Os05g0112000 - Revision history

192.168.72.52: /* Structured Information */

2015-06-12T07:27:29Z

‎Structured Information

Xwjessica at 15:05, 8 June 2014

2014-06-08T15:05:54Z

Xwjessica at 15:02, 8 June 2014

2014-06-08T15:02:43Z

Xwjessica at 14:43, 8 June 2014

2014-06-08T14:43:51Z

Xwjessica: /* Evolution */

2014-06-08T13:51:35Z

‎Evolution

Xwjessica at 13:22, 8 June 2014

2014-06-08T13:22:32Z

Xwjessica at 13:20, 8 June 2014

2014-06-08T13:20:37Z

Xwjessica at 13:19, 8 June 2014

2014-06-08T13:19:14Z

Xwjessica at 13:18, 8 June 2014

2014-06-08T13:18:50Z

Xwjessica at 13:18, 8 June 2014

2014-06-08T13:18:17Z

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 </references>
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
-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<ref name="ref1">.
+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<ref name="ref1" />.
 ===Expression===
-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<ref name="ref2">.
+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<ref name="ref2" />.
 ===Evolution===
-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<ref name="ref3">. 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<ref name="ref4">.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]
+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<ref name="ref3" />. 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<ref name="ref4" />.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]
 == Knowledge Extension ==
-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<ref name="ref5">. 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<ref name="ref6">.
+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<ref name="ref5" />. 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<ref name="ref6" />.
-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<ref name="ref7">.
+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<ref name="ref7" />.
 ==Labs working on this gene==

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
-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.
+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<ref name="ref1">.
 ===Expression===
-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.
+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<ref name="ref2">.
 ===Evolution===
-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.
+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<ref name="ref3">. 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<ref name="ref4">.[[File:Figure 1.. Phylogenetic analysis of the XB3 family .png]]
 == Knowledge Extension ==
-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.
+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<ref name="ref5">. 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<ref name="ref6">.
-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.
+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<ref name="ref7">.
 ==Labs working on this gene==
@@ Line 29: / Line 25: @@
 ==References==
 <references>
-<ref name="ref1">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
+<ref name="ref1">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.</ref>
-plant defenses. Science 295, 2077–2080.</ref>
+<ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref>
-<ref name="ref2">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
+<ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.</ref>
-disease resistance receptor-like kinase XA21. J. Biol. Chem. 277, 20264–20269.</ref>
+<ref name="ref4">Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.</ref>
-<ref name="ref3">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.</ref>
+<ref name="ref5">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.</ref>
-<ref name="ref4">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.</ref>
+<ref name="ref6">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.</ref>
-<ref name="ref5">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.</ref>
+<ref name="ref7">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.</ref>
 </references>
 ==Structured Information==
 {{JaponicaGene|

@@ Line 28: / Line 28: @@
 ==References==
-Please input cited references here.
+<references>
 ==Structured Information==

@@ Line 9: / Line 9: @@
 ===Evolution===
-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]]
+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.
 == Knowledge Extension ==