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| | ==Annotated Information== | | ==Annotated Information== |
| | ===Function=== | | ===Function=== |
| − | It is a gene encoding RING-C2 type protein in rice, called OsRINGC2-2 located on chromosome 12. | + | It is a gene encoding RING-C2 type protein in rice, called OsRINGC2-2 located on chromosome 12 function as E3 ligases. |
| − | RING (Really Interesting New Gene) finger proteins are believed to play a critical role in mediating the transfer of ubiquitin to heterogeneous substrate(s). While the two canonical types, RING-H2 and RING-HC, have been well-characterized, the molecular functions of the modified types, particularly the RING-C2 types, remain elusive. We isolated two rice genes harboring the RING-C2 domain on the distal parts of rice chromosomes 11 and 12, termed OsRINGC2-1 and OsRINGC2-2, respectively. A comparison of sequence divergences between 10 duplicate pairs on the distal parts of rice chromosomes 11 and 12 and randomly selected duplicate pairs suggested that OsRINGC2-1 and OsRINGC2-2 have evolved in concert via gene conversion. An in vitro ubiquitination assay revealed that both proteins possess E3 ligase activity, suggesting that the innate functions of these RING domains have not been affected by their modifications during evolution. Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution. These results shed light on the molecular functions of OsRINGC2-1 and OsRINGC2-2 and provide insight into their molecular evolution.
| + | |
| | + | The sequences of both genes displayed highly significant identities of 99% (3271/3295) at the nucleotide level (data not shown). In particular, no differences between the two genes were found in both the 5′-and 3′-terminal sequences, indicating that gene-specific primer pairs cannot be designed to clone the full-length |
| | + | genes. We further examined the differences between the sequences, which are recognized by any restriction enzyme, and found that one single nucleotide polymorphism displayed a difference in recognition of the HindIII endonuclease (Fig. 1A). |
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| | + | [[File: liu-Os12g0102400-Fig1.jpg|right|thumb|200px|''Gene identification via enzyme digestion. A: Schematic diagram of the pBIN35S-RINGC2 constructs. Restriction enzyme sites are indicated. B: Restriction profiles of each genes..'']] |
| | + | |
| | ===Expression=== | | ===Expression=== |
| | It is a gene encoding RING-C2 type protein in rice. Two RING-C2 types are the modified types of canonical types RING-H2 and RING-HC. | | It is a gene encoding RING-C2 type protein in rice. Two RING-C2 types are the modified types of canonical types RING-H2 and RING-HC. |
| − | Some modified types of RINGs including RING-v, RING-D, RINGS/T, RING-G, and RING-C2 exist in various plant genomes. Interestingly, only two RING-C2 types exist in the rice genome, whereas 10 occur in Arabidopsis and 10 in apple, respectively. Functions of the modified RING domains remain largely unidentified | + | Some modified types of RINGs including RING-v, RING-D, RINGS/T, RING-G, and RING-C2 exist in various plant genomes. Interestingly, only two RING-C2 types exist in the rice genome, whereas 10 occur in Arabidopsis and 10 in apple, respectively. Functions of the modified RING domains remain largely unidentified. |
| | + | |
| | + | Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution. |
| | | | |
| | ===Evolution=== | | ===Evolution=== |
| − | Complete genome sequences and bioinformatics provide new insights into the evolutionary history of plant genomes. In particular, the Poaceae genome, which includes major food crops such as rice, wheat, corn, and sorghum, is believed to have undergone a pregrass whole-genome duplication event with a common ancestor 70–90 million years ago (Mya)(Paterson et al., 2009; Salse et al., 2008, 2009; | + | Complete genome sequences and bioinformatics provide new insights into the evolutionary history of plant genomes. In particular, the Poaceae genome, which includes major food crops such as rice, wheat, corn, and sorghum, is believed to have undergone a pregrass whole-genome duplication event with a common ancestor 70–90 million years ago (Mya)(Paterson et al., 2009; Salse et al., 2008, 2009; Wang et al., 2005) followed by independent gene loss during speciation. |
| − | Wang et al., 2005) followed by independent gene loss during speciation. | + | |
| | + | Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010). |
| | + | |
| | + | The finding that the distal regions of rice chromosomes 11 and 12 diverged 70–90 Mya and may have undergone frequent illegitimate recombination such as gene conversion raises the question regarding the evolutionary fate of OsRINGC2-1 and OsRINGC2-2 located on the distal parts of these chromosomes.We attempted to choose each of 10 OsRINGC2-1 and OsRINGC2-2 neighboring genes, respectively, and 100 randomly selected duplicate genes, which were generated by whole-genome duplication elsewhere in the genome. Strikingly low Ka, Ks, and dsm values were observed between duplicate genes (but not all) located on the distal parts of chromosomes 11 and 12 as compared to those of random sets (Fig 3). |
| | + | |
| | + | [[File: liu-Os12g0102400-Fig2.jpg|right|thumb|200px|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']] |
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| | + | [[File: liu-Os12g0102400-Fig3.jpg|right|thumb|200px|''Sequence divergence of duplicated genes pairs in upstream and downstream of Os11g01190 and Os12g01190.. (from reference <ref name="Jung" />).'']] |
| | | | |
| | ==Labs working on this gene== | | ==Labs working on this gene== |
| − | Please input related labs here.
| + | Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200‐713, Korea |
| | + | |
| | + | ==Reference== |
| | | | |
| | Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060 | | Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060 |
| | | | |
| − | ==Structured Information==
| + | Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380. |
| − | {{JaponicaGene|
| + | |
| − | GeneName = Os12g0102400|
| + | Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556. |
| − | Description = Zinc finger, RING-type domain containing protein|
| + | |
| − | Version = NM_001071769.1 GI:115486859 GeneID:4351244|
| + | Wang, X., et al., 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946. |
| − | Length = 6708 bp|
| |
| − | Definition = Oryza sativa Japonica Group Os12g0102400, complete gene.|
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| − | Source = Oryza sativa Japonica Group
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| | | | |
| − | ORGANISM Oryza sativa Japonica Group
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| − | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
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| − | Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
| |
| − | clade; Ehrhartoideae; Oryzeae; Oryza.
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| − | |
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| − | Chromosome = [[:category:Japonica Chromosome 12|Chromosome 12]]|
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| − | AP = Chromosome 12:104922..111629|
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| − | CDS = 105119..105120,105421..105520,105598..105725,105939..106101,106198..106310<br>,107026..107109,107193..107241,107331..107422,107680..107809<br>,107906..107982,108058..109676,110024..110221,110287..110825<br>|
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| − | GCID = <gbrowseImage1>
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| − | name=NC_008405:104922..111629
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| − | source=RiceChromosome12
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| − | preset=GeneLocation
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| − | </gbrowseImage1>|
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| − | GSID = <gbrowseImage2>
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| − | name=NC_008405:104922..111629
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| − | source=RiceChromosome12
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| − | preset=GeneLocation
| |
| − | </gbrowseImage2>|
| |
| − | CDNA = <cdnaseq>atgatgaccatgagcgacgatggagaccgcacctgcccgctctgtgctgaggacatggacatcactgaccagcagctcaagccctgcaaatgcggctatgagatttgtgtctggtgctggcaccacatcattgatatggctgagaaagaggacactgagggccgctgccccgcatgccgcactcgctatgacaaagataggattgtcaagatggctgccacttgtgacaggacggtagtggagaaaaatgtggacaagaaacagaagacccaaaaggtcaagtcaaaggccgcggtaactgtggaagctaagaaacatcttgctagcgtcagggttatccagagaaacctcgtgtacataattggactacctgcaaatttatgcaacgaaagcatacttgagcgcagggaatactttggtcagtatggcaaggttctgaaagtttcagtttctcggccgactggggctccttcccagcaggcaccaacaaacaacagtatcagcgtatatattacatatgccaaagaagaagaggccatcaggtgtattcaagctgtacacaattttgttttggaagggaaagtgttaagagcgtgctttggtactacaaagtattgccatgcatggctgcggaacatgacctgtggaaatccagattgtctctatttacatgatgtaggaagccaggaagatagtttcactaaagatgagataatctcagcatatacaaggagtagggttccccaaatggcgtctaatgtttctcaaagacgcgcagggactgtattacctcctccagcagaagatttctcatatagtgcagtggttgcagctaaacatccaatcaagaatggaataactaatactgcaaatcaatccaggctttcgcctccaaacagtagttctgggagatccacacttccaccagctgcttcatgggggcatcgcgatttgaataccaggacaacagcaactggggtggcatcgtcacaatctcttactaaatcaaaagcagatcctcaaagtaattcattctcgagttcttcgactgtttcaagtacaaaactaccttcttcatggaatgatgacacaagcacagttccgaaaatgacggaaggacgagatagtttgtctaaaaccttgaagccatataagcctggtattgcaaaggaaacccaagctgtaacatcactggagtcatcgcttgacatagacttctctaccataccttcagcttggaacgatgatgatgtcacatcagatggcatgtcaaaaggaagtgacgagaagcaggttgtaaatgacaatggaaagtttgaatgttcagtttcttcaaagccagctgaatcagggcatcttacatcgaagtcaacgacatcaccaaagaaagacatcgcagtaaacagtaccaggcaaagtcctctaaattgtgtatcaagtccatcggtttctaaatcagaagtaaaggatggtgatggtgattaccaagtaaccaacatggcttctaaaacatctactttggtaattagaaaggaccaatctaatcaagcagctattgacacagcaaccgaagatactagatctgagagcacggatattgataggctttctgttggagtatcttcagtaacattaagcagaaaagatggggttcaaagtattgccgaaaaccaacaaccggatgcaatcctaagtacttcagttgtggtgccctttagtcagaatttgaaacttgctgagtgtaatgattctacatgtcagcctagttcagataagcatcgtgattggtgttcagatatccagagtagtgtgtctcctcagttaaatgacatagaaagttatgcagtagccactgataaatctcatggtagagtgctggatgctgctgatcaagcttcgtcttcaccatatgtccatttccctaacactgctcctatttcactgtggaatggtaaagagattaaccatacatcaacaagtgatagaacttccacaatgatgcaacctgggctgttatcttcagttgacagcacttctaccatgttaaatggacatcaagaagggctagggactatatatgcacctggtaaggtttctgaacatcctagaatgaaaaaccatcagcctggagcagttggtgcagtgagaattgataacataggcagttttgacaaggctgtaagtgtaaataaggatgagagcagcataattgctgatattttgtctttggagtttgatccatgggatgagtcgtattcaacggctaacaattttgctaagatgcttagtgcatctgaaaagaacgatgtgctttttgatgcacgttcatggaaaacaaaaaccagcaatagtgagtctagattttcatttgctagacaagataatcaaggaagcctcctagattcatctatgagaaattataaaagtgagcagaatttcagtttgccatcccagaattctcatggaaacatttatcagagtggcattgcatttcaatctcctgaggaaggtttctcaaagagcaactctcttactatgttggatatgctagctaccggcacatcaaagcctaaagtatccgcgcctcctggattttcagcaccagcaagagttcctactgggttttcttctggattttcatcccatgaggggttgaatccacctccaggattttcatctcataatgggcctaatccccctcctggattttcttctcagggtgggtctaatcagatctatggttcggcatactcagaaactcgcccatttgatgatcttttgggtataaatactagccattatcaaccacagttagctagacaaacaagtgatatagaatttgttgatcctgctatattggctgtgggtaaagggcggatgcctggaataagtgattcagggttggagatgaaaacttcccatacttttccttcgcagttgcaaacatcaaatgatccaaggtttcaattacttatgcagcagaacatgccttcccatcaaaatgttggatttgcagaacatgttcaagatgcattcaaccctatgaatgataattatcttgcatcccgacttatacctcagaaccatggttctctatcctcttacacacagatgtcactccaacaacctagaagctcacatcttacaaatggtcattgggatggctggggtgatttgagacaagggaataatgtttccatgcctgacatgtcaaggatgttatatccaactgaagcaaacaacttccacatgctgggttcaaatgatctgtataacagagcttttggactgtga</cdnaseq>|
| |
| − | AA = <aaseq>MMTMSDDGDRTCPLCAEDMDITDQQLKPCKCGYEICVWCWHHII DMAEKEDTEGRCPACRTRYDKDRIVKMAATCDRTVVEKNVDKKQKTQKVKSKAAVTVE AKKHLASVRVIQRNLVYIIGLPANLCNESILERREYFGQYGKVLKVSVSRPTGAPSQQ APTNNSISVYITYAKEEEAIRCIQAVHNFVLEGKVLRACFGTTKYCHAWLRNMTCGNP DCLYLHDVGSQEDSFTKDEIISAYTRSRVPQMASNVSQRRAGTVLPPPAEDFSYSAVV AAKHPIKNGITNTANQSRLSPPNSSSGRSTLPPAASWGHRDLNTRTTATGVASSQSLT KSKADPQSNSFSSSSTVSSTKLPSSWNDDTSTVPKMTEGRDSLSKTLKPYKPGIAKET QAVTSLESSLDIDFSTIPSAWNDDDVTSDGMSKGSDEKQVVNDNGKFECSVSSKPAES GHLTSKSTTSPKKDIAVNSTRQSPLNCVSSPSVSKSEVKDGDGDYQVTNMASKTSTLV IRKDQSNQAAIDTATEDTRSESTDIDRLSVGVSSVTLSRKDGVQSIAENQQPDAILST SVVVPFSQNLKLAECNDSTCQPSSDKHRDWCSDIQSSVSPQLNDIESYAVATDKSHGR VLDAADQASSSPYVHFPNTAPISLWNGKEINHTSTSDRTSTMMQPGLLSSVDSTSTML NGHQEGLGTIYAPGKVSEHPRMKNHQPGAVGAVRIDNIGSFDKAVSVNKDESSIIADI LSLEFDPWDESYSTANNFAKMLSASEKNDVLFDARSWKTKTSNSESRFSFARQDNQGS LLDSSMRNYKSEQNFSLPSQNSHGNIYQSGIAFQSPEEGFSKSNSLTMLDMLATGTSK PKVSAPPGFSAPARVPTGFSSGFSSHEGLNPPPGFSSHNGPNPPPGFSSQGGSNQIYG SAYSETRPFDDLLGINTSHYQPQLARQTSDIEFVDPAILAVGKGRMPGISDSGLEMKT SHTFPSQLQTSNDPRFQLLMQQNMPSHQNVGFAEHVQDAFNPMNDNYLASRLIPQNHG SLSSYTQMSLQQPRSSHLTNGHWDGWGDLRQGNNVSMPDMSRMLYPTEANNFHMLGSN DLYNRAFGL</aaseq>|
| |
| − | DNA = <dnaseqindica>198..199#500..599#677..804#1018..1180#1277..1389#2105..2188#2272..2320#2410..2501#2759..2888#2985..3061#3137..4755#5103..5300#5366..5904#acgcgaacacgacgacaccagccagcaagcagcggaggagagagagagagagagagagactccatagacggccatcgatcgtacgcgactccccccatccatccatccacccgccggcgccccctccctctcatcgatcgatcgattcccaccgccgcccccgttttgaccacctacctagggtttcccccatcggaatgtgagtacttcaccctctctgatcccccccttttcttttctgattgttgctccaatccacttgggagcataatagactctttggattggatcctcgatttgaaggatcagcccctgcgcttgcccccccacccctcactttctcgtttattcgatttgatgataggaagcttctctctcttattagggattgattgattacaccgtgttactacagattgttattcccacaaacaaacaatctcatgtactactaataatattatctttcatgtctcctgccgctgaattgctcccgaaggatgaccatgagcgacgatggagaccgcacctgcccgctctgtgctgaggacatggacatcactgaccagcagctcaagccctgcaaatgcggctatgaggtttcttcccttccctccccaccactctactctccacaccccccttccattcacctcccttttgcatctcactgcagatttgtgtctggtgctggcaccacatcattgatatggctgagaaagaggacactgagggccgctgccccgcatgccgcactcgctatgacaaagataggattgtcaagatggctgccacttgtgacaggtccctccatctcaaaccgtcttttttcctttcacctcactaactgcactgacatgcgaagatggccgcacaagagcttagggtcttcagttcaacaaaacgaaacatcacccagttgtcgtgaattgtggtttgcaaagcgccataagcaacttcttttacctgtctatcgcatcggaaattttgtacttatgcttcttttaatggaaacaggacggtagtggagaaaaatgtggacaagaaacagaagacccaaaaggtcaagtcaaaggccgcggtaactgtggaagctaagaaacatcttgctagcgtcagggttatccagagaaacctcgtgtacataattggactacctgcaaatttatgcaacgaaagcgtgagtaccatattgtgcacagacagattcttttcaactgagtaatgtgtatattttgtttctcaccttggcaacacaattcattttttatttcagatacttgagcgcagggaatactttggtcagtatggcaaggttctgaaagtttcagtttctcggccgactggggctccttcccagcaggcaccaacaaacaacagtatcagcgtgtatgtttatgtgaatctcatgccacatgtttatgatgtttctctcatggataaacatgacctattatttcaagtgattagatatatcttaccgtatgtacaagtggtgttttcaagttatgctctcctgtactttccaagcctagagcatttaagcataggtgatttattgttgagaaattatatgcttaaatatagatgaaaatgatggctaattcaaatatgatatgtccatgttcttgcaattaatttcagatttatattacctacttaacagtatgatttgactaaggatcatgaatttccatatccatttgtgaatcagtgaatgccacacctagcagcctagtagccaaagcaaaagatgtagatttctagtgttgaataatcagataaatgcaaacgtgactgcttcagtcatatcatgatcattatattaactatggtatgtactaattgtatgtttacatcataagtctgattgagctcagaacctttgcatatgcagatgtcaggtatttcatagaatttacctcaaggattatcaaaattttcctgtctgagcactttgtagttctttgaatgcagctccatctttctcttaggaatcctcagcatcgactggatccatgtagattccaaaatgtgaaacttagattgtatatagaatgcactgtgtgtgttgaaaatgggctcattattgtgatgttttcagatatattacatatgccaaagaagaagaggccatcaggtgtattcaagctgtacacaattttgttttggaagggaaagtgttaaggtcaccctctatgctttgtagccttattgcagcagttttttttacataacgcagttagcctaatcgttaatggtttgttgcagagcgtgctttggtactacaaagtattgccatgcatggctgcggaacatggtatactcgttgcttcatcctggcagctttatttaccattactctacctactgccatccttctgagggcttttatcttctcttttttagacctgtggaaatccagattgtctctatttacatgatgtaggaagccaggaagatagtttcactaaagatgagataatctcagcatatacaaggtaagctgagctcgttgaacatatgtgtggaaagttccactgttccttattatggcactgtgccagtcctagccatatgtactttttcccctgccaagcctactgctactgttactatataatgctcttctgttctgagaatttgtagtctatcaacttttccctatactatgcatgaattattatgctttgctaaatgctaagattttcagtagttctgattggtgctttcgactcatcatctctcgttcctacaggagtagggttccccaaatggcgtctaatgtttctcaaagacgcgcagggactgtattacctcctccagcagaagatttctcatatagtgcagtggttgcagctaaacatccaatcaagaatggaataactgtatgttttttatactgaaaaatccattgggacactggacatgttcatttctgtttgatttcatgctgctacattaactggtcttattttgtacagaatactgcaaatcaatccaggctttcgcctccaaacagtagttctgggagatccacacttccaccagctgcttcatggtatgatgctgcttagggtctcatgatatgttttaaaatgtgaatttgttgctaaaatttttttggtatgagcagggggcatcgcgatttgaataccaggacaacagcaactggggtggcatcgtcacaatctcttactaaatcaaaagcagatcctcaaagtaattcattctcgagttcttcgactgtttcaagtacaaaactaccttcttcatggaatgatgacacaagcacagttccgaaaatgacggaaggacgagatagtttgtctaaaaccttgaagccatataagcctggtattgcaaaggaaacccaagctgtaacatcactggagtcatcgcttgacatagacttctctaccataccttcagcttggaacgatgatgatgtcacatcagatggcatgtcaaaaggaagtgacgagaagcaggttgtaaatgacaatggaaagtttgaatgttcagtttcttcaaagccagctgaatcagggcatcttacatcgaagtcaacgacatcaccaaagaaagacatcgcagtaaacagtaccaggcaaagtcctctaaattgtgtatcaagtccatcggtttctaaatcagaagtaaaggatggtgatggtgattaccaagtaaccaacatggcttctaaaacatctactttggtaattagaaaggaccaatctaatcaagcagctattgacacagcaaccgaagatactagatctgagagcacggatattgataggctttctgttggagtatcttcagtaacattaagcagaaaagatggggttcaaagtattgccgaaaaccaacaaccggatgcaatcctaagtacttcagttgtggtgccctttagtcagaatttgaaacttgctgagtgtaatgattctacatgtcagcctagttcagataagcatcgtgattggtgttcagatatccagagtagtgtgtctcctcagttaaatgacatagaaagttatgcagtagccactgataaatctcatggtagagtgctggatgctgctgatcaagcttcgtcttcaccatatgtccatttccctaacactgctcctatttcactgtggaatggtaaagagattaaccatacatcaacaagtgatagaacttccacaatgatgcaacctgggctgttatcttcagttgacagcacttctaccatgttaaatggacatcaagaagggctagggactatatatgcacctggtaaggtttctgaacatcctagaatgaaaaaccatcagcctggagcagttggtgcagtgagaattgataacataggcagttttgacaaggctgtaagtgtaaataaggatgagagcagcataattgctgatattttgtctttggagtttgatccatgggatgagtcgtattcaacggctaacaattttgctaagatgcttagtgcatctgaaaagaacgatgtgctttttgatgcacgttcatggaaaacaaaaaccagcaatagtgagtctagattttcatttgctagacaagataatcaaggaagcctcctagattcatctatgagaaattataaaagtgagcagaatttcagtttgccatcccagaattctcatggaaacatttatcagagtggcattgcatttcaatctcctgaggaaggtttctcaaagagcaactctcttactatgttggatatgctagctaccggtgagtagtatgaagttatattacgctgcttgtttattaaattcttaatgaacagtgagatgcagtactgcagttaatgtttttattttaatat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| − | Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071769.1 RefSeq:Os12g0102400]|
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| − | }}
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| | [[Category:Genes]] | | [[Category:Genes]] |
| | [[Category:Japonica mRNA]] | | [[Category:Japonica mRNA]] |
| Line 56: |
Line 47: |
| | [[Category:Japonica Chromosome 12]] | | [[Category:Japonica Chromosome 12]] |
| | [[Category:Chromosome 12]] | | [[Category:Chromosome 12]] |
| | + | |
| | + | == Structured Information == |
Please input one-sentence summary here.
Annotated Information
Function
It is a gene encoding RING-C2 type protein in rice, called OsRINGC2-2 located on chromosome 12 function as E3 ligases.
The sequences of both genes displayed highly significant identities of 99% (3271/3295) at the nucleotide level (data not shown). In particular, no differences between the two genes were found in both the 5′-and 3′-terminal sequences, indicating that gene-specific primer pairs cannot be designed to clone the full-length
genes. We further examined the differences between the sequences, which are recognized by any restriction enzyme, and found that one single nucleotide polymorphism displayed a difference in recognition of the HindIII endonuclease (Fig. 1A).
Gene identification via enzyme digestion. A: Schematic diagram of the pBIN35S-RINGC2 constructs. Restriction enzyme sites are indicated. B: Restriction profiles of each genes.. Expression
It is a gene encoding RING-C2 type protein in rice. Two RING-C2 types are the modified types of canonical types RING-H2 and RING-HC.
Some modified types of RINGs including RING-v, RING-D, RINGS/T, RING-G, and RING-C2 exist in various plant genomes. Interestingly, only two RING-C2 types exist in the rice genome, whereas 10 occur in Arabidopsis and 10 in apple, respectively. Functions of the modified RING domains remain largely unidentified.
Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution.
Evolution
Complete genome sequences and bioinformatics provide new insights into the evolutionary history of plant genomes. In particular, the Poaceae genome, which includes major food crops such as rice, wheat, corn, and sorghum, is believed to have undergone a pregrass whole-genome duplication event with a common ancestor 70–90 million years ago (Mya)(Paterson et al., 2009; Salse et al., 2008, 2009; Wang et al., 2005) followed by independent gene loss during speciation.
Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).
The finding that the distal regions of rice chromosomes 11 and 12 diverged 70–90 Mya and may have undergone frequent illegitimate recombination such as gene conversion raises the question regarding the evolutionary fate of OsRINGC2-1 and OsRINGC2-2 located on the distal parts of these chromosomes.We attempted to choose each of 10 OsRINGC2-1 and OsRINGC2-2 neighboring genes, respectively, and 100 randomly selected duplicate genes, which were generated by whole-genome duplication elsewhere in the genome. Strikingly low Ka, Ks, and dsm values were observed between duplicate genes (but not all) located on the distal parts of chromosomes 11 and 12 as compared to those of random sets (Fig 3).
A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference [1]). 
Sequence divergence of duplicated genes pairs in upstream and downstream of Os11g01190 and Os12g01190.. (from reference [1]). Labs working on this gene
Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200‐713, Korea
Reference
Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060
Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.
Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.
Wang, X., et al., 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946.
Structured Information
- ↑ 1.0 1.1 Cite error: Invalid
<ref> tag;
no text was provided for refs named Jung
