Molecular modeling and active site analysis of SdiA homolog, a putative quorum sensor for salmonella typhimurium pathogenecity reveals specific binding patterns of AHL transcriptional regulators

Journal of Molecular Modeling

Volumn 18, Issue 10, 2012, Pages 4709-4719

  Gnanendra, Shanmugam ^a,c   Anusuya, Shanmugam ^b,c   Natarajan, Jeyakumar ^c  

^a Vivekanandha College of Arts and Sciences for Women   (India)

^b Vinayaka Missions University   (India)

^c BHARATHIAR UNIVERSITY   (India)

Author keywords

AHL auto inducers; Co infection; LuxR family proteins; Quorum sensing; Salmonella typhimurium; Transcriptional regulators

Indexed keywords

ASPARTIC ACID; BACTERIAL PROTEIN; N ACYLHOMOSERINE LACTONE; SDIA HOMOLOG; TRANSCRIPTION FACTOR LUXR; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL VIRULENCE; CHROMOBACTERIUM VIOLACEUM; ENZYME ACTIVE SITE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PSEUDOMONAS AERUGINOSA; QUORUM SENSING; RHIZOBIUM RADIOBACTER; SALMONELLA TYPHIMURIUM; STRUCTURAL HOMOLOGY; TRANSCRIPTION REGULATION;

ACYL-BUTYROLACTONES; AMINO ACID SEQUENCE; AMINO ACIDS; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; HUMANS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; QUORUM SENSING; REPRESSOR PROTEINS; REPRODUCIBILITY OF RESULTS; SALMONELLA TYPHIMURIUM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; VIRULENCE;

AGROBACTERIUM TUMEFACIENS; CHROMOBACTERIUM VIOLACEUM; NEGIBACTERIA; PSEUDOMONAS AERUGINOSA; SALMONELLA TYPHIMURIUM;

EID: 84870525619     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1469-1     Document Type: Article

References (36)

1. Scherer CA, Miller SI (2001) Molecular pathogenesis of salmonellae. In: Groisman EA (ed) Principles of bacterial pathogenesis. Academic, New York, pp 266-333.
2. Grein T, O'Flanagan D, McCarthy T, Bauer D (1999) An outbreak of multidrug-resistant Salmonella typhimurium food poisoning at a wedding reception. Ir Med J 92:238-241.
3. Davies A, O'Neill P, Towers L, Cooke M (1996) An outbreak of Salmonella typhimurium DT104 food poisoning associated with eating beef. Commun Dis Rep CDR Rev 6(11):R159-R162.
4. Molbak K, Baggesen DL, Aarestrup FM, Ebbesen JM, Engberg J, Frydendahl K, Gerner-Smidt P, Petersen AM, Wegener HC (1999) An outbreak of multidrug-resistant, quinolone-resistant Salmonella enterica serotype typhimurium DT104. N Engl J Med 341 (19):1420-1425.
5. Cloeckaert A, Chaslus-Dancla E (2001) Mechanisms of quinolone resistance in Salmonella. Vet Res 32:291-300.
6. Piddock LJ (2002) Fluoroquinolone resistance in Salmonella serovars isolated from humans and food animals. FEMS Microbiol Rev 26:3-16.
7. Coombes BK, Coburn BA, Potter AA, Gomis S, Mirakhur K, Li Y, Finlay BB (2005) Analysis of the contribution of Salmonella pathogenicity islands 1 and 2 to enteric disease progression using a novel bovine ileal loop model and a murine model of infectious enterocolitis. Infect Immun 73:7161-7169.
8. Marketon MM, Gronquist MR, Eberhard A, Gonzales JE (2002) Characterization of the Sinorhizobium meliloti sinR/sinI locus and the production of novel N-acyl homoserine lactone. J Bacteriol 184:5686-5695.
9. Parsek MR, Greenberg EP (2000) Acyl-homoserine lactone quorum sensing in Gram-negative bacteria: a signaling mechanism involved in associations with higher organisms. Proc Natl Acad Sci USA 97:8789-8793.
10. Steindler L, Venturi V (2007) Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors. FEMS Microbiol Lett 266:1-9.
11. Ahmer BMM, Jv R, Timmers CD, Valentine PJ, Heffron F (1998) Salmonella typhimurium encodes an SdiA homolog, a putative quorum sensor of the LuxR family, that regulates genes on the virulence plasmid. J Bacteriol 180:1185-1193.
12. Janssens JC, Metzger K, Daniels R, Ptacek D, Verhoeven T (2007) Synthesis of N-acyl homoserine lactone analogues reveals strong activators of SdiA, the Salmonella enteric serovar Typhimurium LuxR homologue. Appl Environ Microbiol 73:535-544.
13. Smith JN, Ahmer BM (2003) Detection of other microbial species by Salmonella: expression of the SdiA regulon. J Bacteriol 185:1357-1366.
14. Dyszel JL, Smith JN, Lucas DE, Soares JA, Swearingen MC, Vross MA, Young GM, Ahmer BM (2010) Salmonella enteric serovar Typhimurium can detect acyl homoserine lactone production by Yersinia enterocolitica in mice. J Bacteriol 192:29- 37.
15. Smith JN, Dyszel JL, Soares JA, Ellermeier CD, Altier C, Lawhon SD, Adams LG, Konjufca V, Curtiss R III, Slauch JM, Ahmer BM (2008) SdiA, an N-acylhomoserine lactone receptor, becomes active during the transit of Salmonella enteric through the gastrointestinal tract of turtles. PloS ONE 3:e2826.
16. Nicholson B, Low D (2000) DNA methylation-dependent regulation of pef expression in Salmonella typhimurium. Mol Microbiol 35:728-742.
17. Michael B, Smith JN, Swift S, Heffron F, Ahmer BM (2001) SdiA of Salmonella enteric is a LuxR homolog that detects mixed microbial communities. J Bacteriol 183:5733-5742.
18. Jiménez-Gómez P, Pozuelo de Felipe MJ, Llinares Pinell F, García de los Ríos JE (2007) Quorum-sensing in Pseudomonas aeruginosa and Salmonella: active natural compounds as antagonists. Commun Curr Res Edu Topics Trends App Microbiol 1:41-51.
19. NCBI. http://www.ncbi.nlm.nih.gov/.
20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
21. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucl Acids Res 28:235-242.
22. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position- specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673- 4680.
23. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
24. Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) Super- Pose: a simple server for sophisticated structural superposition. Nucleic Acids Res 32(1):W590-W594.
25. Walter RP, Scott PH, Hunenberger IG, Tironi AE, Mark SR, Billeter JF, Torda AE, Huber T, Kruger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103(19):3596-3607.
26. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK a program to check the stereo chemical quality of protein structure. J Appl Cryst 26:283-291.
27. Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83-85.
28. Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511- 1519.
29. SAVES (2011) http://nihserver.mbi.ucla.edu/SAVES.
30. Laskowski RA, Chistyakov VV, Thornton JM (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:D266-D268.
31. Laurie AT, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21:1908-1916.
32. ACD/ChemSketch Freeware, version 11 (2006) Advanced Chemistry Development, Inc. Toronto, ON, Canada, www.acdlabs.com.
33. Weininger D (1988) SMILES, a chemical language and information system. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31-36.
34. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-89.
35. Stierand K, Maab P, Rarey M (2006) Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinformatics 22:1710-1716.
36. Throup JP, Camara M, Briggs GS, Winson MK, Chhabra SR, Bycroft BW, Williams P, Stewart GS (1995) Characterisation of the yenI/yenR locus from Yersinia enterocolitica mediating the synthesis of two nacylhomoserine lactone signal molecules. Mol Microbiol 17:345-356.