In silico structural analysis of quorum sensing genes in Vibrio fischeri

Document Type : Original article

Author

University of Mosul, College of education for pure sciences , Biology department

Abstract

Quorum sensing controls the luminescence of Vibrio fischeri through the transcriptional activator LuxR and the specific autoinducer signal produced by luxI. Amino acid sequences of these two genes were analyzed using bioinformatics tools. LuxI consists of 193 amino acids and appears to contain five α-helices and six ß-sheets when analyzed by SSpro8. LuxI belongs to the autoinducer synthetase family and contains an acetyltransferase domain extending from residues 24 to 110 as MOTIF predicted.  LuxR, on the other hand, contains 250 amino acids and has ten α-helices and four ß-sheets. MOTIF predicted LuxR to possess functional motifs; the inducer binding site extending from amino acid residues 23 to 147 and the LuxR activator site extending between amino acids 182 and 236. The InterProScan5 server identified a winged helix-turn-helix DNA binding motif.

Keywords

References

1. Fuqua WC, Winans SC, Greenberg EP. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 1994;176: 269-275.
2. Fuqua WC, Winans SC, Greenberg EP. Census and consensus in bacterial ecosystems: The luxR-luxI family of quorum-sensing transcriptional regulators. Annu Rev Micrbiol 1996;50:727-751.
3. Miller MB, Bassler, BL. Quorum sensing in bacteria. Annu Rev Micrbiol 2001;55: 165-199.
4. Nealson KH, Hastings JW. Bacterial bioluminescence: its control and ecological significance. Microbiol Rev 1979;43:469-518.
5. Ruby EG. Lessons from a cooperative bacterial-animal association: the Vibrio fischeri-Euprymna scolopes light organ symbioses. Annu Rev Microbiol 1996;50: 591-624.
6. Dunlap PV, Greenberg EP. Control of Vibrio fischeri lux gene transcription by a cyclic AMP receptor protein-LuxR protein regulatory circuit. J Bacteriol 1988; 170:4040-4046.
7. Henke JM, Bassler BL. Bacterial social engagements. Trends cell Biol 2004;14:648-656.
8. Waters CM, Bassler, BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 2005;21:319-346.
9. Bassler BL, Losick R. Bacterial speaking. Cell 2006;125:237-246.
10. Engebrecht J, Silverman M. Nucleotide sequence of the regulatory locus controlling expression of bacterial genes for bioluminescence. Nucleic acid Res 1987;15:10455-10467
11. Kaplan HB, Greenberg EP. Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system. J Bacteriol 1985;163:1210-1214.
12. Salmond GPC, Bycraft BW, Stewart GS, Williams P. The bacterial ‘enigma’: Cracking the code of cell-cell communication. Mol Micrbiol 1995;16:615-624.
13. Engebrecht J, Silverman M. Identification of genes and gene products necessary for bacterial bioluminescence. Proc Natl Acad Sci USA 1984;81:4154-4158.
14. Engebrecht J, Nealson K, Silverman M. Bacterial bioluminescence: Isolation and genetic analysis of functions from Vibrio fischeri. Cell 1983;32:773-781.
15. Kievit TR, Iglewski BH. Bacterial quorum sensing in pathogenic relationships. Infect Immun 2000;68:4839-4849.
16. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005;33:W72–W76.
17. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22: 2577–2637.
18. Kelley LA, Sternberg MJ.Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 2009;4:363-371.
19. Bateman A, Birney E, Cerrruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshal M, Sonnhammer ELL. The Pfam protein families’ database. Nucleic Acid Res 2000;30:276-280.
20. Xiong J. ”Essential Bioinformatics”. Cambridge University Press, Cambridge 2006; pp. 85-94.
21. Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001;17:847-848.
22. Morè MI, Finger LD, Stryker JL, Fuqua C, Eberhard A, Winans SC . Enzymatic synthesis of a quorum-sensing autoinducer through use of defined substrates. Science 1996;272:1655-1658.
23. Schaefer AL, Val DL, Hanzelka BL, Cronan JE Jr, Greenberg EP. Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. Proc Natl Acad Sci USA, 1996;93:9505-9509.
24. Fuqua C, Greenberg EP. Listening in on bacteria: Acylhomoserine lactone signaling. Mol Cell Biol 2002;3:685-695.
25. Watson WT, Minogue TD, Val DL, von Bodman SB, Churchill MEA. Structural basis and specificity of Acyl-homoserine lactone signal production in bacterial quorum sensing. Mol Cell 2002;9:685-694.
26. Luscombe NM, Austin SE, Berman HM, Thornton JM. An overview of the sruc- tures of protein-DNA complexes.Genome Biol 2001;1:1-37.
27. Jones S, Thornton JM. Protein–DNA Interactions: The story so far and a new method for prediction. Comp Funct Genomics 2003;4:428-431.
28. Berman, HM, Westbrook J, Feng Z, Gilliland G, Bhat, TN, Weissig H, Shindyalov, IN, Bourne, PE. The Protein Data Bank.Nucleic Acid Res 2000;28:235-242.
29. Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh S -H., Srinivasan AR, Schneider B. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophs J 1992;63:751-759.
30. Pabo CO, Sauer RT. Transcription factors: structural families and principles of DNA recognition.  Annu Rev Biochem 1992;61:1053-1095.
31. Steitz TA, Ohlendorf DH, Mckay DB, Anderson WF, Mathews BW. Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor protein. Proc Natl Acad Sci USA 1982;79:3097-3100.
32. Berman RG. DNA recognition by the helix–turn–helix motif. Curr Opin Struct Biol 1992;2:100-108.
33. Rosinski JA, Atchley WR. Molecular evolution of helix–turn–helix proteins. J Mol Evol 1999;49:301-309.
34. Gehring WJ.The homeobox in perspective.Trends Biochem Sci 1992;17:277-280.
35. Gehring WJ. Exploring the homeobox. Gene 1993;135:215-221.
36. Henikoff S, Wallace JC, Brown JP. Finding protein similarities with nucleotide sequence databases. Methods Enzymol 1990;183:111-132.
37. Shadel GS, Young R, Baldwin TO. Use of regulated cell lysis in a lethal genetic selection in Escherichia coli: identification of the autoinducer-binding region of the LuxR protein from Vibrio fischeri ATCC 7744. J Bacteriol 1990;172:3980-3987.
38. Slock J, Van Riet D., Kolibackuk D, Greenberg EP. Critical regions of the Vibrio fischeri luxR protein defined by mutational analysis. J Bacteriol 1990;172:3974-3979.
39. Stout V, Torres-Cabassa A, Maurizi MR, Gutnick D, Gottesman S. RcsA, an unstable positive regulator of capsular polysaccharide synthesis. J Bacteriol 1991;173:1738-1747.
40. Kahn D, Ditta G. Modular structure of FixJ: homology of the transcriptional activator domain with the - 35 binding domain of sigma factors Mol Micrbiol 1991; 5:987-997.
41. Helman JO, Chamberlin MJ. Structure and function of bacterial sigma factors. Annu Rev Biochem 1988;57:839-872.
42. Gajiwala K, Burley SK.Winged helix proteins. Curr Opin Str Biol 2000;10:110-116.
43. Clark KL, Halay ED, Lai E, Burley S.K. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature 1993;364:412-420.
 
Molecular Biology Research Communications
Volume 4, Issue 3 - Serial Number 3
September 2015
Pages 115-124

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