Annotation of the m. tuberculosis hypothetical orfeome: Adding functional information to more than half of the uncharacterized proteins

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Doerks, Tobias ^a   van Noort, Vera ^a   Minguez, Pablo ^a   Bork, Peer ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HYBRID PROTEIN; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENETICS; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OPEN READING FRAME; OPERON; ORFEOME; ORTHOLOGY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; BIOSYNTHESIS; CELL WALL; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PROTEIN PROTEIN INTERACTION;

MYCOBACTERIUM TUBERCULOSIS;

BACTERIAL PROTEINS; BIOSYNTHETIC PATHWAYS; CELL WALL; MOLECULAR SEQUENCE ANNOTATION; MYCOBACTERIUM TUBERCULOSIS; OPEN READING FRAMES; OPERON; PHYLOGENY; PROTEIN INTERACTION MAPS; SEQUENCE ANALYSIS, DNA;

EID: 84859260583     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034302     Document Type: Article

References (38)

1. Roberts RJ, (2004) Identifying protein function - a call for community action. PloS 2: E42.
2. Doerks T, Andrade MA, Lathe W 3rd, von Mering C, Bork P, (2004) Global analysis of bacterial transcription factors to predict cellular target processes. Trends Genet 20: 126-131.
3. Galperin MY, Koonin EV, (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452-63.
4. Southwick F, (2007) "Chapter 4: Pulmonary Infections". Infectious Diseases: A Clinical Short Course, 2nd ed. McGraw-Hill Medical Publishing Division ISBN 0071477225.
5. "Tuberculosis Fact sheet N°104". World Health Organization. Available: (http://who.int/mediacentre/factsheets/fs104/en/) Accessed November 2010.
6. Kumar V, Abbas AK, Fausto N, Mitchell RN, (2007) Robbins Basic Pathology (8th ed.). pp. 516-522 Saunders Elsevier ISBN 978-1-4160-2973-1.
7. Lew JM, Kapopoulou A, Jones LM, Cole ST, (2011) TubercuList- 10 years after.Tuberculosis (Edinb). Jan 91 (1): 1-7.
8. Eisen JA, (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167.
9. Huynen MA, Snel B, von Mering C, Bork P, (2003) Function prediction and protein networks. Curr Opin Cell Bio 15: 191-198.
10. Koonin EM, (2005) Orthologs, paralogs and evolutionary genomics. Annu Rev Genet 39: 309-338.
11. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, et al. (2010) eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 38: D190-5.
12. Bork P, Koonin EV, (1998) Predicting functions from protein sequences-where are the bottlenecks? Nat Genet 18: 313-8.
13. Dandekar T, Snel B, Huynen M, Bork P, (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328.
14. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA, (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
15. Huynen MA, Bork P, (1998) Measuring genome evolution. Proc Natl Acad Sci U S A 95: 5849-56.
16. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D, (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86.
17. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci 96: 2896-2901.
18. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
19. Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C, (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res 30: 306-309.
20. Date SV, Marcotte EM, (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 21: 1055-1062.
21. von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, et al. (2003) Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A 100: 15428-15433.
22. Huynen M, Snel B, Lathe W 3rd, Bork P, (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10: 1204-1210.
23. Mazandu GK, Mulder NJ, (2011) Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction. Infect Genet Evol [Epub ahead of print].
24. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
25. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31: 258-261.
26. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39 (Database issue): D561-8 Epub 2010 Nov 2.
27. Camus J, Pryor MJ, Médigue C, Cole ST, (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis. H37RvMicrobiology 148: 2967-2973.
28. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-44.
29. Jackson M, Crick DC, Brennan PJ, (2000) Phosphatidylinositol is an essential phospholipid of mycobacteria. J Biol Chem 2000 29: 30092-9.
30. Spraggon G, Pantazatos D, Klock HE, Wilson IA, Woods VL Jr, et al. (2004) On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171. Protein Sci 13: 3187-99.
31. Beloqui A, Pita M, Polaina J, Martínez-Arias A, Golyshina OV, et al. (2006) Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. J Biol Chem 281: 22933-42.
32. Roberts SA, Weichsel A, Grass G, Thakali K, Hazzard JT, et al. (2002) Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in Escherichia coli. Proc Natl Acad Sci U S A 99: 2766-71.
33. Boyle DS, Khattar MM, Addinall SG, Lutkenhaus J, Donachie WD, (1997) ftsW is an essential cell-division gene in Escherichia coli. Mol Microbiol 24: 1263-73.
34. Anishettya S, Pulimia M, Pennathur G, (2005) Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysisis. Comput Biol Chem 29: 368-378.
35. Honrubia MP, Ramos A, Gil JA, (2001) The cell division genes ftsQ and ftsZ, but not the three downstream open reading frames YFIH, ORF5 and ORF6, are essential for growth and viability in Brevibacterium lactofermentum ATCC 13869. Mol Genet Genomics 265 (6): 1022-30.
36. White EL, Southworth K, Ross L, Cooley S, Gill RB, et al. (2006) A novel inhibitor of Mycobacterium tuberculosis pantothenate synthetase. J Biomol Screen 12: 100-5.
37. Goulding CW, Apostol MI, Sawaya MR, Phillips M, Parseghian A, et al. (2005) Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme. J Mol Biol 349: 61-72.
38. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-D360.