Natural selection of protein structural and functional properties: A single nucleotide polymorphism perspective

Genome Biology

Volumn 9, Issue 4, 2008, Pages

  Liu, Jinfeng ^a   Zhang, Yan ^a   Lei, Xingye ^a   Zhang, Zemin ^a  

^a GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIN; G PROTEIN COUPLED RECEPTOR; GLUTATHIONE TRANSFERASE; GLYCOSYLTRANSFERASE; HISTONE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; MELANOMA ANTIGEN; MESSENGER RNA; PLEXIN; PROTEIN KINASE; REGULATOR PROTEIN; RHODOPSIN; SIGNAL PEPTIDE; TETRASPANIN; ZINC FINGER PROTEIN; PROTEIN;

ARTICLE; CELL NUCLEUS; CONTROLLED STUDY; CYTOPLASM; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOUSE; NATURAL SELECTION; NONHUMAN; OLFACTORY RECEPTOR; PHYLOGENY; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECRETION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TASTE BUD; BIOLOGY; CHEMISTRY; GENETIC SELECTION; GENETICS; METHODOLOGY; PHYSIOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; SELECTION, GENETIC;

EID: 47149102754     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-4-r69     Document Type: Article

References (74)

1. Hurst LD The Ka/Ks ratio: Diagnosing the form of sequence evolution. Trends Genet 2002, 18:486. 10.1016/S0168-9525(02)02722-1 12175810
2. Li W-H Molecular Evolution Sunderland, Massachusetts: Sinauer Associates, Inc. 1997.
3. Jordan IK Rogozin IB Wolf YI Koonin EV Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12:962-968. 1383730 12045149 10.1101/gr.87702. Article published online before print in May 2002
4. Zhang L Li WH Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 2004, 21:236-239. 10.1093/molbev/ msh010 14595094
5. Mouse Genome Sequencing Consortium Waterston RH Lindblad-Toh K Birney E Rogers J Abril JF Agarwal P Agarwala R Ainscough R Alexandersson M An P Antonarakis SE Attwood J Baertsch R Bailey J Barlow K Beck S Berry E Birren B Bloom T Bork P Botcherby M Bray N Brent MR Brown DG Brown SD Bult C Burton J Butler J Campbell RD Carninci P et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. 10.1038/nature01262 12466850
6. Sherry ST Ward MH Kholodov M Baker J Phan L Smigielski EM Sirotkin K dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 2001, 29:308-311. 29783 11125122 10.1093/nar/29.1.308
7. Jiang R Duan J Windemuth A Stephens JC Judson R Xu C Genome-wide evaluation of the public SNP databases. Pharmacogenomics 2003, 4:779-789. 10.1517/phgs.4.6.779.22821 14596641
8. Freudenberg-Hua Y Freudenberg J Winantea J Kluck N Cichon S Bruss M Propping P Nöthen MM Systematic investigation of genetic variability in 111 human genes-implications for studying variable drug response. Pharmacogenomics J 2005, 5:183-192. 10.1038/sj.tpj.6500306 15809674
9. Kimura M The neutral theory of molecular evolution. Evolution of Genes and Proteins Sunderland, Massachusetts: Sinauer Associates, Inc. Nei M, Koehn RK 1983, 208-233.
10. Fay JC Wyckoff GJ Wu CI Positive and negative selection on the human genome. Genetics 2001, 158:1227-1234. 1461725 11454770
11. Zhang L Li WH Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol 2005, 22:2504-2507. 10.1093/molbev/msi240 16107590
12. Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87. 10.1038/nature04072 16136131
13. Ensembl http://www.ensembl.org
14. Gibbons JD Nonparametric Measures of Association Newbury Park: Sage Publications 1993.
15. Altschul SF Madden TL Shäffer 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, 25:3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
16. Rocha EP Danchin A An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol 2004, 21:108-116. 10.1093/molbev/msh004 14595100
17. Pál C Papp B Hurst LD Highly expressed genes in yeast evolve slowly. Genetics 2001, 158:927-931. 1461684 11430355
18. Subramanian S Kumar S Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 2004, 168:373-381. 1448110 15454550 10.1534/genetics.104.028944
19. 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
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. 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
22. Duret L Mouchiroud D Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 2000, 17:68-74. 10666707
23. Lercher MJ Chamary JV Hurst LD Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res 2004, 14:1002-1013. 419778 15173108 10.1101/ gr.1597404
24. Su AI Wiltshire T Batalov S Lapp H Ching KA Block D Zhang J Soden R Hayakawa M Kreiman G Cooke MP Walker JR Hogenesch JB A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 395923 15075390 10.1073/pnas.0400782101
25. Kondrashov FA Rogozin IB Wolf YI Koonin EV Selection in the evolution of gene duplications. Genome Biol 2002, 3. research0008.1 0008.9 10.1186/ gb-2002-3-2-research0008
26. Lynch M Conery JS The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155. 10.1126/science.290.5494.1151 11073452
27. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Geer LY Kapustin Y Khovayko O Landsman D Lipman DJ Madden TL Maglott DR Ostell J Miller V Pruitt KD Schuler GD Sequeira E Sherry ST Sirotkin K Souvorov A Starchenko G Tatusov RL Tatusova TA Wagner L Yaschenko E Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, 35: Database issue D5-D12. 1781113 17170002 10.1093/nar/gkl1031
28. HomoloGene http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene
29. Albà MM Castresana J Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol 2005, 22:598-606. 10.1093/ molbev/msi045 15537804
30. Albà MM Castresana J On homology searches by protein Blast and the characterization of the age of genes. BMC Evol Biol 2007, 7:53. 1855329 17408474 10.1186/1471-2148-7-53
31. Elhaik E Sabath N Graur D The "inverse relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence. Mol Biol Evol 2006, 23:1-3. 10.1093/molbev/msj006 16151190
32. 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
33. Lemos B Bettencourt BR Meiklejohn CD Hartl DL Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol 2005, 22:1345-1354. 10.1093/ molbev/msi122 15746013
34. Larracuente AM Sackton TB Greenberg AJ Wong A Singh ND Sturgill D Zhang Y Oliver B Clark AG Evolution of protein-coding genes in Drosophila. Trends Genet 2008, 24:114-123. 10.1016/j.tig.2007.12.001 18249460
35. Zhang J Protein-length distributions for the three domains of life. Trends Genet 2000, 16:107-109. 10.1016/S0168-9525(99)01922-8 10689349
36. Liao BY Scott NM Zhang J Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol 2006, 23:2072-2080. 10.1093/molbev/msl076 16887903
37. Lipman DJ Souvorov A Koonin EV Panchenko AR Tatusova TA The relationship of protein conservation and sequence length. BMC Evol Biol 2002, 2:20. 137605 12410938 10.1186/1471-2148-2-20
38. Ferrer-Costa C Orozco M de la Cruz X Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 2002, 315:771-786. 10.1006/ jmbi.2001.5255 11812146
39. Wang Z Moult J SNPs, protein structure, and disease. Hum Mutat 2001, 17:263-270. 10.1002/humu.22 11295823
40. Rost B How to use protein 1D structure predicted by PROFphd. The Proteomics Protocols Handbook Totowa NJ: Humana Walker JE 2005, 875-901.
41. Jones DT Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292:195-202. 10.1006/jmbi.1999.3091 10493868
42. Dunker AK Lawson JD Brown CJ Williams RM Romero P Oh JS Oldfield CJ Campen AM Ratliff CM Hipps KW Ausio J Nissen MS Reeves R Kang C Kissinger CR Bailey RW Griswold MD Chiu W Garner EC Obradovic Z Intrinsically disordered protein. J Mol Graph Model 2001, 19:26-59. 10.1016/S1093-3263(00)00138-8 11381529
43. Ward JJ Sodhi JS McGuffin LJ Buxton BF Jones DT Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645. 10.1016/ j.jmb.2004.02.002 15019783
44. Liu J Tan H Rost B Loopy proteins appear conserved in evolution. J Mol Biol 2002, 322:53-64. 10.1016/S0022-2836(02)00736-2 12215414
45. Dunker AK Cortese MS Romero P Iakoucheva LM Uversky VN Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148. 10.1111/j.1742-4658.2005.04948.x 16218947
46. Wootton JC Federhen S Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996, 266:554-571. 8743706
47. Ramensky V Bork P Sunyaev S Human non-synonymous SNPs: Server and survey. Nucleic Acids Res 2002, 30:3894-3900. 137415 12202775 10.1093/ nar/gkf493
48. Julenius K Pedersen AG Protein evolution is faster outside the cell. Mol Biol Evol 2006, 23:2039-2048. 10.1093/molbev/msl081 16891379
49. Bendtsen JD Nielsen H von Heijne G Brunak S Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795. 10.1016/ j.jmb.2004.05.028 15223320
50. Krogh A Larsson B von Heijne G Sonnhammer EL Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 2001, 305:567-580. 10.1006/jmbi.2000.4315 11152613
51. Nair R Rost B Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol 2005, 348:85-100. 10.1016/ j.jmb.2005.02.025 15808855
52. Camon E Magrane M Barrell D Lee V Dimmer E Maslen J Binns D Harte N Lopez R Apweiler R The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, 32: Database issue D262-D266. 308756 14681408 10.1093/nar/gkh021
53. Finn RD Mistry J Schuster-Bockler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Eddy SR Sonnhammer EL Bateman A Pfam: Clans, web tools and services. Nucleic Acids Res 2006, 34: Database issue D247-D251. 1347511 16381856 10.1093/nar/gkj149
54. Smith NG Eyre-Walker A Human disease genes: Patterns and predictions. Gene 2003, 318:169-175. 10.1016/S0378-1119(03)00772-8 14585509
55. Huang H Winter EE Wang H Weinstock KG Xing H Goodstadt L Stenson PD Cooper DN Smith D Alba MM Ponting CP Fechtel K Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol 2004, 5:R47. 463309 15239832 10.1186/gb-2004-5-7-r47
56. Kondrashov FA Ogurtsov AY Kondrashov AS Bioinformatical assay of human gene morbidity. Nucleic Acids Res 2004, 32:1731-1737. 390328 15020709 10.1093/nar/gkh330
57. Futreal PA Coin L Marshall M Down T Hubbard T Wooster R Rahman N Stratton MR A census of human cancer genes. Nat Rev Cancer 2004, 4:177-183. 10.1038/nrc1299 14993899
58. Forbes S Clements J Dawson E Bamford S Webb T Dogan A Flanagan A Teague J Wooster R Futreal PA Stratton MR COSMIC 2005. Br J Cancer 2006, 94:318-322. 10.1038/sj.bjc.6602928 16421597
59. Tu Z Wang L Xu M Zhou X Chen T Sun F Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 2006, 7:31. 1397819 16504025 10.1186/1471-2164-7-31
60. 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
61. Jordan IK Wolf YI Koonin EV No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly. BMC Evol Biol 2003, 3:1. 140311 12515583 10.1186/1471-2148-3-1
62. 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
63. Batada NN Hurst LD Tyers M Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2006, 2:e88. 1500817 16839197 10.1371/ journal.pcbi.0020088
64. Kerrien S Alam-Faruque Y Aranda B Bancarz I Bridge A Derow C Dimmer E Feuermann M Friedrichsen A Huntley R Kohler C Khadake J Leroy C Liban A Lieftink C Montecchi-Palazzi L Orchard S Risse J Robbe K Roechert B Thorneycroft D Zhang Y Apweiler R Hermjakob H IntAct - open source resource for molecular interaction data. Nucleic Acids Res 2007, 35: Database issue D561-D565. 1751531 17145710 10.1093/nar/gkl958
65. Parmley JL Urrutia AO Potrzebowski L Kaessmann H Hurst LD Splicing and the evolution of proteins in mammals. PLoS Biol 2007, 5:e14. 1790955 17298171 10.1371/journal.pbio.0050014
66. Koonin EV Wolf YI Evolutionary systems biology: Links between gene evolution and function. Curr Opin Biotechnol 2006, 17:481-487. 10.1016/ j.copbio.2006.08.003 16962765
67. Gene Expression Atlas http://wombat.gnf.org/index.html
68. Yanai I Benjamin H Shmoish M Chalifa-Caspi V Shklar M Ophir R Bar-Even A Horn-Saban S Safran M Domany E Lancet D Shmueli O Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005, 21:650-659. 10.1093/ bioinformatics/bti042 15388519
69. GOA slim ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/goslim/goaslim.map
70. IntAct ftp://ftp.ebi.ac.uk/pub/databases/intact/
71. Cancer Gene Census http://www.sanger.ac.uk/genetics/CGP/Census/
72. Catalogue Of Somatic Mutations In Cancer http://www.sanger.ac.uk/ genetics/CGP/cosmic/
73. OMIM http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
74. Miyata T Yasunaga T Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol 1980, 16:23-36. 10.1007/BF01732067 6449605