A Walk into the LuxR Regulators of Actinobacteria: Phylogenomic Distribution and Functional Diversity

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Santos, Catarina Lopes ^a   Correia Neves, Margarida ^b,c   Moradas Ferreira, Pedro ^a,d   Mendes, Marta Vaz ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF MINHO   (Portugal)

^c UNIVERSITY OF MINHO   (Portugal)

^d UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR LUXR;

ACTINOBACTERIA; ARTICLE; BACTERIAL VIRULENCE; BIODIVERSITY; ECOLOGICAL NICHE; GENE SEQUENCE; GENETIC CODE; GRAM NEGATIVE BACTERIUM; NONHUMAN; PHYLOGENOMICS; PROTEIN DOMAIN; QUORUM SENSING; SIGNAL TRANSDUCTION;

ACTINOBACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; PHYLOGENY; REPRESSOR PROTEINS; TRANS-ACTIVATORS;

EID: 84867322158     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046758     Document Type: Article

References (54)

1. Nealson KH, Platt T, Hastings JW, (1970) Cellular Control of the Synthesis and Activity of the Bacterial Luminescent System. J Bacteriol 104: 313-322.
2. Fuqua C, Greenberg EP, (1998) Self perception in bacteria: quorum sensing with acylated homoserine lactones. Curr Opin Microbiol 1: 183-189.
3. Fuqua C, Winans SC, Greenberg EP, (1996) Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators. Annu Rev Microbiol 50: 727-751.
4. Patankar AV, Gonzalez JE, (2009) Orphan LuxR regulators of quorum sensing. FEMS Microbiol Rev 33: 739-756.
5. Gray KM, Garey JR, (2001) The evolution of bacterial LuxI and LuxR quorum sensing regulators. Microbiology 147: 2379-2387.
6. Lerat E, Moran NA, (2004) The Evolutionary History of Quorum-Sensing Systems in Bacteria. Mol Biol Evol 21: 903-913.
7. Sturme MH, Kleerebezem M, Nakayama J, Akkermans AD, Vaugha EE, et al. (2002) Cell to cell communication by autoinducing peptides in Gram-positive bacteria. Antonie Van Leeuwenhoek 81: 233-243.
8. Fuqua C, Parsek MR, Greenberg EP, (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 35: 439-468.
9. Sturme MH, Francke C, Siezen RJ, de Vos WM, Kleerebezem M, (2007) Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. Microbiology 153: 3939-3947.
10. Schuster M, Greenberg EP, (2006) A network of networks: Quorum-sensing gene regulation in Pseudomonas aeruginosa. IJMM 296: 73-81.
11. Daniels R, Vanderleyden J, Michiels J, (2004) Quorum sensing and swarming migration in bacteria. FEMS Microbiol Rev 28: 261-289.
12. Gonzalez JE, Keshavan ND, (2006) Messing with bacterial quorum sensing. Microbiol Mol Biol Rev 70: 859-875.
13. Subramoni S, Venturi V, (2009) LuxR-family 'solos': bachelor sensors/regulators of signalling molecules. Microbiology 155: 1377-1385.
14. Guerra SM, Rodriguez-Garcia A, Santos-Aberturas J, Vicente CM, Payero TD, et al. (2012) LAL regulators SCO0877 and SCO7173 as pleiotropic modulators of phosphate starvation response and actinorhodin biosynthesis in Streptomyces coelicolor. PLoS One 7: e31475.
15. Kato JY, Funa N, Watanabe H, Ohnishi Y, Horinouchi S, (2007) Biosynthesis of gamma-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc Natl Acad Sci U S A 104: 2378-2383.
16. Galperin MY, (2010) Diversity of structure and function of response regulator output domains. Curr Opin Microbiol 13: 150-159.
17. Adekambi T, Butler RW, Hanrahan F, Delcher AL, Drancourt M, et al. (2011) Core Gene Set As the Basis of Multilocus Sequence Analysis of the Subclass Actinobacteridae. PLoS ONE 6: e14792.
18. Gao B, Gupta RS, (2012) Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 76: 66-112.
19. Alm E, Huang K, Arkin A, (2006) The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. PLoS Comput Biol 2: e143.
20. Yanai I, Wolf YI, Koonin EV (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 3.
21. Mirny LA, Gelfand MS, (2002) Using orthologous and paralogous proteins to identify specifity-determining residues in bacterial transcription factors. J Mol Biol 321: 7-20.
22. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM, (2005) The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 29: 231-262.
23. Williams P, Camara M, (2009) Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules. Curr Opin Microbiol 12: 182-191.
24. Eberl L, Winson MK, Sternberg C, Stewart GSAB, Christiansen G, et al. (1996) Involvement of N-acyl-L-homoserine lactone autoinducers in controlling the multicellular behaviour of Serratia liquefaciens. Mol Microbiol 20: 127-136.
25. Joelsson A, Kan B, Zhu J, (2007) Quorum sensing enhances the stress response in Vibrio cholerae. Appl Environ Microbiol 73: 3742-3746.
26. Ohsawa T, Tsukahara K, Sato T, Ogura M, (2006) Superoxide stress decreases expression of srfA through inhibition of transcription of the comQXP quorum-sensing locus in Bacillus subtilis. J Biochem 139: 203-211.
27. Wen ZT, Burne RA, (2004) LuxS-Mediated Signaling in Streptococcus mutans is Involved in Regulation of Acid and Oxidative Stress Tolerance and Biofilm Formation. J Bacteriol 186: 2682-2691.
28. Pomposiello PJ, Demple B, (2001) Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 19: 109-114.
29. Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J, (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29: 147-167.
30. Santos CL, Tavares F, Thioulouse J, Normand P, (2009) A phylogenomic analysis of bacterial helix-turn-helix transcription factors. FEMS Microbiol Rev 33: 411-429.
31. Guo J, Zhao J, Li L, Chen Z, Wen Y, et al. (2010) The pathway-specific regulator AveR from Streptomyces avermitilis positively regulates avermectin production while it negatively affects oligomycin biosynthesis. Molecular Genetics and Genomics 283: 123-133.
32. Anton N, Santos-Aberturas J, Mendes MV, Guerra SM, Martin JF, et al. (2007) PimM, a PAS domain positive regulator of pimaricin biosynthesis in Streptomyces natalensis. Microbiology 153: 3174-3183.
33. Laureti L, Song L, Huang S, Corre C, Leblond P, et al. (2011) Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens. Proc Natl Acad Sci U S A 108: 6258-6263.
34. Lechner A, Eustáquio Alessandra S, Gulder Tobias AM, Hafner M, Moore Bradley S, (2011) Selective Overproduction of the Proteasome Inhibitor Salinosporamide A via Precursor Pathway Regulation. Chem Biol 18: 1527-1536.
35. Dubern JF, Diggle SP, (2008) Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species. Molecular Biosystems 4: 882-888.
36. Ferluga S, Bigirimana J, Höfte M, Venturi V, (2007) A LuxR homologue of Xanthomonas oryzae pv. oryzae is required for optimal rice virulence. Mol Plant Path 8: 529-538.
37. Zhu J, Miller MB, Vance RE, Dziejman M, Bassler BL, et al. (2002) Quorum-sensing regulators control virulence gene expression in Vibrio cholerae. Proc Natl Acad Sci U S A 99: 3129-3134.
38. Linder JU, Schultz JE, (2003) The class III adenylyl cyclases: multi-purpose signalling modules. Cell Signal 15: 1081-1089.
39. Muttucumaru DGN, Smith DA, McMinn EJ, Reese V, Coler RN, et al. (2011) Mycobacterium tuberculosis Rv0198c, a putative matrix metalloprotease is involved in pathogenicity. Tuberculosis 91: 111-116.
40. Parish T, Smith DA, Roberts G, Betts J, Stoker NG, (2003) The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology 149: 1423-1435.
41. Castro LI, Hermsen C, Schultz JE, Linder JU, (2005) Adenylyl cyclase Rv0386 from Mycobacterium tuberculosis H37Rv uses a novel mode for substrate selection. FEBS Journal 272: 3085-3092.
42. Agarwal N, Lamichhane G, Gupta R, Nolan S, Bishai WR, (2009) Cyclic AMP intoxication of macrophages by a Mycobacterium tuberculosis adenylate cyclase. Nature 460: 98-102.
43. Hartkoorn RC, Sala C, Uplekar S, Busso P, Rougemont J, et al. (2012) Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis. J Bacteriol 194: 2001-2009.
44. Geier H, Mostowy S, Cangelosi GA, Behr MA, Ford TE, (2008) Autoinducer-2 triggers the oxidative stress response in Mycobacterium avium, leading to biofilm formation. Appl Environ Microbiol 74: 1798-1804.
45. Banaiee N, Jacobs WR Jr, Ernst JD, (2006) Regulation of Mycobacterium tuberculosis whiB3 in the mouse lung and macrophages. Infect Immun 74: 6449-6457.
46. Alonso-Hearn M, Eckstein TM, Sommer S, Bermudez LE, (2010) A Mycobacterium avium subsp. paratuberculosis LuxR regulates cell envelope and virulence. Innate Immun 16: 235-247.
47. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-D222.
48. Galperin MY, (2004) Bacterial signal transduction network in a genomic perspective. Environmental Microbiology 6: 552-567.
49. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK,et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-D229.
50. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, et al. (2011) Geneious v5.4, Available: http://www.geneious.com/.Accessed 2012 May 18.
51. Jukes TH, Cantor CR (1969) Evolution of Protein Molecules; Munro HN, editor: Academy Press.
52. Guindon S, Gascuel O, (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Syst Biol 52: 696-704.
53. Whelan S, Goldman N, (2001) A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach. Mol Biol Evol 18: 691-699.
54. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.