ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: A census in prokaryotic genomes

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Dogsa, Iztok ^a   Choudhary, Kumari Sonal ^b   Marsetic, Ziva ^a   Hudaiberdiev, Sanjarbek ^b   Vera, Roberto ^b,c   Pongor, Sándor ^b,c   Mandic Mulec, Ines ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^c PÁZMÁNY PÉTER CATHOLIC UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARTILAGE OLIGOMERIC MATRIX PROTEIN; COMA PROTEIN; COMQ PROTEIN; COMX PROTEIN; UNCLASSIFIED DRUG; GAMMA BUTYROLACTONE DERIVATIVE;

ARTICLE; BACILLUS SUBTILIS; CLADISTICS; CLOSTRIDIALES; COMA GENE; COMP GENE; COMQ GENE; COMX GENE; FIRMICUTES; GENE LOCUS; GENE SEQUENCE; MICROBIAL GENOME; NONHUMAN; QUORUM SENSING; SEQUENCE ANALYSIS; BACTERIAL GENOME; CONSENSUS SEQUENCE; CYTOLOGY; GENETIC VARIABILITY; GENETICS; GENOMICS; METABOLISM;

ACYL-BUTYROLACTONES; BACILLUS SUBTILIS; CONSENSUS SEQUENCE; GENETIC LOCI; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; QUORUM SENSING;

EID: 84900399690     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096122     Document Type: Article

References (43)

1. Mongkolthanaruk W (2012) Classification of Bacillus beneficial substances related to plants, humans and animals. J Microbiol Biotechnol 22: 1597-1604.
2. Thoendel M, Horswill AR (2010) Biosynthesis of peptide signals in gram-positive bacteria. In: Gadd, Geoffrey; Sariaslani S, editor. Advances in applied microbiology. Iowa City, Iowa: Elsevier Inc., Vol. 71. pp. 91-112.
3. Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 176: 269-275. (Pubitemid 24034041)
4. Bacon Schneider K, Palmer TM, Grossman AD (2002) Characterization of comQ and comX, two genes required for production of ComX pheromone in Bacillus subtilis. J Bacteriol 184: 410-419. (Pubitemid 34027380)
5. Comella N, Grossman AD (2005) Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis. Mol Microbiol 57: 1159-1174. (Pubitemid 41139873)
6. Piazza F, Tortosa P, Dubnau D (1999) Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development. J Bacteriol 181: 4540-4548. (Pubitemid 29357934)
7. Tortosa P, Logsdon L, Kraigher B, Itoh Y, Mandic-Mulec I, et al. (2001) Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system. J Bacteriol 183: 451-460. doi:10.1128/JB.183.2.451-460.2001 (Pubitemid 32048102)
8. Weinrauch Y, Msadek T, Kunst F, Dubnau D (1991) Sequence and properties of comQ, a new competence regulatory gene of Bacillus subtilis. J Bacteriol 173: 5685-5693.
9. Magnuson R, Solomon J, Grossman AD (1994) Biochemical and genetic characterization of a competence pheromone from B. subtilis. Cell 77: 207-216. (Pubitemid 24138618)
10. Solomon JM, Magnuson R, Srivastava A, Grossman AD (1995) Convergent sensing pathways mediate response to two extracellular competence factors in Bacillus subtilis. Genes Dev 9: 547-558.
11. Ryan RP, Dow JM (2008) Diffusible signals and interspecies communication in bacteria. Microbiology 154: 1845-1858. doi:10.1099/mic.0.2008/017871-0
12. Taga ME, Bassler BL (2003) Chemical communication among bacteria. Proc Natl Acad Sci U S A 100 Suppl: 14549-14554. doi:10.1073/pnas.1934514100 (Pubitemid 37499280)
13. López D, Vlamakis H, Losick R, Kolter R (2009) Paracrine signaling in a bacterium. Genes Dev 23: 1631-1638. doi:10.1101/gad.1813709
14. Shank E, Kolter R (2011) Extracellular signaling and multicellularity in Bacillus subtilis. Curr Opin Microbiol 14: 741-747. doi:10.1016/j.mib.2011.09. 016.Extracellular
15. Dubnau D (1991) Genetic competence in Bacillus subtilis. Microbiol Rev 55: 395-424.
16. Nakano MM, Zuber P (1991) The primary role of comA in establishment of the competent state in Bacillus subtilis is to activate expression of srfA. J Bacteriol 173: 7269-7274.
17. Zafra O, Lamprecht-Grandío M, de Figueras CG, González- Pastor JE (2012) Extracellular DNA release by undomesticated Bacillus subtilis is regulated by early competence. PLoS One 7: e48716. doi:10.1371/journal.pone. 0048716
18. Ansaldi M, Marolt D, Stebe T, Mandic-Mulec I, Dubnau D (2002) Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants. Mol Microbiol 44: 1561-1573. (Pubitemid 34639433)
19. Oslizlo A, Stefanic P, Dogsa I, Mandic-Mulec I (2014) Private link between signal and response in Bacillus subtilis quorum sensing. Proc Natl Acad Sci U S A 2013: 1-6. doi:10.1073/pnas.1316283111
20. Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526-529. doi:10.1126/science.1140818 (Pubitemid 47196119)
21. Tran LS, Nagai T, Itoh Y (2000) Divergent structure of the ComQXPA quorum-sensing components: molecular basis of strain-specific communication mechanism in Bacillus subtilis. Mol Microbiol 37: 1159-1171.
22. Mandic-Mulec I, Kraigher B, Cepon U, Mahne I (2003) Variability of the Quorum Sensing System in Natural Isolates of Bacillus sp. FOOD Technol Biotechnol 41: 23-28. (Pubitemid 36381749)
23. Stefanic P, Mandic-Mulec I (2009) Social interactions and distribution of Bacillus subtilis pherotypes at microscale. J Bacteriol 191: 1756-1764. doi:10.1128/JB.01290-08
24. Stefanic P, Decorosi F, Viti C, Petito J, Cohan FM, et al. (2012) The quorum sensing diversity within and between ecotypes of Bacillus subtilis. Environ Microbiol 14: 1378-1389. doi:10.1111/j.1462-2920.2012.02717.x
25. Okada M, Yamaguchi H, Sato I, Tsuji F, Dubnau D, et al. (2008) Chemical structure of posttranslational modification with a farnesyl group on tryptophan. Biosci Biotechnol Biochem 72: 914-918. (Pubitemid 351463662)
26. Okada M, Sato I, Cho SJ, Iwata H, Nishio T, et al. (2005) Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX. Nat Chem Biol 1: 23-24. doi:10.1038/nchembio709
27. Tsuji F, Ishihara A, Kurata K, Nakagawa A, Okada M, et al. (2012) Geranyl modification on the tryptophan residue of ComXRO-E-2 pheromone by a cell-free system. FEBS Lett 586: 174-179. doi:10.1016/j.febslet.2011.12.012
28. Weinrauch Y, Penchev R, Dubnau E, Smith I, Dubnau D (1990) A Bacillus subtilis regulatory gene product for genetic competence and sporulation resembles sensor protein members of the bacterial two-component signal-transduction systems. Genes Dev 4: 860-872.
29. Roggiani M, Dubnau D (1993) ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA. J Bacteriol 175: 3182-3187. (Pubitemid 23148756)
30. Johnson ZI, Chisholm SW (2004) Properties of overlapping genes are conserved across microbial genomes. Genome Res 14: 2268-2272. doi:10.1101/gr.2433104 (Pubitemid 39517333)
31. Fukuda Y, Nakayama Y, Tomita M (2003) On dynamics of overlapping genes in bacterial genomes. Gene 323: 181-187. (Pubitemid 37501098)
32. Martin A (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-3682. doi:10.1128/AEM.68.8.3673
33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739. doi:10.1093/molbev/msr121
34. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
35. Choudhary KS, Hudaiberdiev S, Gelencsér Z, Gonçalves Coutinho B, Venturi V, et al. (2013) The Organization of the Quorum Sensing luxI/R Family Genes in Burkholderia. Int J Mol Sci 14: 13727-13747. doi:10.3390/ijms140713727
36. Gelencsér Z, Galbáts B, Gonzalez JF, Choudhary KS, Hudaiberdiev S, et al. (2012) Chromosomal arrangement of AHL.driven quorum sensing circuits in Pseudomonas. ISRN Microbiol 2012: 1-6.
37. Gelencsér Z, Choudhary KS, Coutinho BG, Hudaiberdiev S, Galbáts B, et al. (2012) Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes. Sensors 12: 5432-5444.
38. Maddison WP, Maddison DR (1989) Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol (Basel) 53: 190-202.
39. Slatkin WPM (1991) Null Models for the Number of Evolutionary Steps in a Character on a Phylogenetic Tree. Evolution (N Y) 45: 1184-1197.
40. Edwards S (1993) Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the grey-crowned babbler (Pomatostomus temporalis). Evolution (N Y) 47: 1118-1137.
41. Edwards S (1993) Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the grey-crowned babbler (Pomatostomus temporalis). Evolution (N Y) 47: 1118-1137.
42. Sonego P, Pacurar M, Dhir S, Kertész-Farkas A, Kocsor A, et al. (2007) A Protein Classification Benchmark collection for machine learning. Nucleic Acids Res 35: D232-6. doi:10.1093/nar/gkl812 (Pubitemid 46056205)
43. Pintar A, Carugo O, Pongor S (2003) Atom depth in protein structure and function. Trends Biochem Sci 28: 593-597. (Pubitemid 38352805)