Buffering by gene duplicates: An analysis of molecular correlates and evolutionary conservation

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Hannay, Kevin ^a   Marcotte, Edward M ^a   Vogel, Christine ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENETICS; CAENORHABDITIS ELEGANS; CONSERVATION GENETICS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; FUNGAL GENETICS; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; MOLECULAR GENETICS; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA GENITALIUM; NONHUMAN; PSEUDOMONAS AERUGINOSA; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; ANIMAL; BACTERIUM; BIOLOGICAL MODEL; GENETICS; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

BACILLUS SUBTILIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EUKARYOTA; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; MUS MUSCULUS; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA GENITALIUM; PSEUDOMONAS AERUGINOSA; SACCHAROMYCES CEREVISIAE;

ANIMALS; BACTERIA; CAENORHABDITIS ELEGANS; CONSERVED SEQUENCE; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION; MICE; MODELS, GENETIC; MULTIGENE FAMILY; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 59449097316     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-609     Document Type: Article

References (71)

1. Hartman JL Garvik B Hartwell L Principles for the buffering of genetic variation Science 2001, 291(5506):1001-1004. 11232561
2. Pal C Papp B Lercher MJ An integrated view of protein evolution Nat Rev Genet 2006, 7(5):337-348. 16619049
3. Wilkins AS Canalization: A molecular genetic perspective Bioessays 1997, 19(3):257-262. 9080776
4. Tautz D Redundancies, development and the flow of information Bioessays 1992, 14(4):263-266. 1596275
5. Ohno S Evolution by Gene Duplication New York: Springer-Verlag 1970.
6. Wolfe KH Li WH Molecular evolution meets the genomics revolution Nat Genet 2003, 33(Suppl):255-265. 12610535
7. Lynch M Katju V The altered evolutionary trajectories of gene duplicates Trends Genet 2004, 20(11):544-549. 15475113
8. Wagner A Robustness against mutations in genetic networks of yeast Nat Genet 2000, 24(4):355-361. 10742097
9. Hartman JLt Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism Proc Natl Acad Sci USA 2007, 104(28):11700-11705. 1913885 17606896
10. Giaever G Chu AM Ni L Connelly C Riles L Veronneau S Dow S Lucau-Danila A Anderson K Andre B et al Functional profiling of the Saccharomyces cerevisiae genome Nature 2002, 418(6896):387-391. 12140549
11. Gu Z Steinmetz LM Gu X Scharfe C Davis RW Li WH Role of duplicate genes in genetic robustness against null mutations Nature 2003, 421(6918):63-66. 12511954
12. Papp B Pal C Hurst LD Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast Nature 2004, 429(6992):661-664. 15190353
13. Ihmels J Collins SR Schuldiner M Krogan NJ Weissman JS Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss Mol Syst Biol 2007, 3:86. 1847942 17389874
14. Blank LM Kuepfer L Sauer U Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast Genome Biol 2005, 6(6):R49. 1175969 15960801
15. Kuepfer L Sauer U Blank LM Metabolic functions of duplicate genes in Saccharomyces cerevisiae Genome Res 2005, 15(10):1421-1430. 1240085 16204195
16. Tong AH Lesage G Bader GD Ding H Xu H Xin X Young J Berriz GF Brost RL Chang M et al Global mapping of the yeast genetic interaction network Science 2004, 303(5659):808-813. 14764870
17. Wong SL Zhang LV Tong AH Li Z Goldberg DS King OD Lesage G Vidal M Andrews B Bussey H et al Combining biological networks to predict genetic interactions Proc Natl Acad Sci USA 2004, 101(44):15682-15687. 524818 15496468
18. Liang H Li WH Gene essentiality, gene duplicability and protein connectivity in human and mouse Trends Genet 2007, 23(8):375-378. 17512629
19. Liao BY Zhang J Mouse duplicate genes are as essential as singletons Trends Genet 2007, 23(8):378-381. 17559966
20. Kafri R Bar-Even A Pilpel Y Transcription control reprogramming in genetic backup circuits Nat Genet 2005, 37(3):295-299. 15723064
21. He X Zhang J Higher duplicability of less important genes in yeast genomes Mol Biol Evol 2006, 23(1):144-151. 16151181
22. Nowak MA Boerlijst MC Cooke J Smith JM Evolution of genetic redundancy Nature 1997, 388(6638):167-171. 9217155
23. Seoighe C Wolfe KH Yeast genome evolution in the post-genome era Curr Opin Microbiol 1999, 2(5):548-554. 10508730
24. Conant GC Wagner A Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans Proc Biol Sci 2004, 271(1534):89-96. 1691561 15002776
25. Kamath RS Fraser AG Dong Y Poulin G Durbin R Gotta M Kanapin A Le Bot N Moreno S Sohrmann M et al Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Nature 2003, 421(6920):231-237. 12529635
26. Lehner B Crombie C Tischler J Fortunato A Fraser AG Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways Nat Genet 2006, 38(8):896-903. 16845399
27. Wolfe KH Shields DC Molecular evidence for an ancient duplication of the entire yeast genome Nature 1997, 387(6634):708-713. 9192896
28. Kellis M Birren BW Lander ES Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae Nature 2004, 428(6983):617-624. 15004568
29. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
30. Stark C Breitkreutz BJ Reguly T Boucher L Breitkreutz A Tyers M BioGRID: a general repository for interaction datasets Nucleic Acids Res 2006, 34(Database):D535-539. 1347471 16381927
31. Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes is accurate, extensive, and highly modular Science 2004, 306(5701):1555-1558. 15567862
32. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314(5):1041-1052. 11743721
33. Tischler J Lehner B Chen N Fraser AG Combinatorial RNA interference in C. elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution Genome Biol 2006, 7(8):R69. 1779603 16884526
34. Guan Y Dunham MJ Troyanskaya OG Functional Analysis of Gene Duplications in Saccharomyces cerevisiae Genetics 2007, 175(2):933-943. 1800624 17151249
35. Boutros M Kiger AA Armknecht S Kerr K Hild M Koch B Haas SA Paro R Perrimon N Genome-wide RNAi analysis of growth and viability in Drosophila cells Science 2004, 303(5659):832-835. 14764878
36. Glass JI Assad-Garcia N Alperovich N Yooseph S Lewis MR Maruf M Hutchison CA 3rd Smith HO Venter JC Essential genes of a minimal bacterium Proc Natl Acad Sci USA 2006 ,103(2):425-430. 1324956 16407165
37. Mushegian AR Koonin EV A minimal gene set for cellular life derived by comparison of complete bacterial genomes Proc Natl Acad Sci USA 1996, 93(19):10268-10273. 38373 8816789
38. Pal C Papp B Hurst LD Genomic function: Rate of evolution and gene dispensability Nature 2003, 421(6922):496-497. discussion 497-498 12556881
39. Wilson D Madera M Vogel C Chothia C Gough J The SUPERFAMILY database in 2007: Families and functions Nucleic Acids Res 2007, 35(Database):D308-313. 1669749 17098927
40. Kobayashi K Ehrlich SD Albertini A Amati G Andersen KK Arnaud M Asai K Ashikaga S Aymerich S Bessieres P et al Essential Bacillus subtilis genes Proc Natl Acad Sci USA 2003, 100(8):4678-4683. 153615 12682299
41. Gerdes SY Scholle MD Campbell JW Balazsi G Ravasz E Daugherty MD Somera AL Kyrpides NC Anderson I Gelfand MS et al Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J Bacteriol 2003, 185(19):5673-5684. 193955 13129938
42. Winzeler EA Liang H Shoemaker DD Davis RW Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization Novartis Found Symp 2000, 229:105-109. discussion 109-111 11084935
43. Salama NR Shepherd B Falkow S Global transposon mutagenesis and essential gene analysis of Helicobacter pylori J Bacteriol 2004, 186(23):7926-7935. 529078 15547264
44. Liberati NT Urbach JM Miyata S Lee DG Drenkard E Wu G Villanueva J Wei T Ausubel FM An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants Proc Natl Acad Sci USA 2006, 103(8):2833-2838. 1413827 16477005
45. Sassetti CM Boyd DH Rubin EJ Genes required for mycobacterial growth defined by high density mutagenesis Mol Microbiol 2003, 48(1):77-84. 12657046
46. Akerley BJ Rubin EJ Novick VL Amaya K Judson N Mekalanos JJ A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae Proc Natl Acad Sci USA 2002, 99(2):966-971. 117414 11805338
47. Eppig JT Blake JA Bult CJ Kadin JA Richardson JE The mouse genome database (MGD): New features facilitating a model system Nucleic Acids Res 2007, 35(Database):D630-637. 1751527 17135206
48. Tong AH Evangelista M B PA Xu H Bader GD Page N Robinson M Raghibizadeh S Hogue CW Bussey H et alSystematic genetic analysis with ordered arrays of yeast deletion mutants Science 2001, 294(5550):2364-2368. 11743205
49. Pan X P Y Yuan DS Wang X Bader JS Boeke JD A DNA integrity network in the yeast Saccharomyces cerevisiae Cell 2006, 124(5):1069-1081. 16487579
50. Krogan NJ Keogh MC Datta N Sawa C Ryan OW Ding H Haw RA Pootoolal J Tong AH Canadien V A et al Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1 Molecular Cell 2003, 12(6):1565-1576. 14690608
51. Lesage G Shapiro J Specht CA Sdicu AM Menard P Hussein S Tong AH Boone C Bussey H An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae BMC Genet 2005, 6(1):8. 554099 15715908
52. Daniel JA Keyes BE Ng YP Freeman CO Burke DJ Diverse functions of spindle assembly checkpoint genes in Saccharomyces cerevisiae Genetics 2006, 172(1):53-65. 1456180 16157669
53. Lesage G Sdicu AM Menard P Shapiro J Hussein S Bussey H Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin Genetics 2004, 167(1):35-49. 1470839 15166135
54. Zhao R Davey M Hsu YC Kaplanek P Tong A Parsons AB Krogan N Cagney G Mai D Greenblatt J et al Navigating the chaperone network: An integrative map of physical and genetic interactions mediated by the hsp90 chaperone Cell 2005, 120(5):715-727. 15766533
55. Friesen H Humphries C Ho Y Schub O Colwill K Andrews B Characterization of the yeast amphiphysins Rvs161p and Rvs167p reveals roles for the Rvs heterodimer in vivo Mol Biol Cell 2006, 17(3):1306-1321. 1382319 16394103
56. Loeillet S Palancade B Cartron M Thierry A Richard GF Dujon B Doye V Nicolas A Genetic network interactions among replication, repair and nuclear pore deficiencies in yeast DNA Repair (Amst) 2005, 4(4):459-468. 15725626
57. Pan X Yuan DS Xiang D Wang X Sookhai-Mahadeo S Bader JS Hieter P Spencer F Boeke JD A robust toolkit for functional profiling of the yeast genome Mol Cell 2004, 16(3):487-496 15525520
58. Ingvarsdottir K Krogan NJ Emre NC Wyce A Thompson NJ Emili A Hughes TR Greenblatt JF Berger SL H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex Mol Cell Biol 2005, 25(3):1162-1172 544016 15657441
59. Menon BB Sarma NJ Pasula S Deminoff SJ Willis KA Barbara KE Andrews B Santangelo GM Reverse recruitment: The Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation Proc Natl Acad Sci USA 2005, 102(16):5749-5754 556015 15817685
60. Suter B Tong A Chang M Yu L Brown GW Boone C Rine J The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae Genetics 2004, 167(2):579-591 1470908 15238513
61. Byrne AB Weirauch MT Wong V Koeva M Dixon SJ Stuart JM Roy PJ A global analysis of genetic interactions in Caenorhabditis elegans J Biol 2007, 6(3):8 2373897 17897480
62. CodonW http://sourceforge.net/projects/codonw/
63. McGary KL Lee I Marcotte EM Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes Genome Biol 2007, 8(12):R258 2246260 18053250
64. 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(Pt 7):2175-2187 16000708
65. Robinson MD Grigull J Mohammad N Hughes TR FunSpec: A web-based cluster interpreter for yeast BMC Bioinformatics 2002, 3(1):35 139976 12431279
66. Nash R Weng S Hitz B Balakrishnan R Christie KR Costanzo MC Dwight SS Engel SR Fisk DG Hirschman JE et al Expanded protein information at SGD: new pages and proteome browser Nucleic Acids Res 2007 35 Database D468-471 1669759 17142221
67. Lu P Vogel C Wang R Yao X Marcotte EM Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat Biotechnol 2007, 25(1):117-124 17187058
68. Fraser HB Hirsh AE Giaever G Kumm J Eisen MB Noise minimization in eukaryotic gene expression PLoS Biol 2004, 2(6):e137 400249 15124029
69. Belle A Tanay A Bitincka L Shamir R O'Shea EK Quantification of protein half-lives in the budding yeast proteome Proc Natl Acad Sci USA 2006, 103(35):13004-13009 1550773 16916930
70. 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(15):5483-5488 555735 15800036
71. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM et al Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415(6868):141-147 11805826