Reevaluation of the evolutionary events within recA/RAD51 phylogeny

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Chintapalli, Sree V ^a,b   Bhardwaj, Gaurav ^a,b   Babu, Jagadish ^c   Hadjiyianni, Loukia ^b   Hong, Yoojin ^c   Todd, George K ^a,b   Boosalis, Casey A ^a,b   Zhang, Zhenhai ^c   Zhou, Xiaofan ^c   Ma, Hong ^c   Anishkin, Andriy ^c   van Rossum, Damian B ^c   Patterson, Randen L ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Phylogenetic inference; RAD51; recA; Recombinase

Indexed keywords

RAD51 PROTEIN; RECA PROTEIN;

ARTICLE; MOLECULAR EVOLUTION; MOLECULAR MODEL; MOLECULAR PHYLOGENY; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; SEQUENCE HOMOLOGY;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; PHYLOGENY; RAD51 RECOMBINASE; REC A RECOMBINASES;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 84875946720     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-240     Document Type: Article

References (41)

1. Thompson LH, Schild D. Homologous recombinational repair of DNA ensures mammalian chromosome stability. Mutat Res 2001, 477(1-2):131-153.
2. van den Bosch M, Lohman PH, Pastink A. DNA double-strand break repair by homologous recombination. Biol Chem 2002, 383(6):873-892.
3. Thacker J. The RAD51 gene family, genetic instability and cancer. Cancer Lett 2005, 219(2):125-135. 10.1016/j.canlet.2004.08.018, 15723711.
4. Bishop DK, Park D, Xu L, Kleckner N. DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 1992, 69(3):439-456. 10.1016/0092-8674(92)90446-J, 1581960.
5. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 1992, 69(3):457-470. 10.1016/0092-8674(92)90447-K, 1581961.
6. Eisen JA. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 1995, 41(6):1105-1123. 3188426, 8587109.
7. DiRuggiero J, Brown JR, Bogert AP, Robb FT. DNA repair systems in archaea: mementos from the last universal common ancestor?. J Mol Evol 1999, 49(4):474-484. 10.1007/PL00006570, 10486005.
8. Komori K, Miyata T, DiRuggiero J, Holley-Shanks R, Hayashi I, Cann IK, Mayanagi K, Shinagawa H, Ishino Y. Both RadA and RadB are involved in homologous recombination in Pyrococcus furiosus. J Biol Chem 2000, 275(43):33782-33790. 10.1074/jbc.M004557200, 10903318.
9. Golubovskaya IN, Hamant O, Timofejeva L, Wang CJ, Braun D, Meeley R, Cande WZ. Alleles of afd1 dissect REC8 functions during meiotic prophase I. J Cell Sci 2006, 119(Pt 16):3306-3315.
10. Affonso DD, Mayberry LJ, Lovett SM, Paul S. Cognitive adaptation to stressful events during pregnancy and postpartum: development and testing of the CASE instrument. Nurs Res 1994, 43(6):338-343.
11. Game JC. DNA double-strand breaks and the RAD50-RAD57 genes in Saccharomyces. Semin Canc Biol 1993, 4(2):73-83.
12. Gaasbeek EJ, van der Wal FJ, van Putten JP, de Boer P, van der Graaf-van BL, de Boer AG, Vermaning BJ, Wagenaar JA. Functional characterization of excision repair and RecA-dependent recombinational DNA repair in Campylobacter jejuni. J Bacteriol 2009, 191(12):3785-3793. 10.1128/JB.01817-08, 2698403, 19376866.
13. Tsuzuki T, Fujii Y, Sakumi K, Tominaga Y, Nakao K, Sekiguchi M, Matsushiro A, Yoshimura Y. Morita T: Targeted disruption of the Rad51 gene leads to lethality in embryonic mice. Proc Natl Acad Sci USA 1996, 93(13):6236-6240. 10.1073/pnas.93.13.6236, 39005, 8692798.
14. Li W, Ma H. Double-stranded DNA breaks and gene functions in recombination and meiosis. Cell Res 2006, 16(5):402-412. 10.1038/sj.cr.7310052, 16699536.
15. Stassen NY, Logsdon JM, Vora GJ, Offenberg HH, Palmer JD, Zolan ME. Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs. Curr Genet 1997, 31(2):144-157. 10.1007/s002940050189, 9021132.
16. Lin Z, Kong H, Nei M, Ma H. Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc Natl Acad Sci USA 2006, 103(27):10328-10333. 10.1073/pnas.0604232103, 1502457, 16798872.
17. Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One 2011, 6(3):e18011. 10.1371/journal.pone.0018011, 3060911, 21437252.
18. Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME. PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. PLoS One 2012, 7(4):e34261. 10.1371/journal.pone.0034261, 3325999, 22514627.
19. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008, 57(5):758-771. 10.1080/10635150802429642, 18853362.
20. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17(8):754-755. 10.1093/bioinformatics/17.8.754, 11524383.
21. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 2011, 39:D225-229. 10.1093/nar/gkq1189, 3013737, 21109532.
22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
23. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
24. Jagadish B, Loukia H, Yoojin H, Zhenhai Z, Xiaofan Z, Hong M, Andriy A, Randen L, Sree V. Chintapalli GB Patterson: Extraction of Deep Phylogenetic Signal and Improved Resolution of Evolutionary Events within the recA/RAD51 Phylogeny. arXiv 2012, (1206.3340):21. Sree V. Chintapalli GB.
25. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
26. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
27. Felsenstein J. PHYLIP (Phylogeny Inference Package) vol. version 3.5c. Department of Genetics 1993, Seattle: University of Washington, Distributed by the author.
28. Felsenstein J. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
29. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8(3):275-282.
30. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007, 5(3):e16. 10.1371/journal.pbio.0050016, 1821046, 17355171.
31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
32. Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 2012, 335(6070):843-847. 10.1126/science.1213561, 22344442.
33. Nakazato E, Fukuzawa H, Tabata S, Takahashi H, Tanaka K. Identification and expression analysis of cDNA encoding a chloroplast recombination protein REC1, the chloroplast RecA homologue in Chlamydomonas reinhardtii. Biosci Biotechnol Biochem 2003, 67(12):2608-2613. 10.1271/bbb.67.2608, 14730139.
34. Asamizu E, Nakamura Y, Sato S, Fukuzawa H, Tabata S. A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res Int J Rapid publ Genes Genomes 1999, 6(6):369-373.
35. Cerutti H, Osman M, Grandoni P, Jagendorf AT. A homolog of Escherichia coli RecA protein in plastids of higher plants. Proc Natl Acad Sci USA 1992, 89(17):8068-8072. 10.1073/pnas.89.17.8068, 49857, 1518831.
36. Li W, Ma H. Double-stranded DNA breaks and gene functions in recombination and meiosis. Cell Res 2006, 16(5):402-412. 10.1038/sj.cr.7310052, 16699536.
37. Hamant O, Ma H, Cande WZ. Genetics of meiotic prophase I in plants. Annu Rev Plant Biol 2006, 57:267-302. 10.1146/annurev.arplant.57.032905.105255, 16669763.
38. Tsuzuki T, Fujii Y, Sakumi K, Tominaga Y, Nakao K, Sekiguchi M, Matsushiro A, Yoshimura Y. MoritaT: Targeted disruption of the Rad51 gene leads to lethality in embryonic mice. Proc Natl Acad Sci USA 1996, 93(13):6236-6240. 10.1073/pnas.93.13.6236, 39005, 8692798.
39. Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC. RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. Genes Dev 1998, 12(9):1248-1253. 10.1101/gad.12.9.1248, 316774, 9573041.
40. Li W, Chen C, Markmann-Mulisch U, Timofejeva L, Schmelzer E, Ma H, Reiss B. The Arabidopsis AtRAD51 gene is dispensable for vegetative development but required for meiosis. Proc Natl Acad Sci USA 2004, 101(29):10596-10601. 10.1073/pnas.0404110101, 489980, 15249667.
41. Liu N, Schild D, Thelen MP, Thompson LH. Involvement of Rad51C in two distinct protein complexes of Rad51 paralogs in human cells. Nucleic Acids Res 2002, 30(4):1009-1015. 10.1093/nar/30.4.1009, 100342, 11842113.