Evolution of a membrane protein regulon in saccharomyces

Molecular Biology and Evolution

Volumn 29, Issue 7, 2012, Pages 1747-1756

  Martin, Hilary C ^a,b   Roop, Jeremy I ^a   Schraiber, Joshua G ^a   Hsu, Tiffany Y ^a   Brem, Rachel B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

natural selection; regulatory variation; Saccharomyces

Indexed keywords

MEMBRANE PROTEIN; MESSENGER RNA;

ALLELE; ARTICLE; DNA SEQUENCE; GENE EXPRESSION; GENE LOCUS; NATURAL SELECTION; NONHUMAN; PHYLOGENY; PROMOTER REGION; REGULON; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS;

EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; MEMBRANE PROTEINS; PROMOTER REGIONS, GENETIC; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS;

EID: 84863562763     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss017     Document Type: Article

References (42)

1. Arthur RK, Ruvinsky I. 2011. Evidence that purifying selection acts on promoter sequences. Genetics 189:1121-1126.
2. Baker CR, Tuch BB, Johnson AD. 2011. Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc Natl Acad Sci U S A. 108:7493-7498.
3. Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. 2008. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet. 4:e1000271.
4. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. 2007. Divergence of transcription factor binding sites across related yeast species. Science 317:815-819. (Pubitemid 47257921)
5. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. 2009. Fast statistical alignment. PLoS Comput Biol. 5:e1000392.
6. Bullard JH, Mostovoy Y, Dudoit S, Brem RB. 2010. Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A. 107:5058-5063.
7. Bustamante CD, Wakeley J, Sawyer S, Hartl DL. 2001. Directional selection and the site-frequency spectrum. Genetics 159:1779-1788. (Pubitemid 34087614)
8. Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, Thomas WK. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet. 37:544-548. (Pubitemid 40617285)
9. Dowell RD. 2010. Transcription factor binding variation in the evolution of gene regulation. Trends Genet. 26:468-475.
10. Elyashiv E, Bullaughey K, Sattath S, Rinott Y, Przeworski M, Sella G. 2010. Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species. Genome Res. 20:1558-1573.
11. Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, Schadt EE. 2011. Systematic detection of polygenic cis-regulatory evolution. PLoS Genet. 7:e1002023.
12. Fraser HB, Moses AM, Schadt EE. 2010. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci U S A. 107:2977-2982.
13. Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. 2004. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2:e398.
14. He BZ, Holloway AK, Maerkl SJ, Kreitman M. 2011. Does positive selection drive transcription factor binding site turnover?. A test with Drosophila cis-regulatory modules. PLoS Genet. 7:e1002053.
15. Hinman VF, Nguyen A, Davidson EH. 2007. Caught in the evolutionary act:precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. Dev Biol. 312:584-595. (Pubitemid 350183970)
16. Hittinger CT, Goncalves P, Sampaio JP, Dover J, Johnston M, Rokas A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464:54-58.
17. Hodgins-Davis A, Townsend JP. 2009. Evolving gene expression:from G to E to GxE. Trends Ecol Evol. 24:649-658.
18. Hogues H, LavoieH, Sellam A,MangosM, Roemer T, Purisima E,NantelA, Whiteway M. 2008. Transcription factor substitution during the evolution of fungal ribosome regulation. Mol CE.L.L. 29:552-562. (Pubitemid 351374685)
19. Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, Barkai N. 2005. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309:938-940. (Pubitemid 41099931)
20. Kohn MH, Fang S, Wu CI. 2004. Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes. Mol Biol Evol. 21:374-383. (Pubitemid 38314625)
21. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. 2010. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 20:1672-1678.
22. Lavoie H, Hogues H, Mallick J, Sellam A, Nantel A, Whiteway M. 2010. Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol. 8:e1000329.
23. Liti G, Carter DM, Moses AM, et al. (26 co-authors). 2009. Population genomics of domestic and wild yeasts. Nature 458:337-341.
24. Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M. 2005. Functional evolution of a cis-regulatory module. PLoS Biol. 3:e93.
25. Orr HA. 1998. Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics 149:2099-2104. (Pubitemid 28375975)
26. Perez JC, Groisman EA. 2009. Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proc Natl Acad Sci U S A. 106:4319-4324.
27. Piasecki BP, Burghoorn J, Swoboda P. 2010. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals. Proc Natl Acad Sci U S A. 107:12969-12974.
28. Rockman MV, Kruglyak L. 2006. Genetics of global gene expression. Nat Rev Genet. 7:862-872. (Pubitemid 44607102)
29. Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. 2011. The awesome power of yeast evolutionary genetics:new genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 1:11-25.
30. Takahasi KR, Matsuo T, Takano-Shimizu-Kouno T. 2011. Two types of cis-trans compensation in the evolution of transcriptional regulation. Proc Natl Acad Sci U S A. 108:15276-15281.
31. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5:molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
32. Tanay A, Regev A, Shamir R. 2005. Conservation and evolvability in regulatory networks:the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A. 102:7203-7208. (Pubitemid 40696358)
33. Tirosh I, Reikhav S, Levy AA, Barkai N. 2009. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324:659-662.
34. Tirosh I, Weinberger A, Carmi M, Barkai N. 2006. A genetic signature of interspecies variations in gene expression. Nat Genet. 38:830-834. (Pubitemid 43980606)
35. Tirosh I, Wong KH, Barkai N, Struhl K. 2011. Extensive divergence of yeast stress responses through transitions between induced and constitutive activation. Proc Natl Acad Sci U S A. 108:16693-16698.
36. Torgerson DG, Boyko AR, Hernandez RD, et al. (11 co-authors). 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet. 5:e1000592.
37. Tsong AE, Tuch BB, Li H, Johnson AD. 2006. Evolution of alternative transcriptional circuits with identical logic. Nature 443:415-420. (Pubitemid 44477273)
38. Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD. 2008. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6:e38.
39. Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. 2011. Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol. 28:2615-2627.
40. Weiss KM. 2008. Tilting at quixotic trait loci (QTL): An evolutionary perspective on genetic causation. Genetics 179:1741-1756.
41. Wilson MD, Odom DT. 2009. Evolution of transcriptional control in mammals. Curr Opin Genet Dev. 19:579-585.
42. Yang Z. 2007. PAML 4:phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)