcactgtctctgtcagtgccactgtccatcgtcgtccggctgttacagccggattgttactgctagtaattggcttccttcgttcgttcgtgatggcatcagcatcagattgtttcttttcttcaggctgataaaatgaagactgttgttgcctgtagctgtatggttgtccttgcgatctgtaccttctcttgtgctcctacctgcagtgatattgtgagatccaggagtagcataatttttctatcgacaaatcataccactacatttcacttggaaagatggacttagcatcataggtttaggtgagactgaggaccaactctgattaacactgaagtctgccgtgtggattgggtttagattgaaagaaattcatggagataacaagaatttttgtggcaaaagctttgttgttatgcagagtttaaggactaggagatgactatatgagacacaagccaagtgctactgtagtttgttttgaccaggacacagcacacaacttggaatttggaaaccttccaagtcatggctgcaattccacgtcaggcttggtgatcgacctagtagttcttttgcttcttgtgacgaactgacgataacacggacagatatttgtgaagctttggccattctatagtccatatgatcactcaagcaaaaaatatcttggtgccacacctcatcatgtgacagaaactaactaataatttcaaagtgcgattaatt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060984.1 RefSeq:Os05g0112000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 5]]<br /> [[Category:Chromosome 5]]</div> Xwjessica https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os11g47210&diff=181047 Os11g47210 2014-06-08T09:23:27Z <p>Xwjessica: Created page with &quot;''Os05g0107700'', named as ''xa5'', is a recessive gene associated with resistance to rice bacterial leaf blight. ==Annotated Information== ===Function=== Xa3/Xa26 mediates r...&quot;</p> <hr /> <div>''Os05g0107700'', named as ''xa5'', is a recessive gene associated with resistance to rice bacterial leaf blight.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Xa3/Xa26 mediates resistance to bacterial blight, a disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which is a significant agronomic problem in rice-growing regions.The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.). This family encodes leucine-rich repeat (LRR) receptor kinasetype proteins. Asian-cultivated rice consists of two major subspecies, indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica). <br /> <br /> <br /> <br /> ===Expression===<br /> The indica plants carrying Xa3/Xa26 were highly susceptible in four-leaf stage, but become resistant or moderately resistant to these Xoo races at booting stage. The development-controlled Xa3/Xa26 activity is also associated with its expression level (Cao et al. 2007).<br /> ===Evolution===<br /> The orthologs (alleles) of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza species O. officinalis (CC genome) and O. minuta (BBCC genome), respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91–99% sequence identity and 94–99% sequence similarity.<br /> <br /> == Knowledge Extension ==<br /> <br /> Xa3/Xa26 was first identified in the indica rice cultivar Minghui 63 and named Xa26. Further study revealed that Xa3, an R gene conferring resistance against Xoo, and Xa26 are actually the same gene and then it was renamed Xa3/Xa26. Xa3/Xa26 has been an important resistance gene for both indica and japonica rice production in China for a long time.<br /> <br /> <br /> ==Labs working on this gene==<br /> <br /> ==Structured Information==</div> Xwjessica