What makes species unique? The contribution of proteins with obscure features

Genome Biology

Volumn 7, Issue 7, 2006, Pages

  Gollery, Martin ^a   Harper, Jeff ^a   Cushman, John ^a   Mittler, Taliah ^a   Girke, Thomas ^b   Zhu, Jian Kang ^b   Bailey Serres, Julia ^b   Mittler, Ron ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; PROTEIN;

AMINO ACID SEQUENCE; ANALYSIS OF VARIANCE; ARABIDOPSIS; ARTICLE; BIOCHEMISTRY; BUDDING; CHIMPANZEE; COMPARATIVE STUDY; CONTROLLED STUDY; EUKARYOTE; FLY; GENOME; HUMAN; MOSQUITO; MOUSE; NONHUMAN; PHENOTYPE; PREDICTION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; RAT; RICE; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SPECIES DIFFERENTIATION; WORM; YEAST; ANIMAL; BIOLOGICAL MODEL; GENETICS; PROTEOMICS; SPECIES DIFFERENCE;

ARABIDOPSIS; EUKARYOTA; SCHIZOSACCHAROMYCES POMBE;

ANIMALS; HUMANS; MODELS, GENETIC; PROTEINS; PROTEOMICS; SPECIES SPECIFICITY;

EID: 33747262040     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-7-r57     Document Type: Article

References (40)

1. Fay JC, Wu CI: Sequence divergence, functional constraint, and selection in protein evolution. Annu Rev Genomics Hum Genet 2003, 4:213-235.
2. Yang Z: Inference of selection from multiple species alignments. Curr Opin Genet Dev 2002, 12:688-694.
3. Robichaux RH, Purugganan MD: Accelerated regulatory gene evolution in an adaptive radiation. Proc Natl Acad Sci USA 2001, 98:10208-10213.
4. Liti, Louis EJ: Yeast evolution and comparative genomics. Annu Rev Microbiol 2005, 59:13 5-153.
5. Orengo CA, Thornton JM: Protein families and their evolution-a structural perspective. Annu Rev Biochem 2005, 74:867-900.
6. Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA: Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res 2006, 34:1066-1080.
7. Roberts RJ: Identifying protein function - a call for community action. PLoS Biol 2004, 2:E42.
8. Galperin MY, Koonin EV: 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 2004, 32:5452-5463.
9. 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, 421:231-237.
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, 418:387-391.
11. The Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87.
12. 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, 303:808-813.
13. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, et al.: A map of theinteractome network of the metazoan C. elegans. Science 2004, 303:540-543.
14. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, et al.: Intrinsically disordered protein. J Mol Graph Model 2001, 19:26-59.
15. Tompa P, Csermely P: The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004, 18:1169-1175.
16. Dunker AK, Brown CJ, Lawson JD, lakoucheva LM, Obradovic Z: Intrinsic disorder and protein function. Biochemistry 2002, 41:6573-6582.
17. Gunasekaran K, Tsai CJ, Kumar S, Zanuy D, Nussinov R: Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci 2003, 28:81-85.
18. Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, Oldfield CJ, Williams CJ, Dunker AK: Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 2002, 55:104-110.
19. Dyson HJ, Wright PE: Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6:197-208.
20. Fischer D, Eisenberg D: Finding families for genomic ORFans. Bioinformatics 1999, 15:759-762.
21. Siew N, Fischer D: Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 2003, 531:241-251.
22. Siew N, Fischer D: Structural biology sheds light on the puzzle of genomic ORFans. J Mol Biol 2004, 342:369-373.
23. NCBI Index [ftp://ftp.ncbi.nlm.nih.govn/]
24. The Arabidopsis Information Resource [http://www.arabidopsis.org/]
25. Ensembl [http://www.ensembl.org]
26. HMMER [http://hmmer.wustl.edu/]
27. Pfam [http://www.sanger.ac.uk/Software/Pfam/]
28. TIGR Protein Families [http://www.tigr.org/TIGFAMs/]
29. SMART [http://smart.embl-heidelberg.de/]
30. SUPERFAMILY: Main page [http://supfam.org/SUPERFAMILY/]
31. Chothia C, Gough J, Vogel C, Teichmann SA: Evolution of the protein repertoire. Science 2003, 300:1701-1703.
32. TimeLogic [http://www.timelogic.com]
33. NCBI BLAST [http://www.ncbi.nlm.nih.gov/blast/]
34. Database of Interacting Proteins [http://dip.doe-mbi.ucla.edu/]
35. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB: Protein disorder prediction: implications for structural proteomics. Structure 2003, 11:1453-1459.
36. DisEMBL [http://dis.embl.de]
37. Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias A: Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. J Biol Chem 2000, 275:5668-5674.
38. SAS 9 Documentation [http://support.sas.com/documentation/onlinedoc/ sas9doc.html]
39. Hartigan J: Clustering Algorithms New York, USA: Wiley; 1975.
40. Everitt BS: Cluster Analysis London, UK: Edward Arnold; 1998.