The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes

Biology Direct

Volumn 5, Issue , 2010, Pages

  Wu, Xuechang ^a   Chi, Xiaoqin ^a   Wang, Pinmei ^a   Zheng, Daoqiong ^a   Ding, Rui ^a   Li, Yudong ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; FUNGAL GENOME; GENETICS; MOLECULAR EVOLUTION; OSMOLARITY; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

EVOLUTION, MOLECULAR; GENOME, FUNGAL; OSMOLAR CONCENTRATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 77954334909     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-5-46     Document Type: Article

References (39)

1. Bahn YS, Xue C, Idnurm A, Rutherford JC, Heitman J, Cardenas ME. Sensing the environment: lessons from fungi. Nat Rev Microbiol 2007, 5:57-69. 10.1038/nrmicro1578, 17170747.
2. Gasch AP. Comparative genomics of the environmental stress response in ascomycete fungi. Yeast 2007, 24:961-976. 10.1002/yea.1512, 17605132.
3. Singh AH, Wolf DM, Wang P, Arkin AP. Modularity of stress response evolution. Proc Natl Acad Sci USA 2008, 105:7500-7505. 10.1073/pnas.0709764105, 2396705, 18495925.
4. Jin Y, Weining S, Nevo E. A MAPK gene from Dead Sea fungus confers stress tolerance to lithium salt and freezing-thawing: Prospects for saline agriculture. Proc Natl Acad Sci USA 2005, 102:18992-18997. 10.1073/pnas.0509653102, 1323214, 16365289.
5. Westfall PJ, Ballon DR, Thorner J. When the stress of your environment makes you go HOG wild. Science 2004, 306:1511-1512. 10.1126/science.1104879, 15567851.
6. Chen RE, Thorner J. Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 2007, 1773:1311-1340. 10.1016/j.bbamcr.2007.05.003, 2031910, 17604854.
7. Krantz M, Becit E, Hohmann S. Comparative genomics of the HOG-signalling system in fungi. Curr Genet 2006, 49:137-151. 10.1007/s00294-005-0038-x, 16468042.
8. O'Rourke S, Herskowitz I. Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. Molecular Biology of the Cell 2004, 15:532-542. 10.1091/mbc.E03-07-0521, 329229, 14595107.
9. Hersen P, McClean MN, Mahadevan L, Ramanathan S. Signal processing by the HOG MAP kinase pathway. Proc Natl Acad Sci USA 2008, 105:7165-7170. 10.1073/pnas.0710770105, 2386076, 18480263.
10. Nikolaou E, Agrafioti I, Stumpf M, Quinn J, Stansfield I, Brown AJ. Phylogenetic diversity of stress signalling pathways in fungi. BMC Evol Biol 2009, 9:44. 10.1186/1471-2148-9-44, 2666651, 19232129.
11. Wolf MY, Wolf YI, Koonin EV. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol Direct 2008, 3:40. 10.1186/1745-6150-3-40, 2572155, 18840284.
12. Ingvarsson PK. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol 2007, 24:836-844. 10.1093/molbev/msl212, 17204548.
13. Graur D, Li W. Fundamentals of molecular evolution 2000, Sunderland, MA: Sinauer Associates.
14. Alvarez-Ponce D, Aguade M, Rozas J. Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Res 2009, 19:234-242. 10.1101/gr.084038.108, 2652205, 19141596.
15. Yang YH, Zhang FM, Ge S. Evolutionary rate patterns of the Gibberellin pathway genes. BMC Evol Biol 2009, 9:206. 10.1186/1471-2148-9-206, 2794029, 19689796.
16. Beskow A, Wright AP. Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 2006, 23:929-935. 10.1002/yea.1413, 17072884.
17. Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624. 10.1038/nature02424, 15004568.
18. Li YD, Liang H, Gu Z, Lin Z, Guan W, Zhou L, Li YQ, Li WH. Detecting positive selection in the budding yeast genome. J Evol Biol 2009, 22:2430-2437. 10.1111/j.1420-9101.2009.01851.x, 19878412.
19. Jovelin R, Dunham JP, Sung FS, Phillips PC. High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in caenorhabditis. Genetics 2009, 181:1387-1397. 10.1534/genetics.107.082651, 2666507, 19001295.
20. Jovelin R, Phillips PC. Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol 2009, 10:R35. 10.1186/gb-2009-10-4-r35, 2688926, 19358738.
21. Sackton TB, Lazzaro BP, Schlenke TA, Evans JD, Hultmark D, Clark AG. Dynamic evolution of the innate immune system in Drosophila. Nat Genet 2007, 39:1461-1468. 10.1038/ng.2007.60, 17987029.
22. Muzzey D, Gomez-Uribe CA, Mettetal JT, van Oudenaarden A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 2009, 138:160-171. 10.1016/j.cell.2009.04.047, 19596242.
23. Rausher M, Miller R, Tiffin P. Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. SMBE 1999, 16:266-274.
24. Ramsay H, Rieseberg LH, Ritland K. The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis. Mol Biol Evol 2009, 26:1045-1053. 10.1093/molbev/msp021, 19188263.
25. O'Rourke S, Herskowitz I, O'Shea E. Yeast go the whole HOG for the hyperosmotic response. Trends in Genetics 2002, 18:405-412. 10.1016/S0168-9525(02)02723-3, 12142009.
26. Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA. Activated signal transduction kinases frequently occupy target genes. Science 2006, 313:533-536. 10.1126/science.1127677, 16873666.
27. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. SGD: Saccharomyces Genome Database. Nucleic Acids Res 1998, 26:73-79. 10.1093/nar/26.1.73, 147204, 9399804.
28. Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. The Candida Genome Database (CGD), acommunity resource for Candida albicans gene and protein information. Nucleic Acids Res 2005, 33:D358-363. 10.1093/nar/gki003, 539957, 15608216.
29. Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 2005, 15:1456-1461. 10.1101/gr.3672305, 1240090, 16169922.
30. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
31. Li YD, Xie ZY, Du YL, Zhou Z, Mao XM, Lv LX, Li YQ. The rapid evolution of signal peptides is mainly caused by relaxed selection on non-synonymous and synonymous sites. Gene 2009, 436:8-11. 10.1016/j.gene.2009.01.015, 19393172.
32. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
33. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
34. Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804. 10.1038/nature02053, 14574403.
35. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574. 10.1093/bioinformatics/btg180, 12912839.
36. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591. 10.1093/molbev/msm088, 17483113.
37. Wong WS, Yang Z, Goldman N, Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 2004, 168:1041-1051. 10.1534/genetics.104.031153, 1448811, 15514074.
38. Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 1994, 11:725-736.
39. Connallon T, Knowles LL. Recombination rate and protein evolution in yeast. BMC Evol Biol 2007, 7:235. 10.1186/1471-2148-7-235, 2211315, 18042299.