Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica

Nucleic Acids Research

Volumn 32, Issue 3, 2004, Pages 1059-1064

  Malek, Joel A ^a   Wierzbowski, Jamey M ^a   Tao, Wei ^a   Bosak, Stephanie A ^a   Saranga, David J ^a   Doucette Stamm, Lynn ^a   Smith, Douglas R ^a   McEwan, Paul J ^a   McKernan, Kevin J ^a  

^a Agencourt Bioscience Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRULENCE FACTOR; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOACCUMULATION; CONTROLLED STUDY; CYTOLYSIS; DATA ANALYSIS; ENDOTHELIUM CELL; FEVER; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; MOLECULAR MECHANICS; NONHUMAN; PATHOGENICITY; PRIORITY JOURNAL; PROGENY; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN SECRETION; PROTEOMICS; RICKETTSIA; RICKETTSIA SIBIRICA; SEQUENCE ANALYSIS; TWO HYBRID SYSTEM; EVALUATION; GENE LIBRARY; GENETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE;

BACTERIA (MICROORGANISMS); RICKETTSIA; RICKETTSIA SIBIRICA; RICKETTSIA SIBIRICA 246; SPOTTED FEVER GROUP;

BACTERIAL PROTEINS; BASE SEQUENCE; GENOME, BACTERIAL; GENOMIC LIBRARY; PROTEIN INTERACTION MAPPING; RICKETTSIA;

EID: 2342620064     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh254     Document Type: Article

References (25)

1. Eisenberg,D., Marcotte,E.M., Xenarios,I. and Yeates,T.O. (2000) Protein function in the post-genomic era. Nature, 405, 823-826.
2. Oliver,S. (2000) Proteomics: guilt-by-association goes global. Nature, 403, 601-603.
3. Walhout,A.J., Reboul,J., Shtanko,O., Bertin,N., Vaglio,P., Ge,H., Lee,H., Doucette-Stamm,L., Gunsalus,K.C., Schetter,A.J. et al. (2000) Protein interaction mapping in C.elegans using proteins involved in vulval development. Science, 287, 116-122.
4. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
5. Ito,T., Tashiro,K., Muta,S., Ozawa,R., Chiba,T., Nishizawa,M., Yamamoto,K., Kuhara,S. and Sakaki,Y. (2000) Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA, 97, 1143-1147.
6. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
7. Reboul,J., Vaglio,P., Rual,J.F., Lamesch,P., Martinez,M., Armstrong,C.M., Li,S., Jacotot,L., Bertin,N., Janky,R. et al. (2003) C.elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nature Genet., 34, 35-41.
8. Rain,J.C., Selig,L., De Reuse,H., Battaglia,V., Reverdy,C., Simon,S., Lenzen,G., Petel,F., Wojcik,J., Schachter,V. et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
9. Ward,D.V., Draper,O., Zupan,J.R. and Zambryski,P.C. (2002) Peptide linkage mapping of the Agrobacterium tumefaciens vir-encoded type IV secretion system reveals protein subassemblies. Proc. Natl Acad. Sci. USA, 99, 11493-11500.
10. Hu,J.C., Kornacker,M.G. and Hochschild,A. (2000) Escherichia coli one- and two-hybrid systems for the analysis and identification of protein-protein interactions. Methods, 20, 80-94.
11. Ladant,D. and Karimova,G. (2000) Genetic systems for analyzing protein-protein interactions in bacteria. Res. Microbiol., 151, 711-720.
12. Dove,S.L., Joung,J.K. and Hochschild,A. (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature, 386, 627-630.
13. Dove,S.L. and Hochschild,A. (1998) Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev., 12, 745-754.
14. Dove,S.L. and Hochschild,A. (2001) Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. J. Bacteriol., 183, 6413-6421.
15. Shaywitz,A.J., Dove,S.L., Kornhauser,J.M., Hochschild,A. and Greenberg,M.E. (2000) Magnitude of the CREB-dependent transcriptional response is determined by the strength of the interaction between the kinase-inducible domain of CREB and the KIX domain of CREB-binding protein. Mol. Cell. Biol., 20, 9409-9422.
16. Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
17. Ogata,H., Audic,S., Renesto-Audiffren,P., Fournier,P.E., Barbe,V., Samson,D., Roux,V., Cossart,P., Weissenbach,J., Claverie,J.M. and Raoult,D. (2001) Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science, 293, 2093-2098.
18. Lander,E.S. and Waterman,M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
19. Magalon,A., Frixon,C., Pommier,J., Giordano,G. and Blasco,F. (2002) In vivo interactions between gene products involved in the final stages of molybdenum cofactor biosynthesis in Escherichia coli. J. Biol. Chem., 277, 48199-48204.
20. Ohashi,N., Zhi,N., Lin,Q. and Rikihisa,Y. (2002) Characterization and transcriptional analysis of gene clusters for a type IV secretion machinery in human granulocytic and monocytic ehrlichiosis agents. Infect. Immun., 70, 2128-2138.
21. Das,A. and Xie,Y.H. (2000) The Agrobacterium T-DNA transport pore proteins VirB8, VirB9 and VirB10 interact with one another. J. Bacteriol., 182, 758-763.
22. Christie,P.J. (2001) Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Mol. Microbiol., 40, 294-305.
23. Matthews,L.R., Vaglio,P., Reboul,J., Ge,H., Davis,B.P., Garrels,J., Vincent,S. and Vidal,M. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or 'interologs'. Genome Res., 11, 2120-2126.
24. Mahan,M.J., Tobias,J.W., Slauch,J.M., Hanna,P.C., Collier,R.J. and Mekalanos,J.J. (1995) Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl Acad. Sci. USA, 92, 669-673.
25. Ideker,T., Ozier,O., Schwikowski,B. and Siegel,A.F. (2002) Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics, 18, S233-S240.