The binary protein interactome of Treponema pallidum - The syphilis spirochete

PLoS ONE

Volumn 3, Issue 5, 2008, Pages

  Titz, Björn ^a,d   Rajagopala, Seesandra V ^a,b   Goll, Johannes ^a   Häuser, Roman ^a   McKevitt, Matthew T ^c   Palzkill, Timothy ^c   Uetz, Peter ^a,b  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b J CRAIG VENTER INSTITUTE   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; AMINO ACID TRANSFER RNA LIGASE; BACTERIAL PROTEIN; CHAPERONE; DNA A; DNA B; DNA METHYLTRANSFERASE; DNA PRIMASE; DNA TOPOISOMERASE (ATP HYDROLYSING) A; DNA TOPOISOMERASE (ATP HYDROLYSING) B; EPIMERASE; EXONUCLEASE; HELICASE; HU PROTEIN; OXIDOREDUCTASE; PHOSPHORIBOSYLTRANSFERASE; PROTEIN HRPA; RIBULOSE 3 P EPIMERASE; RNA HELICASE; SINGLE STRANDED DNA; TRANSFER RNA METHYLTRANSFERASE; BACTERIAL DNA; PROTEOME;

ARTICLE; CAMPYLOBACTER JEJUNI; DNA METABOLISM; DNA PROTEIN COMPLEX; DNA REPLICATION; ESCHERICHIA COLI; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENE LOCUS; GENE SEQUENCE; NONHUMAN; OPERON; ORTHOLOGY; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TREPONEMA PALLIDUM; TWO HYBRID SYSTEM; GENETICS; METABOLISM; PROTEIN BINDING; QUALITY CONTROL;

BACTERIA (MICROORGANISMS); EUKARYOTA; SPIROCHAETALES; TREPONEMA PALLIDUM;

BACTERIAL PROTEINS; DNA, BACTERIAL; PROTEIN BINDING; PROTEOME; QUALITY CONTROL; TREPONEMA PALLIDUM; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 48249128882     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002292     Document Type: Article

References (43)

1. Galperin MY, Koonin EV (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452-5463.
2. Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18: 1257-1261.
3. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
4. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
5. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686-691.
6. Goll J, Uetz P (2006) The elusive yeast interactome. Genome Biol 7: 223.
7. Parrish JR, Yu J, Liu G, Hines JA, Chan JE, et al. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol 8: R130.
8. Gandhi TKB (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics 38: 285-293.
9. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, et al. (2001) The proteinprotein interaction map of Helicobacter pylori. Nature 409: 211-215.
10. Sato S, Shimoda Y, Muraki A, Kohara M, Nakamura Y, et al. (2007) A Large-scale Protein-protein Interaction Analysis in Synechocystis sp. PCC6803. DNA Research 14: 207-216.
11. Shimoda Y, Shinpo S, Kohara M, Nakamura Y, Tabata S, et al. (2008) A Large Scale Analysis of Protein-Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti. DNA Research 15: 13-23.
12. Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, et al. (2002) Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet 18: 529-536.
13. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
14. Rajagopala SV, Titz B, Goll J, Parrish JR, Wohlbold K, et al. (2007) The protein network of bacterial motility. Molecular Systems Biology 3: 128.
15. Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, et al. (1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281: 375-388.
16. Peeling RW, Mabey DC (2004) Syphilis. Nat Rev Microbiol 2: 448-449.
17. Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239-242.
18. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-362.
19. Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
20. Gaillard M, Vallaeys T, Vorholter FJ, Minoia M, Werlen C, et al. (2006) The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol 188: 1999-2013.
21. Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100: 12123-12128.
22. Deaconescu AM, Savery N, Darst SA (2007) The bacterial transcription repair coupling factor. Curr Opin Struct Biol 17: 96-102.
23. Trautinger BW, Jaktaji RP, Rusakova E, Lloyd RG (2005) RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 19: 247-258.
24. Boubrik F, Rouviere-Yaniv J (1995) Increased sensitivity to gamma irradiation in bacteria lacking protein HU. Proc Natl Acad Sci U S A 92: 3958-3962.
25. Harmon FG, Kowalczykowski SC (1998) RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. Genes Dev 12: 1134-1144.
26. Harmon FG, Kowalczykowski SC (2001) Biochemical characterization of the DNA helicase activity of the escherichia coli RecQ helicase. J Biol Chem 276: 232-243.
27. Huisman O, Faelen M, Girard D, Jaffe A, Toussaint A, et al. (1989) Multiple defects in Escherichia coli mutants lacking HU protein. J Bacteriol 171: 3704-3712.
28. Sikder D, Unniraman S, Bhaduri T, Nagaraja V (2001) Functional cooperation between topoisomerase I and single strand DNA-binding protein. J Mol Biol 306: 669-679.
29. Umezu K, Nakayama H (1993) RecQ DNA helicase of Escherichia coli. Characterization of the helix-unwinding activity with emphasis on the effect of single-stranded DNA-binding protein. J Mol Biol 230: 1145-1150.
30. Takahashi S, Hours C, Chu A, Denhardt DT (1979) The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can J Biochem 57: 855-866.
31. Heller RC, Marians KJ (2005) The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart. Mol Cell 17: 733-743.
32. Connelly JC, Kirkham LA, Leach DR (1998) The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA. Proc Natl Acad Sci U S A 95: 7969-7974.
33. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354-357.
34. Titz B, Rajagopala SV, Ester C, Hauser R, Uetz P (2006) A novel conserved assembly factor of the bacterial flagellum. J Bacteriol 188: 7700-7706.
35. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, et al. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res 11: 2120-2126.
36. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, et al. (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A 102: 1974-1979.
37. McKevitt M, Patel K, Smajs D, Marsh M, McLoughlin M, et al. (2003) Systematic cloning of Treponema pallidum open reading frames for protein expression and antigen discovery. Genome Res 13: 1665-1674.
38. Noirot-Gros MF, Dervyn E, Wu LJ, Mervelet P, Errington J, et al. (2002) An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A 99: 8342-8347.
39. Uchiyama I (2007) MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res 35: D343-346.
40. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
41. Deka RK, Brautigam CA, Yang XF, Blevins JS, Machius M, et al. (2006) The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum. J Biol Chem 281: 8072-8081.
42. Noens EE, Mersinias V, Willemse J, Traag BA, Laing E, et al. (2007) Loss of the controlled localization of growth stage-specific cell-wall synthesis pleiotropically affects developmental gene expression in an ssgA mutant of Streptomyces coelicolor. Mol Microbiol 64: 1244-1259.
43. Yoshida Y, Nakano Y, Nezu T, Yamashita Y, Koga T (1999) A novel NDP-6-deoxyhexosyl-4-ulose reductase in the pathway for the synthesis of thymidine diphosphate-D-fucose. J Biol Chem 274: 16933-16939.