A large-scale protein-protein interaction analysis in synechocystis sp. PCC6803

DNA Research

Volumn 14, Issue 5, 2007, Pages 207-216

  Sato, Shusei ^a   Shimoda, Yoshikazu ^a   Muraki, Akiko ^a   Kohara, Mitsuyo ^a   Nakamura, Yasukazu ^a   Tabata, Satoshi ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

Protein protein interactions; Synechocystis sp. strain PCC6803; Yeast two hybrid system

Indexed keywords

ARABIDOPSIS PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; PRIMER DNA;

ARABIDOPSIS; ARTICLE; BACTERIAL GENOME; COMPARATIVE STUDY; GENETICS; GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; STATISTICS; SYNECHOCYSTIS; TWO HYBRID SYSTEM;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BACTERIAL PROTEINS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; GENOME, BACTERIAL; GENOME, PLANT; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; SYNECHOCYSTIS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 39749105401     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsm021     Document Type: Article

References (39)

1. Kaneko, T., Sato, S., Kotani, H., et al. 1996, Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions, DNA Res., 3, 109-136.
2. Ikeuchi, M. and Tabata, S. 2001, Synechocystis sp. PCC 6803 - a useful tool in the study of the genetics of cyanobac-teria, Photosynth Res., 70, 73-83.
3. Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A. and Ikeuchi, M. 2001, DNA microarray analysis of cyanobacterial gene expression during acclimation to high light, Plant Cell, 13, 793-806.
4. Sazuka, T., Yamaguchi, M. and Ohara, O. 1999, Cyano2Dbase updated: linkage of 234 protein spots to corresponding genes through N-terminal microsequencing, Electrophoresis, 20, 2160-2171.
5. Nakamura, Y., Kaneko, T., Miyajima, N. and Tabata, S. 1999, Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803, Nucleic Acids Res., 27, 66-68.
6. Nakamura, Y., Kaneko, T. and Tabata, S. 2000, CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000, Nucleic Acids Res., 28, 72.
7. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., et al. 2000, A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature, 403, 623-627.
8. 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.
9. Walhout, A. J., Sordella, R., Lu, X., et al. 2000, Protein interaction mapping in C. elegans using proteins involved in vulval development, Science, 287, 116-122.
10. Rain, J. C., Selig, L., De Reuse, H., et al. 2001, The protein - protein interaction map of Helicobacter pylori, Nature, 409, 211-215.
11. Giot, L., Bader, J. S., Brouwer, C., et al. 2003, A protein interaction map of Drosophila melanogaster, Science, 302, 1727-1736.
12. LaCount, D. J., Vignali, M., Chettier, R., et al. 2005, A protein interaction network of the malaria parasite Plasmodium falciparum, Nature, 438, 103-107.
13. Parrish, J. R., Yu, J., Liu, G., et al. 2007, A proteome-wide protein interaction map for Campylobacter jejuni, Genome Biol., 8, R130.
14. Mizuno, T., Kaneko, T and Tabata, S. 1996, Compilation of all genes encoding bacterial two-component signal transducers in the genome of the cyanobacterium, Synechocystis sp. strain PCC 6803, DNA Res., 3, 407-414.
15. Murata, N. and Suzuki, I. 2006, Exploitation of genomic sequences in a systematic analysis to access how cyano-bacteria sense environmental stress, J. Exp. Bot., 57, 235-247.
16. Rujan, T. and Martin, W. 2000, How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies, Trends Genet., 17, 113-120.
17. Martin, W., Rujan, T., Richly, E., et al. 2002, Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyano-bacterial genes in the nucleus, Proc. Natl Acad. Sci. USA, 99, 12246-12251.
18. Fromont-Racine, M., Rain, J.-C. and Legrain, P. 1997, Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet., 16, 277-282.
19. Ito, H., Fukuda, Y., Murata, K. and Kimura, A. 1983, Transformation of intact yeast cells treated with alkali cations, J. Bacteriol., 153, 163-168.
20. Uetz, P. and Hughes, R. E. 2000, Systematic and large-scale two-hybrid screens, Curr. Opin. Microbiol., 3, 303-308.
21. Saito, R., Suzuki, H. and Hayashizaki, Y. 2002, Interaction generality, a measurement to assess the reliability of a protein-protein interaction, Nucleic Acids Res., 30, 1163-1168.
22. Fields, S. 2005, High-throughput two-hybrid analysis. The promise and the peril, FEBS J., 272, 5391-5399.
23. Suzuki, H., Fukunishi, Y., Kagawa, I., et al. 2007, Proteinprotein interaction panel using mouse full-length cDNAs, Genome Res., 11, 1758-1765.
24. Ng, S. K., Zhang, Z., Tan, S.H. and Lin, K. 2003, InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes, Nucleic Acids Res. 31, 251-254.
25. Arifuzzaman, M., Maeda, M., Itoh, A., et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12, Genome Res., 16, 686-691.
26. Shannon, P., Markiel, A., Ozier, O., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498-2504.
27. Snel, B., Bork, P. and Huynen, M. A. 2002, The identification of functional modules from the genomic association of genes, Proc. Natl Acad. Sci., 99, 5890-5895.
28. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. and Maltsev, N. 1999, The use of gene clusters to infer functional coupling, Proc. Natl Acad. Sci., 96, 2896-2901.
29. Helmann, J. D. 2002, The extracytoplasmic function (ECF) sigma factors, Adv. Microb. Physiol., 46, 47-110.
30. Ispolatov, I., Yuryev, A., Mazo, I. and Maslov, S. 2005, Binding properties and evolution of homodimers in protein-protein interaction networks, Nucleic Acids Res. 33, 3629-3635.
31. Alex, L. A. and Simon, M. I. 1994, Protein histidine kinases and signal transduction in prokaryotes and eukaryotes, Trends Genet., 10, 133-138.
32. Parkinson, J. S. and Kofoid, E. C. 1992, Communication modules in bacterial signaling proteins, Annu. Rev. Genet., 26, 71-112.
33. Wanner, B.L. 1992, Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria, J. Bacteriol., 174, 2053-2058.
34. Suzuki, I., Los, D. A., Kanesaki, Y., Mikami, K. and Murata, N. 2000, The pathway for perception and transduction of low-temperature signals in Synechocystis, EMBO J., 19, 1327-1334.
35. Paithoonrangsarid, K., Shoumskaya, M. A., Kanesaki, Y., et al. 2004, Five histidine kinases perceive osmotic stress and regulate distinct sets of genes in Synechocystis, J. Biol. Chem., 279, 53078-53086.
36. Shoumskaya, M. A., Paithoonrangsarid, K., Kanesaki, Y., et al. 2005, Identical Hik-Rre systems are involved in perception and transduction of salt signals and hyperosmotic signals but regulate the expression of individual genes to different extents in Synechocystis, J. Biol. Chem., 280, 21531-21538.
37. Sasaki, Y. and Nagano, Y. 2004, Plant acetyl-CoA carboxylase: Structure, biosynthesis, regulation, and gene manipulation for plant breeding, Biosci. Biotechnol. Biochem., 68, 1175-1184.
38. Yamaguchi, K. and Subramanian, A. R. 2003, Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit, Eur. J. Biochem., 270, 190-205.
39. Osanai, T., Sato, S., Tabata, S. and Tanaka, K. 2005, Identification of PamA as a PII-binding membrane protein important in nitrogen-related and sugar-catabolic gene expression in Synechocystis sp. PCC 6803, J. Biol. Chem., 280, 34684-34690.