Abstract
Quorum sensing (QS) is a cell–cell communication process that enables bacteria to track cell population density and orchestrate collective behaviors. QS relies on the production and detection of, and the response to, extracellular signal molecules called autoinducers. In Vibrio cholerae, multiple QS circuits control pathogenesis and biofilm formation. Here, we identify and characterize a new QS autoinducer–receptor pair. The autoinducer is 3,5-dimethylpyrazin-2-ol (DPO). DPO is made from threonine and alanine, and its synthesis depends on threonine dehydrogenase (Tdh). DPO binds to and activates a transcription factor, VqmA. The VqmA–DPO complex activates expression of vqmR, which encodes a small regulatory RNA. VqmR represses genes required for biofilm formation and toxin production. We propose that DPO allows V. cholerae to regulate collective behaviors to, among other possible roles, diversify its QS output during colonization of the human host.
Similar content being viewed by others
Change history
04 April 2017
In the version of this article initially published, the compound structure immediately upstream of DPO in the biosynthetic scheme in Figure 4e was redrawn incorrectly during production. The structure was missing a methyl group. The error has been corrected in the HTML and PDF versions of the article.
23 August 2017
In the version of this article initially published, the trace shown in Figure 4b was mislabeled as the RNA VqmR instead of the protein VqmA. The error has been corrected in the HTML and PDF versions of the article.
References
Bassler, B.L. & Losick, R. Bacterially speaking. Cell 125, 237–246 (2006).
Higgins, D.A. et al. The major Vibrio cholerae autoinducer and its role in virulence factor production. Nature 450, 883–886 (2007).
Zhu, J. et al. Quorum-sensing regulators control virulence gene expression in Vibrio cholerae. Proc. Natl. Acad. Sci. USA 99, 3129–3134 (2002).
Miller, M.B., Skorupski, K., Lenz, D.H., Taylor, R.K. & Bassler, B.L. Parallel quorum sensing systems converge to regulate virulence in Vibrio cholerae. Cell 110, 303–314 (2002).
Jung, S.A., Chapman, C.A. & Ng, W.L. Quadruple quorum-sensing inputs control Vibrio cholerae virulence and maintain system robustness. PLoS Pathog. 11, e1004837 (2015).
Chen, X. et al. Structural identification of a bacterial quorum-sensing signal containing boron. Nature 415, 545–549 (2002).
Surette, M.G., Miller, M.B. & Bassler, B.L. Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. Proc. Natl. Acad. Sci. USA 96, 1639–1644 (1999).
Rutherford, S.T. & Bassler, B.L. Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb. Perspect. Med. 2, a012427 (2012).
Pereira, C.S., Thompson, J.A. & Xavier, K.B. AI-2-mediated signalling in bacteria. FEMS Microbiol. Rev. 37, 156–181 (2013).
Schauder, S., Shokat, K., Surette, M.G. & Bassler, B.L. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol. Microbiol. 41, 463–476 (2001).
Miller, S.T. et al. Salmonella typhimurium recognizes a chemically distinct form of the bacterial quorum-sensing signal AI-2. Mol. Cell 15, 677–687 (2004).
Bassler, B.L., Wright, M. & Silverman, M.R. Sequence and function of LuxO, a negative regulator of luminescence in Vibrio harveyi. Mol. Microbiol. 12, 403–412 (1994).
Freeman, J.A. & Bassler, B.L. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. Mol. Microbiol. 31, 665–677 (1999).
Lenz, D.H. et al. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69–82 (2004).
Lilley, B.N. & Bassler, B.L. Regulation of quorum sensing in Vibrio harveyi by LuxO and sigma-54. Mol. Microbiol. 36, 940–954 (2000).
Rutherford, S.T., van Kessel, J.C., Shao, Y. & Bassler, B.L. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev. 25, 397–408 (2011).
Feng, L. et al. A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics. Cell 160, 228–240 (2015).
Tsou, A.M., Cai, T., Liu, Z., Zhu, J. & Kulkarni, R.V. Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs. Nucleic Acids Res. 37, 2747–2756 (2009).
Waters, C.M., Lu, W., Rabinowitz, J.D. & Bassler, B.L. Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. J. Bacteriol. 190, 2527–2536 (2008).
Krasteva, P.V. et al. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 327, 866–868 (2010).
Zhu, J. & Mekalanos, J.J. Quorum sensing-dependent biofilms enhance colonization in Vibrio cholerae. Dev. Cell 5, 647–656 (2003).
Papenfort, K. & Bassler, B.L. Quorum sensing signal-response systems in Gram-negative bacteria. Nat. Rev. Microbiol. 14, 576–588 (2016).
Liu, Z., Hsiao, A., Joelsson, A. & Zhu, J. The transcriptional regulator VqmA increases expression of the quorum-sensing activator HapR in Vibrio cholerae. J. Bacteriol. 188, 2446–2453 (2006).
Papenfort, K., Förstner, K.U., Cong, J.P., Sharma, C.M. & Bassler, B.L. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc. Natl. Acad. Sci. USA 112, E766–E775 (2015).
González, J.F. & Venturi, V. A novel widespread interkingdom signaling circuit. Trends Plant Sci. 18, 167–174 (2013).
Brameyer, S., Kresovic, D., Bode, H.B. & Heermann, R. LuxR solos in Photorhabdus species. Front. Cell. Infect. Microbiol. 4, 166 (2014).
Venturi, V. & Ahmer, B.M. Editorial: LuxR solos are becoming major players in cell–cell communication in bacteria. Front. Cell. Infect. Microbiol. 5, 89 (2015).
Subramoni, S., Florez Salcedo, D.V. & Suarez-Moreno, Z.R. A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. Front. Cell. Infect. Microbiol. 5, 16 (2015).
Hsiao, A. et al. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. Nature 515, 423–426 (2014).
Henry, J.T. & Crosson, S. Ligand-binding PAS domains in a genomic, cellular, and structural context. Annu. Rev. Microbiol. 65, 261–286 (2011).
Shcherbo, D. et al. Bright far-red fluorescent protein for whole-body imaging. 4, 741–746 (2007).
Finn, R.D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).
Mukherjee, J.J. & Dekker, E.E. Purification, properties, and N-terminal amino acid sequence of homogeneous Escherichia coli 2-amino-3-ketobutyrate CoA ligase, a pyridoxal phosphate-dependent enzyme. J. Biol. Chem. 262, 14441–14447 (1987).
Johnson, A.R. & Dekker, E.E. Site-directed mutagenesis of histidine-90 in Escherichia coli L-threonine dehydrogenase alters its substrate specificity. Arch. Biochem. Biophys. 351, 8–16 (1998).
Boylan, S.A. & Dekker, E.E. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. J. Biol. Chem. 256, 1809–1815 (1981).
Heidelberg, J.F. et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483 (2000).
Cameron, D.E., Urbach, J.M. & Mekalanos, J.J. A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc. Natl. Acad. Sci. USA 105, 8736–8741 (2008).
Reitzer, L. Catabolism of amino acids and related compounds. EcoSal Plus 1 http://dx.doi.org/10.1128/ecosalplus.3.4.7 (2005).
Kelly, R.C. et al. The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA. Nat. Chem. Biol. 5, 891–895 (2009).
Thiel, V., Kunze, B., Verma, P., Wagner-Döbler, I. & Schulz, S. New structural variants of homoserine lactones in bacteria. ChemBioChem 10, 1861–1868 (2009).
Fong, J.C., Syed, K.A., Klose, K.E. & Yildiz, F.H. Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis. Microbiology 156, 2757–2769 (2010).
Casper-Lindley, C. & Yildiz, F.H. VpsT is a transcriptional regulator required for expression of vps biosynthesis genes and the development of rugose colonial morphology in Vibrio cholerae O1 El Tor. J. Bacteriol. 186, 1574–1578 (2004).
Müller, R. & Rappert, S. Pyrazines: occurrence, formation and biodegradation. Appl. Microbiol. Biotechnol. 85, 1315–1320 (2010).
Besson, I., Creuly, C., Gros, B.J. & Larroche, C. Pyrazine production by Bacillus subtilis in solid-state fermentation on soybeans. Appl. Microbiol. Biotechnol. 47, 489–495 (1997).
Vannini, A. et al. The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO J. 21, 4393–4401 (2002).
Neiditch, M.B. et al. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 126, 1095–1108 (2006).
Neiditch, M.B., Federle, M.J., Miller, S.T., Bassler, B.L. & Hughson, F.M. Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Mol. Cell 18, 507–518 (2005).
Deng, Y. et al. Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover. Proc. Natl. Acad. Sci. USA 109, 15479–15484 (2012).
Neidhardt, F.C., Bloch, P.L. & Smith, D.F. Culture medium for enterobacteria. J. Bacteriol. 119, 736–747 (1974).
Pédelacq, J.D., Cabantous, S., Tran, T., Terwilliger, T.C. & Waldo, G.S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2006).
Kazachkov, M. & Yu, P.H. A novel HPLC procedure for detection and quantification of aminoacetone, a precursor of methylglyoxal, in biological samples. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 824, 116–122 (2005).
van Kessel, J.C., Ulrich, L.E., Zhulin, I.B. & Bassler, B.L. Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. MBio 4, e00378-13 (2013).
Acknowledgements
This work was supported by the Howard Hughes Medical Institute, NIH Grant 2R37GM065859, and National Science Foundation Grant MCB-0948112 (to B.L.B.). K.P. was supported by a career development award from the Human Frontiers Science Program (CDA00024/2016-C) and DFG Grant PA2820/1. J.E.S. was supported by the Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) program. M.R.S. gratefully acknowledges support from the Pew Biomedical Scholars Program. K.R.S. was supported by the Eli Lilly–Edward C. Taylor Fellowship in Chemistry. We thank the members of the Bassler lab for helpful discussions. We especially thank M. Donia, T. Srikumar, I. Pelczer, and S. Kyin for help in initial analyses of DPO.
Author information
Authors and Affiliations
Contributions
K.P., J.E.S., M.R.S. and B.L.B. designed the experiments and K.P., J.E.S., K.R.S., J.-P.C. and M.R.S. performed the experiments. Specifically, K.P., J.E.S. and J.P.S. performed northern and western blot experiments; K.P., J.E.S., K.R.S. and M.R.S. were involved in the autoinducer-capture experiments; K.P., J.E.S., K.R.S., J.P.S., M.R.S. and B.L.B. analyzed the data; and K.P., J.E.S., M.R.S. and B.L.B. wrote the paper.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Results, Supplementary Tables 1–6 and Supplementary Figures 1–8 (PDF 3858 kb)
Rights and permissions
About this article
Cite this article
Papenfort, K., Silpe, J., Schramma, K. et al. A Vibrio cholerae autoinducer–receptor pair that controls biofilm formation. Nat Chem Biol 13, 551–557 (2017). https://doi.org/10.1038/nchembio.2336
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nchembio.2336
- Springer Nature America, Inc.
This article is cited by
-
Insights into the regulatory role of bacterial sncRNA and its extracellular delivery via OMVs
Applied Microbiology and Biotechnology (2024)
-
Small protein modules dictate prophage fates during polylysogeny
Nature (2023)
-
Global transcriptomic response of the AI-3 isomers 3,5-DPO and 3,6-DPO in Salmonella Typhimurium
Archives of Microbiology (2023)
-
An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae
Nature Communications (2022)
-
Mechanisms of interactions between bacteria and bacteriophage mediate by quorum sensing systems
Applied Microbiology and Biotechnology (2022)