Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors

Journal of Bacteriology

Volumn 193, Issue 17, 2011, Pages 4338-4345

  Draper, Jenny ^a   Karplus, Kevin ^a   Ottemann, Karen M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CHEMORECEPTOR ZINC BINDING DOMAIN PROTEIN TLPD; CYCLIC GMP; CYTOPLASMIC RECEPTOR; NITRATE; NITRITE; UNCLASSIFIED DRUG; ZINC BINDING PROTEIN;

ARTICLE; ATOMIC EMISSION SPECTROMETRY; CHEMORECEPTOR; CHEMOTAXIS; CONTROLLED STUDY; DISSOCIATION CONSTANT; HELICOBACTER PYLORI; HETEROLOGOUS EXPRESSION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; SIGNAL TRANSDUCTION;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; CHEMOTAXIS; CLONING, MOLECULAR; CYCLIC GMP; CYSTEINE; CYTOPLASM; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; HELICOBACTER PYLORI; HISTIDINE; MUTATION; PROTEIN BINDING; RECEPTORS, CYTOPLASMIC AND NUCLEAR; SIGNAL TRANSDUCTION; ZINC;

BACTERIA (MICROORGANISMS); HELICOBACTER PYLORI;

EID: 80052321528     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05140-11     Document Type: Article

References (44)

1. Alexandre, G., S. Greer-Phillips, and I. B. Zhulin. 2004. Ecological role of energy taxis in microorganisms. FEMS Microbiol. Rev. 28:113-126.
2. Alm, R. A., et al. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-180.
3. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Anantharaman, V., and L. Aravind. 2001. The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci. 26:579-582.
5. Andermann, T. M., Y.-T. Chen, and K. M. Ottemann. 2002. Two predicted chemoreceptors promote Helicobacter pylori infection. Infect. Immun. 70: 5877-5881.
6. Auld, D. S. 2001. Zinc coordination sphere in biochemical zinc sites. Bio-Metals 14:271-313.
7. Bellucci, M., B. Zambelli, F. Musiani, P. Turano, and S. Ciurli. 2009. Helicobacter pylori UreE, a urease accessory protein: specific Ni(2+)- and Zn(2+)-binding properties and interaction with its cognate UreG. Biochem. J. 422:91-100.
8. Boehm, A., et al. 2009. Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress. Mol. Microbiol. 72:1500-1516.
9. Castillo, A. R., A. J. Woodruff, L. E. Connolly, W. E. Sause, and K. M. Ottemann. 2008. Recombination-based in vivo expression technology identifies Helicobacter pylori genes important for host colonization. Infect. Immun. 76:5632-5644.
10. Cerda, O., A. Rivas, and H. Toledo. 2003. Helicobacter pylori strain ATCC700392 encodes a methyl-accepting chemotaxis receptor protein (MCP) for arginine and sodium bicarbonate. FEMS Microbiol. Lett. 224: 175-181.
11. Croxen, M. A., G. Sisson, R. Melano, and P. S. Hoffman. 2006. The Helicobacter pylori chemotaxis receptor TlpB (HP0103) is required for pH taxis and for colonization of the gastric mucosa. J. Bacteriol. 188:2656-2665.
12. Finn, R. D., et al. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
13. Foynes, S., et al. 2000. Helicobacter pylori possesses two CheY response regulators and a histidine kinase sensor, CheA, which are essential for chemotaxis and colonization of the gastric mucosa. Infect. Immun. 68:2016- 2023.
14. Galperin, M. Y., A. N. Nikolskaya, and E. V. Koonin. 2001. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol. Lett. 203:11-21.
15. Hazelbauer, G. L., J. J. Falke, and J. S. Parkinson. 2008. Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem. Sci. 33:9-19.
16. Hecht, G. B., and A. Newton. 1995. Identification of a novel response regulator required for the swarmer-to-stalked-cell transition in Caulobacter crescentus. J. Bacteriol. 177:6223-6229.
17. Heger, A., and L. Holm. 2003. Exhaustive enumeration of protein domain families. J. Mol. Biol. 328:749-767.
18. Hou, S., et al. 2000. Myoglobin-like aerotaxis transducers in Archaea and Bacteria. Nature 403:540-544.
19. Hulo, N., et al. 2006. The PROSITE database. Nucleic Acids Res. 34:D227- D230.
20. Jakob, U., M. Eser, and J. C. A. Bardwell. 2000. Redox switch of Hsp33 has a novel zinc-binding motif. J. Biol. Chem. 275:38302-38310.
21. Jonas, K., et al. 2008. The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins. Mol. Microbiol. 70:236-257.
22. Karplus, K. 2009. SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res. 37:W492-W497.
23. Karplus, K., et al. 2005. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 61(Suppl. 7):135-142.
24. Katzman, S., C. Barrett, G. Thiltgen, R. Karchin, and K. Karplus. 2008. PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics 24:2453-2459.
25. Letunic, I., T. Doerks, and P. Bork. 2009. SMART 6: recent updates and new developments. Nucleic Acids Res. 37:D229-D232.
26. Marchler-Bauer, A., et al. 2009. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 37:D205-D210.
27. Maret, W., and Y. Li. 2009. Coordination dynamics of zinc in proteins. Chem. Rev. 109:4682-4707.
28. Martell, A. E., and R. M. Smith. 1974. Critical stability constants. Plenum Press, New York, NY.
29. McGee, D. J., et al. 2005. Colonization and inflammation deficiencies in Mongolian gerbils infected by Helicobacter pylori chemotaxis mutants. Infect. Immun. 73:1820-1827.
30. Merkel, T., C. Barros, and S. Stibitz. 1998. Characterization of the bvgR locus of Bordetella pertussis. J. Bacteriol. 180:1682-1690.
31. Miller, L. D., M. H. Russell, and G. Alexandre. 2009. Diversity in bacterial chemotactic responses and niche adaptation. Adv. Appl. Microbiol. 66:53-75.
32. Mougel, C., and I. B. Zhulin. 2001. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci. 26:582-584.
33. Outten, C. E., and T. V. O'Halloran. 2001. Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis. Science 292:2488-2492.
34. Schultz, J., F. Milpetz, P. Bork, and C. P. Ponting. 1998. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. U. S. A. 95:5857-5864.
35. Schweinitzer, T., et al. 2008. Functional characterization and mutagenesis of the proposed behavioral sensor TlpD of Helicobacter pylori. J. Bacteriol. 190:3244-3255.
36. Shu, C. J., L. E. Ulrich, and I. B. Zhulin. 2003. The NIT domain: a predicted nitrate-responsive module in bacterial sensory receptors. Trends Biochem. Sci. 28:121-124.
37. Taylor, B. L., and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63:479-506.
38. Terry, K., S. M. Williams, L. Connolly, and K. M. Ottemann. 2005. Chemotaxis plays multiple roles in Helicobacter pylori animal infection. Infect. Immun. 73:803-811.
39. Testerman, T. L., D. J. McGee, and H. L. Mobley. 2001. Helicobacter pylori growth and urease detection in the chemically defined medium Ham's F-12 nutrient mixture. J. Clin. Microbiol. 39:3842-3850.
40. Tomb, J.-F., et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
41. Van Wart, H. E., and H. Birkedal-Hansen. 1990. The cysteine switch: a principle of regulation of metalloproteinase activity with potential applicability to the entire matrix metalloproteinase gene family. Proc. Natl. Acad. Sci. U. S. A. 87:5578-5582.
42. Wadhams, G. H., and J. P. Armitage. 2004. Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5:1024-1037.
43. Williams, S. M., et al. 2007. Helicobacter pylori chemotaxis modulates inflammation and bacterium-gastric epithelium interactions in infected mice. Infect. Immun. 75:3747-3757.
44. Wuichet, K., R. P. Alexander, and I. B. Zhulin. 2007. Comparative genomic and protein sequence analysis of a complex system controlling bacterial chemotaxis. Methods Enzymol. 422:1-31.