Regular patterns for proteome-wide distribution of protein abundance across species

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Zhong, Fan ^a,b   Yang, Dong ^a,c   Hao, Yunwei ^a,c   Lin, Chengzhao ^b   Jiang, Ying ^a,c   Ying, Wantao ^a,c   Wu, Songfeng ^a,c   Zhu, Yunping ^a,c   Liu, Siqi ^d   Yang, Pengyuan ^b   Qian, Xiaohong ^a,c   He, Fuchu ^a,b,c  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b FUDAN UNIVERSITY   (China)

^c National Engineering Research Center for Protein Drugs   (China)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; PROTEIN;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DOMAIN COVERAGE; DOMAIN NUMBER; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENETIC CONSERVATION; HUMAN; HUMAN TISSUE; INTRACELLULAR SIGNALING; MOLECULAR PHYLOGENY; MOUSE; NONHUMAN; PROTEIN ABUNDANCE; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SPECIES DIFFERENCE; ANIMAL; BIODIVERSITY; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; NONPARAMETRIC TEST; PROTEIN TERTIARY STRUCTURE;

ANIMALS; BIODIVERSITY; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; HUMANS; MICE; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; STATISTICS, NONPARAMETRIC;

EID: 84863248733     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032423     Document Type: Article

References (37)

1. Cox J, Mann M, (2007) Is proteomics the new genomics? Cell 130: 395-398.
2. Eriksson J, Fenyö D, (2007) Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs. Nat Biotechnol 25 (6): 651-655.
3. Yang D, Jiang Y, He F, (2009) An integrated view of the correlations between genomic and phenomic variables. J Genet Genomics 36: 645-651.
4. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH, (2005) Why highly expressed proteins evolve slowly? Proc Natl Acad Sci USA 102: 14338-14343.
5. Tuller T, Kupiec M, Ruppin E, (2007) Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 3: e248.
6. Drummond DA, Wilke CO, (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
7. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA, (2002) Selection for short introns in highly expressed genes. Nat Genet 31: 415-418.
8. Urrutia AO, Hurst LD, (2003) The signature of selection mediated by expression on human genes. Genome Res 3: 2260-2264.
9. Warringer J, Blomberg A, (2006) Evolutionary constraints on yeast protein size. BMC Evol Biol 6: 61.
10. Greenbaum D, Jansen R, Gerstein M, (2002) Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18: 585-596.
11. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9: 102.
12. Ingvarsson PK, (2007) Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol 24: 836-844.
13. Urrutia AO, Hurst LD, (2001) Codon bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159: 1191-1199.
14. Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, et al. (2011) The quantitative proteome of a human cell line. Mol Syst Biol 7: 549.
15. He F, (2005) Human liver proteome project: plan progress and perspectives. Mol Cell Proteomics 4: 1841-1848.
16. Jiang Y, Ying W, Wu S, Chen M, Zhong F, et al. (2010) First insight into the human liver proteome from PROTEOME(SKY)-LIVER(Hu) 1.0 a publicly available database. J Proteome Res 9: 79-94.
17. Lai KK, Kolippakkam D, Beretta L, (2008) Comprehensive and quantitative proteome profiling of the mouse liver and plasma. Hepatology 47: 1043-1051.
18. Zhao Y, Denner L, Haidacher SJ, LeJeune WS, Tilton RG, (2008) Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC-tandem mass spectrometry. Proteome Sci 6: 15.
19. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, et al. (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25: 576-583.
20. Merrihew GE, Davis C, Ewing B, Williams G, Kall L, et al. (2008) Use of shotgun proteomics for the identification confirmation and correction of C elegans gene annotations. Genome Res 18: 1660-1669.
21. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741.
22. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
23. Hedges SB, (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-849.
24. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
25. Basu MK, Carmel L, Rogozin IB, Koonin EV, (2008) Evolution of protein domain promiscuity in eukaryotes. Genome Res 18: 449-461.
26. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36 (Database issue): D281-288.
27. Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34 (Database issue): D257-260.
28. Ng SK, Zhang Z, Tan SH, Lin K, (2003) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res 31: 251-254.
29. Wang Z, Zhang J, (2009) Why is the correlation between gene importance and gene evolutionary rate so weak? PLoS Genet 5: e1000329.
30. Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, et al. (2009) Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 7: e48.
31. Koonin EV, Aravind L, Kondrashov AS, (2000) The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
32. Koonin EV, Wolf YI, Karev GP, (2002) The structure of the protein universe and genome evolution. Nature 420: 218-223.
33. Xia K, Fu Z, Hou L, Han JD, (2008) Impacts of protein-protein interaction domains on organism and network complexity. Genome Res 18: 1500-1508.
34. Oakley TH, Rivera AS, (2008) Genomics and the evolutionary origins of nervous system complexity. Curr Opin Genet Dev 18: 479-492.
35. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
36. Altshuler D, Daly M J, Lander ES, (2008) Genetic mapping in human disease. Science 322: 881-888.
37. Saeed R, Deane CM, (2006) Protein protein interactions, evolutionary rate, abundance and age. BMC Bioinformatics 7: 128.