Evolutionary rates and centrality in the yeast gene regulatory network

Genome Biology

Volumn 10, Issue 4, 2009, Pages

  Jovelin, Richard ^a   Phillips, Patrick C ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; TRANSCRIPTION FACTOR; SACCHAROMYCES CEREVISIAE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; EVOLUTIONARY RATE; FUNGAL GENETICS; FUNGAL METABOLISM; FUNGAL STRAIN; GENE DELETION; GENE EXPRESSION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC VARIABILITY; NONHUMAN; PHENOTYPE; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PROTEIN BINDING; SACCHAROMYCES;

DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENOME, FUNGAL; PROTEIN BINDING; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 65449187535     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-4-r35     Document Type: Article

References (52)

1. Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization. Nat Rev Genet 2004 5 101-113 10.1038/nrg1272 14735121
2. Davidson EH Rast JP Oliveri P Ransick A Calestani C Yuh CH Minokawa T Amore G Hinman V Arenas-Mena C Otim O Brown CT Livi CB Lee PY Revilla R Rust AG Pan Z Schilstra MJ Clarke PJ Arnone MI Rowen L Cameron RA McClay DR Hood L Bolouri H A genomic regulatory network for development. Science 2002 295 1669-1678 10.1126/science.1069883 11872831
3. Proulx SR Promislow DE Phillips PC Network thinking in ecology and evolution. Trends Ecol Evol 2005 20 345-353 10.1016/j.tree.2005.04.004 16701391
4. Hahn MW Kern AD Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005 22 803-806 10.1093/molbev/msi072 15616139
5. Vitkup D Kharchenko P Wagner A Influence of metabolic network structure and function on enzyme evolution. Genome Biol 2006 7 R39 1779518 16684370 10.1186/gb-2006-7-5-r39
6. Lu C Zhang Z Leach L Kearsey MJ Luo ZW Impacts of yeast metabolic network structure on enzyme evolution. Genome Biol 2007 8 407 2374984 17692134 10.1186/gb-2007-8-8-407
7. Fraser HB Hirsh AE Steinmetz LM Scharfe C Feldman MW Evolutionary rate in the protein interaction network. Science 2002 296 750-752 10.1126/ science.1068696 11976460
8. Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks. Nature 2001 411 41-42 10.1038/35075138 11333967
9. Wagner A How the global structure of protein interaction networks evolves. Proc Biol Sci 2003 270 457-466 1691265 12641899 10.1098/ rspb.2002.2269
10. Proulx SR Phillips PC The opportunity for canalization and the evolution of genetic networks. Am Nat 2005 165-147 162 10.1086/426873 15729647
11. Keller EF Revisiting "scale-free" networks. Bioessays 2005 27 1060-1068 10.1002/bies.20294 16163729
12. Davidson EH The Regulatory Genome Amsterdam, Boston, Heidelberg, London, New York, Oxford, Paris, San Diego, San Francisco, Singapore, Sydney, Tokyo: Academic Press 2006
13. Guelzim N Bottani S Bourgine P Kepes F Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002 31 60-63 10.1038/ng873 11967534
14. Balaji S Iyer LM Aravind L Babu MM Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J Mol Biol 2006 360 204-212 10.1016/j.jmb.2006.04.026 16730024
15. Yu H Gerstein M Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci USA 2006 103 14724-14731 1595419 17003135 10.1073/pnas.0508637103
16. Rocha EP The quest for the universals of protein evolution. Trends Genet 2006 22 412-416 10.1016/j.tig.2006.06.004 16808987
17. Pál C Papp B Lercher MJ An integrated view of protein evolution. Nat Rev Genet 2006 7 337-348 10.1038/nrg1838 16619049
18. Pál C Papp B Hurst LD Highly expressed genes in yeast evolve slowly. Genetics 2001 158 927-931 1461684 11430355
19. Wall DP Hirsh AE Fraser HB Kumm J Giaever G Eisen MB Feldman MW Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci USA 2005 102 5483-5488 555735 15800036 10.1073/pnas.0501761102
20. Drummond DA Bloom JD Adami C Wilke CO Arnold FH Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 2005 102 14338-14343 1242296 16176987 10.1073/pnas.0504070102
21. Drummond DA Raval A Wilke CO A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 2006 23 327-337 10.1093/molbev/ msj038 16237209
22. Pál C Papp B Hurst LD Genomic function: Rate of evolution and gene dispensability. Nature 2003 421 496-497 discussion 497-498. 10.1038/ 421496b 12556881
23. Hirsh AE Fraser HB Protein dispensability and rate of evolution. Nature 2001 411 1046-1049 10.1038/35082561 11429604
24. Plotkin JB Fraser HB Assessing the determinants of evolutionary rates in the presence of noise. Mol Biol Evol 2007 24 1113-1121 10.1093/molbev/ msm044 17347158
25. Kim SH Yi SV Understanding relationship between sequence and functional evolution in yeast proteins. Genetica 2007 131 151-156 10.1007/ s10709-006-9125-2 17160620
26. Bloom JD Adami C Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol Biol 2003 3 21 270031 14525624 10.1186/ 1471-2148-3-21
27. Fraser HB Hirsh AE Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol 2004 4 13 420460 15165289 10.1186/1471-2148-4-13
28. Bloom JD Adami C Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response. BMC Evol Biol 2004 4 14 443507 15171796 10.1186/1471-2148-4-14
29. Giaever G Chu AM Ni L Connelly C Riles L Veronneau S Dow S Lucau-Danila A Anderson K Andre B Arkin AP Astromoff A El-Bakkoury M Bangham R Benito R Brachat S Campanaro S Curtiss M Davis K Deutschbauer A Entian KD Flaherty P Foury F Garfinkel DJ Gerstein M Gotte D Güldener U Hegemann JH Hempel S Herman Z Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002 418 387-391 10.1038/nature00935 12140549
30. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000 25 25-29 10.1038/75556 10802651
31. Dwight SS Harris MA Dolinski K Ball CA Binkley G Christie KR Fisk DG Issel-Tarver L Schroeder M Sherlock G Sethuraman A Weng S Botstein D Cherry JM Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 2002 30 69-72 99086 11752257 10.1093/nar/30.1.69
32. Sauer U Heinemann M Zamboni N Genetics. Getting closer to the whole picture. Science 2007 316 550-551 10.1126/science.1142502 17463274
33. Wagner A Wright J Alternative routes and mutational robustness in complex regulatory networks. Biosystems 2007 88 163-172 10.1016/ j.biosystems.2006.06.002 16860925
34. Ishii N Nakahigashi K Baba T Robert M Soga T Kanai A Hirasawa T Naba M Hirai K Hoque A Ho PY Kakazu Y Sugawara K Igarashi S Harada S Masuda T Sugiyama N Togashi T Hasegawa M Takai Y Yugi K Arakawa K Iwata N Toya Y Nakayama Y Nishioka T Shimizu K Mori H Tomita M Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007 316 593-597 10.1126/science.1132067 17379776
35. Choi JK Kim SC Seo J Kim S Bhak J Impact of transcriptional properties on essentiality and evolutionary rate. Genetics 2007 175 199-206 1775009 17057246 10.1534/genetics.106.066027
36. Promislow D A regulatory network analysis of phenotypic plasticity in yeast. Am Nat 2005 165 515-523 10.1086/429161 15795849
37. Fraser HB Modularity and evolutionary constraint on proteins. Nat Genet 2005 37 351-352 10.1038/ng1530 15750592
38. Flowers JM Sezgin E Kumagai S Duvernell DD Matzkin LM Schmidt PS Eanes WF Adaptive evolution of metabolic pathways in Drosophila. Mol Biol Evol 2007 24 1347-1354 10.1093/molbev/msm057 17379620
39. Yip KY Yu H Kim PM Schultz M Gerstein M The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks. Bioinformatics 2006 22 2968-2970 10.1093/ bioinformatics/btl488 17021160
40. Goffeau A Barrell BG Bussey H Davis RW Dujon B Feldmann H Galibert F Hoheisel JD Jacq C Johnston M Louis EJ Mewes HW Murakami Y Philippsen P Tettelin H Oliver SG Life with 6000 genes. Science 1996 274 546-567 10.1126/science.274.5287.546 8849441
41. 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
42. 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
43. 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 147204 9399804 10.1093/nar/26.1.73
44. Hall TA BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999 41 95-98
45. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997 13 555-556 9367129
46. Hirsh AE Fraser HB Wall DP Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 2005 22 174-177 10.1093/molbev/msh265 15371530
47. Ghaemmaghami S Huh WK Bower K Howson RW Belle A Dephoure N O'Shea EK Weissman JS Global analysis of protein expression in yeast. Nature 2003 425 737-741 10.1038/nature02046 14562106
48. Holstege FC Jennings EG Wyrick JJ Lee TI Hengartner CJ Green MR Golub TR Lander ES Young RA Dissecting the regulatory circuitry of a eukaryotic genome. Cell 1998 95 717-728 10.1016/S0092-8674(00)81641-4 9845373
49. Sharp PM Li WH The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987 15 1281-1295 340524 3547335 10.1093/nar/15.3.1281
50. Coghlan A Wolfe KH Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000 16 1131-1145 10.1002/1097-0061(20000915)16:12<1131::AID-YEA609>3.0.CO;2-F 10953085
51. Wu G Culley DE Zhang W Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 2005 151 2175-2187 10.1099/mic.0.27833-0 16000708
52. Carbone A Zinovyev A Kepes F Codon adaptation index as a measure of dominating codon bias. Bioinformatics 2003 19 2005-2015 10.1093/ bioinformatics/btg272 14594704