PreprintCited by 58Bacterial biofilms and quorum sensingBacterial Genetics and BiotechnologyEscherichia coli research studies

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Autoinducer-2 and bile salts induce c-di-GMP synthesis to repress the T3SS via the CesD/SycD/LcrH family of chaperones

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Preprint — published as 10.1038/s41467-022-34607-9 · Paper page

Abstract

Cyclic di-GMP (c-di-GMP) is a bacterial second messenger that transduces extracellular stimuli into intracellular responses, efficiently coordinating a plethora of important biological processes. Low levels of c-di-GMP are often associated with highly virulent behavior that depends on the type III secretion system (T3SS) effectors encoded, whereas elevated levels of c-di-GMP lead to the repression of T3SSs. However, extracellular signals that modulate c-di-GMP metabolism to control T3SSs and the underlying mechanisms remain largely obscure. Here, we identify a GAPES1 domain-containing diguanylate cyclase (DGC) YeaJ that senses the quorum sensing signal autoinducer-2 (AI-2) to repress T3SS-1 gene expression in Salmonella enterica serovar Typhimurium. YeaJ homologs capable of sensing AI-2 are present in many other species belonging to Enterobacterales. We also reveal that bile components taurocholate and taurodeoxycholate bind to the periplasmic sensory domain of the DGC YedQ to induce intracellular accumulation of c-di-GMP, thus repressing the expression of T3SS-1 genes. Further, we found that c-di-GMP negatively controls the function of T3SSs through binding to the widely conserved CesD/SycD/LcrH family of T3SS chaperones. Our results support a model in which bacteria sense changes in population density and host-derived cues to regulate c-di-GMP synthesis, thereby modulating the activity of T3SSs via a c-di-GMP-responsive T3SS chaperone.

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  1. Jenal, U., Reinders, A. & Lori, C. Cyclic di-GMP: second messenger extraordinaire. Nat. Rev. Microbiol. 15, 271–284 (2017). · DOI
  2. Herbst, S. et al. Transmembrane redox control and proteolysis of PdeC, a novel type of c-di-GMP phosphodiesterase. EMBO J. 37, e97825 (2018). · DOI
  3. Hengge, R. High-specificity local and global c-di-GMP signaling. Trends Microbiol. 29, 993–1003 (2021). · DOI
  4. Srivastava, D. & Waters, C. M. A tangled web: regulatory connections between quorum sensing and cyclic Di-GMP. J. Bacteriol. 194, 4485–4493 (2012). · DOI
  5. Almblad et al. Bacterial cyclic diguanylate signaling networks sense temperature. Nat. Commun. 12,1986 (2021). · DOI
  6. Mills, E., Petersen, E., Kulasekara, B. R. & Miller, S. I. A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic Ê࿽-arginine-sensing pathway. Sci. Signal. 8, ra57 (2015). · DOI
  7. Zhang, L. et al. Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes. Nat. Commun. 11, 5371 (2020). · DOI
  8. 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 <bi>109</bi>, 15479–15484 (2012).
  9. Purcell, E. B. et al. A nutrient-regulated cyclic diguanylate phosphodiesterase controls Clostridium difficile biofilm and toxin production during stationary phase. Infect. Immun. 85, e00347-17 (2017). · DOI
  10. Koestler, B. J. & Waters, C. M. Bile acids and bicarbonate inversely regulate intracellular cyclic di-GMP in Vibrio cholerae. Infect. Immun. 82, 3002–3014 (2014). · DOI
  11. Wang, F. F., Cheng, S. T., Wu, Y., Ren, B. Z. & Qian, W. A bacterial receptor PcrK senses the plant hormone cytokinin to promote adaptation to oxidative stress. Cell Rep. 21, 2940–2951 (2017). · DOI
  12. Ueda, A. & Wood, T. K. Connecting quorum sensing, c-di-GMP, Pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase TpbA (PA3885). PLoS Pathog. 5, e1000483 (2009). · DOI
  13. Papenfort, K. & Bassler, B. L. Quorum sensing signal-response systems in Gram-negative bacteria. Nat. Rev. Microbiol. 14, 576–588 (2016).
  14. Koestler, B. J. & Waters, C. M. Intestinal GPS: bile and bicarbonate control cyclic di-GMP to provide Vibrio cholerae spatial cues within the small intestine. Gut Microbes 5, 775–780 (2014). · DOI
  15. Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411–413 (2008). · DOI
  16. Krasteva, P. V. et al. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 327, 866–868 (2010). · DOI
  17. Lori, C. et al. Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 523, 236–239 (2015). · DOI
  18. Roelofs, K. G. et al. Systematic identification of cyclic-di-GMP binding proteins in Vibrio cholerae reveals a novel class of cyclic-di-GMP-binding ATPases associated with type II secretion systems. PLoS Pathog. 11, e1005232 (2015). · DOI
  19. Shyp, V. et al. Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus. Nat. Microbiol. 6, 59–72 (2021). · DOI
  20. Xu, L. et al. A cyclic di-GMP-binding adaptor protein interacts with a chemotaxis methyltransferase to control flagellar motor switching. Sci. Signal. 9, ra102 (2016).
  21. An, S. Q. et al. Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence. PLoS Pathog. 10, e1004429 (2014). · DOI
  22. Moscoso, J. A., Mikkelsen, H., Heeb, S., Williams, P. & Filloux, A. The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c-di-GMP signalling. Environ. Microbiol. 13, 3128–3138 (2011). · DOI
  23. Lamprokostopoulou, A., Monteiro, C., Rhen, M. & Römling, U. Cyclic di-GMP signalling controls virulence properties of Salmonella enterica serovar Typhimurium at the mucosal lining. Environ. Microbiol. 12, 40–53 (2010). · DOI
  24. Zheng, Y. et al. The EAL domain containing protein STM2215 (rtn) is needed during Salmonella infection and has cyclic di-GMP phosphodiesterase activity. Mol. Microbiol. 89, 403–419 (2013). · DOI
  25. Hall, C. L. & Lee, V. T. Cyclic-di-GMP regulation of virulence in bacterial pathogens. Wiley Interdiscip. Rev. RNA 9, 10 (2018).
  26. 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). · DOI
  27. De Keersmaecker, S. C. et al. Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella Typhimurium. J. Biol. Chem. 280, 19563–19568 (2005). · DOI
  28. Jesudhasan, P. R. et al. Transcriptome analysis of genes controlled by luxS/autoinducer-2 in Salmonella enterica serovar Typhimurium. Foodborne Pathog. Dis. 7<bi>,</bi> 399–410 (2010). · DOI
  29. Amarasinghe, J. J., D'Hondt, R. E., Waters, C. M. & Mantis, N. J. Exposure of Salmonella enterica serovar Typhimurium to a protective monoclonal IgA triggers exopolysaccharide production via a diguanylate cyclase-dependent pathway. Infect. Immun. 81, 653–664 (2013). · DOI
  30. Sanchez-Torres, V., Hu, H. & Wood, T. K. GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli. Appl. Microbiol. Biotechnol. 90, 651–658 (2011). · DOI
  31. Surette, M. G. & Bassler, B. L. Quorum sensing in Escherichia coli and Salmonella Typhimurium. Proc. Natl Acad. Sci. USA <bi>95</bi>, 7046–7050 (1998).
  32. Baisón-Olmo, F., Cardenal-Muñoz, E. & Ramos-Morales, F. PipB2 is a substrate of the Salmonella pathogenicity island 1-encoded type III secretion system. Biochem. Biophys. Res. Commun. 423, 240–246 (2012). · DOI
  33. Perrett, C. A. et al. LuxS-based quorum sensing does not affect the ability of Salmonella enterica serovar Typhimurium to express the SPI-1 type 3 secretion system, induce membrane ruffles, or invade epithelial cells. J. Bacteriol. 191, 7253–7259 (2009). · DOI
  34. Dufresne, K., Saulnier-Bellemare, J. & Daigle, F. Functional analysis of the chaperone-usher fimbrial gene clusters of Salmonella enterica serovar Typhi. Front. Cell. Infect. Microbiol. 8, 26 (2018). · DOI
  35. Lostroh, C. P. & Lee, C. A. The Salmonella pathogenicity island-1 type III secretion system. Microbes Infect. 3, 1281–1291 (2001). · DOI
  36. Prouty, A. M. & Gunn, J. S. Salmonella enterica serovar Typhimurium invasion is repressed in the presence of bile. Infect. Immun. 68, 6763–6769 (2000). · DOI
  37. Prouty, A. M. et al. Transcriptional regulation of Salmonella enterica serovar Typhimurium genes by bile. FEMS Immunol. Med. Microbiol. 2004 41, 177–185. · DOI
  38. Mashruwala, A. A. & Bassler, B. L. The Vibrio cholerae quorum-sensing protein VqmA integrates cell density, environmental, and host-derived cues into the control of virulence. mBio 11, e01572–20 (2020). · DOI
  39. Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010). · DOI · Paper page
  40. Darwin, K. H. & Miller, V. L. The putative invasion protein chaperone SicA acts together with InvF to activate the expression of Salmonella Typhimurium virulence genes. Mol. Microbiol. 35, 949–960 (2000). · DOI
  41. Hersh, D. et al. The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. Proc. Natl Acad. Sci. USA <bi>96</bi>, 2396–2401 (1999).
  42. Hayward, R. D. & Koronakis, V. Direct nucleation and bundling of actin by the SipC protein of invasive Salmonella. EMBO J. 18, 4926–4934 (1999). · DOI
  43. Tucker, S. C. & Galán, J. E. Complex function for SicA, a Salmonella enterica serovar Typhimurium type III secretion-associated chaperone. J Bacteriol. 182, 2262–2268 (2000). · DOI
  44. Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015). · DOI · Paper page
  45. Yu, J., ZHou, Y., Tanaka, I. & Yao, M. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics 26, 46–52 (2010). · DOI
  46. Kozakov, D. et al. The ClusPro web server for protein-protein docking. Nat. Protoc. 12, 255–278 (2017). · DOI
  47. Pallen, M. J., Francis, M. S. & Fütterer, K. Tetratricopeptide-like repeats in type-III-secretion chaperones and regulators. FEMS Microbiol. Lett. 223, 53–60 (2003). · DOI
  48. Lunelli, M., Lokareddy, R. K., Zychlinsky, A. & Kolbe M. IpaB-IpgC interaction defines binding motif for type III secretion translocator. Proc. Natl Acad. Sci. USA <bi>106</bi>, 9661–9666 (2009).
  49. Singh, S. K., Boyle, A. L. & Main, E. R. LcrH, a class II chaperone from the type three secretion system, has a highly flexible native structure. J. Biol. Chem. 288, 4048–4055 (2013). · DOI
  50. Bröms, J. E., Forslund, A. L., Forsberg, A. & Francis, M. S. PcrH of Pseudomonas aeruginosa is essential for secretion and assembly of the type III translocon. J. Infect. Dis. 188, 1909–1921 (2003). · DOI
  51. Song, S. & Wood, T. K. The primary physiological roles of autoinducer 2 in Escherichia coli are chemotaxis and biofilm formation. Microorganisms 9, 386 (2021). · DOI
  52. Pereira, C. S., de Regt, A. K., Brito, P. H., Miller, S. T. & Xavier, K. B. Identification of functional LsrB-like autoinducer-2 receptors. J. Bacteriol. 191, 6975–6987 (2009). · DOI
  53. Pereira, C. S., Thompson, J. A. & Xavier, K. B. AI-2-mediated signalling in bacteria. FEMS Microbiol. Rev. 37, 156–181 (2013). · DOI
  54. Thompson, J. A., Oliveira, R. A., Djukovic, A., Ubeda, C. & Xavier, K. B. Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. Cell Rep. 10, 1861–1871 (2015). · DOI
  55. Eade, C. R. et al. Bile acids function synergistically to repress invasion gene expression in Salmonella by destabilizing the invasion regulator HilD. Infect. Immun. 84, 2198–2208 (2016). · DOI
  56. Römling, U., Galperin, M. Y. & Gomelsky, M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol. Mol. Biol. Rev. 77, 1–52 (2013). · DOI
  57. Trampari, E. et al. Bacterial rotary export ATPases are allosterically regulated by the nucleotide second messenger cyclic-di-GMP. J. Biol. Chem. 290, 24470–24483 (2015). · DOI
  58. Bassler, B. L., Wright, M., Showalter, R. E. & Silverman, M. R. Intercellular signalling in Vibrio harveyi: sequence and function of genes regulating expression of luminescence. Mol. Microbiol. 9, 773–786 (1993). · DOI
  59. Jiang, Y. et al. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl. Environ. Microbiol. 81, 2506–2514 (2015). · DOI · Paper page
  60. Wang, F. F. et al. A three-component signalling system fine-tunes expression kinetics of HPPK responsible for folate synthesis by positive feedback loop during stress response of Xanthomonas campestris. Environ. Microbiol. 16, 2126–2144 (2014). · DOI
  61. Bähre, H. & Kaever, V. Identification and quantification of cyclic di-guanosine monophosphate and its linear metabolites by reversed-phase LC-MS/MS. Methods Mol. Biol. 1657, 45–58 (2017). · DOI
  62. Xu, L. et al. Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector. PLoS Pathog. 6, e1000822 (2010). · DOI
  63. Gutierrez, A, et al. β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity. Nat. Commun. 4, 1610 (2013). · DOI
  64. Pacheco, A. R. et al. Fucose sensing regulates bacterial intestinal colonization. Nature 492, 113–117 (2012). · DOI · Paper page
  65. Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009). · DOI
  66. Laskowski, R. A. & Swindells, M. B. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51, 2778–2786 (2011). · DOI
  67. Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014). · DOI
  68. Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016). · DOI

Metadata

Authors
Li, S., Sun, H., Li, J., Zhao, Y., Wang, R., Xu, L., Duan, C., Li, J., Wang, Z., Liu, Q., Wang, Y., Ouyang, S., Shen, X., & Zhang, L.
Affiliations
  • Northwest A&F University (CN)
  • Fujian Normal University (CN)
Corresponding author
  • Ouyang, Songying
  • Shen, Xihui
  • Zhang, Lei
Venue
Nature Communications
Published
2022-09-22
Volume
13
Issue
1
Pages
6684-6684
ISSN
2041-1723 (ISSN-L)
OpenAlex
W4308451496
Cited by
58
References
1
Citations by year
2026: 17 · 2025: 30 · 2024: 6 · 2023: 5
FWCI
3.35
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Nanyang Technological University
  • National Natural Science Foundation of China (31,725,003, 32170048, 82172287, 82225028, 2018YFA0901200)
  • Chinese Academy of Sciences
  • Northwest A and F University
  • Institute of Microbiology, Chinese Academy of Sciences
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Immunology and Microbiology › Microbiology › Escherichia coli research studies
Keywords
c-di-GMP, autoinducer-2, quorum sensing, type III secretion system, diguanylate cyclase, bile salts, taurocholate, taurodeoxycholic acid, Salmonella typhimurium, Enterobacterales, bacterial virulence regulation
MeSH terms
Bacterial Proteins, Bile Acids and Salts, Cyclic GMP, Salmonella typhimurium, Gene Expression Regulation, Bacterial, Biofilms, Molecular Chaperones, Escherichia coli Proteins

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