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Volume 168, Issue 10

Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Open Access

Abstract

Integrative and conjugative elements (ICEs) are chromosomally encoded mobile genetic elements that can transfer DNA between bacterial strains. Recently, as part of efforts to determine hypothetical gene functions, we have discovered an important regulatory module encoded on an ICE known as TnSmu1 on the chromosome. The regulatory module consists of a cI-like repressor with a helix-turn-helix DNA binding domain (immunity repressor) and a metalloprotease (anti-repressor). It is not possible to create an in-frame deletion mutant of and repression of with CRISPRi (CRISPR interference) causes substantial cell defects. We used a bypass of essentiality (BoE) screen to discover genes that allow deletion of the regulatory module. This revealed that conjugation genes, located within TnSmu1, can restore the viability of an mutant. Deletion of also leads to production of a circular intermediate form of TnSmu1, which is also inducible by the genotoxic agent mitomycin C. To gain further insights into potential regulation of TnSmu1 by ImmR and broader effects on UA159 physiology, we used CRISPRi and RNA-seq. Strongly induced genes included all the TnSmu1 mobile element, genes involved in amino acid metabolism, transport systems and a type I-C CRISPR-Cas system. Lastly, bioinformatic analysis shows that the TnSmu1 mobile element and its associated genes are well distributed across isolates. Taken together, our results show that activation of TnSmu1 is controlled by the module, and that activation is deleterious to , highlighting the complex interplay between mobile elements and their host.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ImmR , integrative and conjugative element , Streptococcus mutans , TnSmu1 and transcriptional regulator
Funding
This study was supported by the:
  • National Institute of Dental and Craniofacial Research (Award DE029882)
    • Principle Award Recipient: RobertColquhoun Shields
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-10-06
2024-05-07
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References

  1. Loesche WJ. Role of Streptococcus mutans in human dental decay. Microbiol Rev 1986; 50:353–380 [View Article] [PubMed]
     [Google Scholar]
  2. Pitts NB, Zero DT, Marsh PD, Ekstrand K, Weintraub JA et al. Dental caries. Nat Rev Dis Primers 2017; 3:17030 [View Article]
     [Google Scholar]
  3. Sheiham A, James WPT. Diet and dental caries: the pivotal role of free sugars reemphasized. J Dent Res 2015; 94:1341–1347 [View Article]
     [Google Scholar]
  4. Shields RC, Zeng L, Culp DJ, Burne RA. Genomewide identification of essential genes and fitness determinants of Streptococcus mutans UA159. mSphere 2018; 3:e00031-18 [View Article]
     [Google Scholar]
  5. Shields RC, Walker AR, Maricic N, Chakraborty B, Underhill SAM et al. Repurposing the Streptococcus mutans CRISPR-Cas9 system to understand essential gene function. PLoS Pathog 2020; 16:e1008344 [View Article]
     [Google Scholar]
  6. Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 2018; 46:D493–D496 [View Article]
     [Google Scholar]
  7. Jongeneel CV, Bouvier J, Bairoch A. A unique signature identifies a family of zinc-dependent metallopeptidases. FEBS Lett 1989; 242:211–214 [View Article] [PubMed]
     [Google Scholar]
  8. Sevin EW, Barloy-Hubler F. RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes. Genome Biol 2007; 8:R155 [View Article]
     [Google Scholar]
  9. Galkin VE, Yu X, Bielnicki J, Ndjonka D, Bell CE et al. Cleavage of bacteriophage lambda cI repressor involves the RecA C-terminal domain. J Mol Biol 2009; 385:779–787 [View Article] [PubMed]
     [Google Scholar]
  10. Bellanger X, Morel C, Decaris B, Guédon G. Derepression of excision of integrative and potentially conjugative elements from Streptococcus thermophilus by DNA damage response: implication of a cI-related repressor. J Bacteriol 2007; 189:1478–1481 [View Article] [PubMed]
     [Google Scholar]
  11. Bose B, Auchtung JM, Lee CA, Grossman AD. A conserved anti-repressor controls horizontal gene transfer by proteolysis. Mol Microbiol 2008; 70:570–582 [View Article] [PubMed]
     [Google Scholar]
  12. Maruyama F, Kobata M, Kurokawa K, Nishida K, Sakurai A et al. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics 2009; 10:358 [View Article] [PubMed]
     [Google Scholar]
  13. Waterhouse JC, Swan DC, Russell RRB. Comparative genome hybridization of Streptococcus mutans strains. Oral Microbiol Immunol 2007; 22:103–110 [View Article] [PubMed]
     [Google Scholar]
  14. Carraro N, Libante V, Morel C, Decaris B, Charron-Bourgoin F et al. Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus. BMC Microbiol 2011; 11:238 [View Article]
     [Google Scholar]
  15. Sambrook J, Russell D. Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001
     [Google Scholar]
  16. Lau PCY, Sung CK, Lee JH, Morrison DA, Cvitkovitch DG. PCR ligation mutagenesis in transformable streptococci: application and efficiency. J Microbiol Methods 2002; 49:193–205 [View Article] [PubMed]
     [Google Scholar]
  17. Ahn S-J, Burne RA. The atlA operon of Streptococcus mutans: role in autolysin maturation and cell surface biogenesis. J Bacteriol 2006; 188:6877–6888 [View Article] [PubMed]
     [Google Scholar]
  18. Shields RC, Mokhtar N, Ford M, Hall MJ, Burgess JG et al. Efficacy of a marine bacterial nuclease against biofilm forming microorganisms isolated from chronic rhinosinusitis. PLoS One 2013; 8:e55339 e55339 [View Article]
     [Google Scholar]
  19. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R et al. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 2007; 35:W71–W74 [View Article]
     [Google Scholar]
  20. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139–140 [View Article] [PubMed]
     [Google Scholar]
  21. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26:841–842 [View Article]
     [Google Scholar]
  22. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  23. R Core Team R: a Language and Environment for Statistical Computing ( https://www.R-project.org/) Vienna: R Foundation for Statistical Computing; 2018
     [Google Scholar]
  24. Valero-Mora PM. ggplot2: elegant graphics for data analysis. J Stat Softw 2010; 35:1–3
     [Google Scholar]
  25. Yu G, Smith DK, Zhu H, Guan Y, Lam T-Y. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36
     [Google Scholar]
  26. Liu M, Li X, Xie Y, Bi D, Sun J et al. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2019; 47:D660–D665 [View Article]
     [Google Scholar]
  27. Wozniak RAF, Waldor MK. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010; 8:552–563 [View Article] [PubMed]
     [Google Scholar]
  28. Koyanagi S, Lévesque CM. Characterization of a Streptococcus mutans intergenic region containing a small toxic peptide and its cis-encoded antisense small RNA antitoxin. PLoS One 2013; 8:e54291 [View Article]
     [Google Scholar]
  29. Patel S, Weaver KE. Addiction toxin Fst has unique effects on chromosome segregation and cell division in Enterococcus faecalis and Bacillus subtilis. J Bacteriol 2006; 188:5374–5384 [View Article]
     [Google Scholar]
  30. Weaver KE, Weaver DM, Wells CL, Waters CM, Gardner ME et al. Enterococcus faecalis plasmid pAD1-encoded Fst toxin affects membrane permeability and alters cellular responses to lantibiotics. J Bacteriol 2003; 185:2169–2177 [View Article]
     [Google Scholar]
  31. Wu C, Cichewicz R, Li Y, Liu J, Roe B et al. Genomic island TnSmu2 of Streptococcus mutans harbors a nonribosomal peptide synthetase-polyketide synthase gene cluster responsible for the biosynthesis of pigments involved in oxygen and H2O2 tolerance. Appl Environ Microbiol 2010; 76:5815–5826 [View Article] [PubMed]
     [Google Scholar]
  32. Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111–1137 [View Article] [PubMed]
     [Google Scholar]
  33. Li J, Wang HT, Wang WT, Zhang XR, Suo F et al. Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. Nat Commun 2019; 10:1002 [View Article]
     [Google Scholar]
  34. van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J et al. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol 2020; 16:e9828 [View Article]
     [Google Scholar]
  35. Hart EM, Silhavy TJ. Functions of the BamBCDE lipoproteins revealed by bypass mutations in BamA. J Bacteriol 2020; 202:e00401-20 [View Article]
     [Google Scholar]
  36. Wang Y, Cao W, Merritt J, Xie Z, Liu H. Characterization of FtsH essentiality in Streptococcus mutans via genetic suppression. Front Genet 2021; 12:659220 [View Article]
     [Google Scholar]
  37. Pichoff S, Du S, Lutkenhaus J. The bypass of ZipA by overexpression of FtsN requires a previously unknown conserved FtsN motif essential for FtsA-FtsN interaction supporting a model in which FtsA monomers recruit late cell division proteins to the Z ring. Mol Microbiol 2015; 95:971–987 [View Article] [PubMed]
     [Google Scholar]
  38. Anupama K, Leela JK, Gowrishankar J. Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol 2011; 82:1330–1348 [View Article] [PubMed]
     [Google Scholar]
  39. Krüger L, Herzberg C, Rath H, Pedreira T, Ischebeck T et al. Essentiality of c-di-AMP in Bacillus subtilis: bypassing mutations converge in potassium and glutamate homeostasis. PLOS Genet 2021; 17:e1009092 [View Article]
     [Google Scholar]
  40. Johnson CM, Grossman AD. Integrative and Conjugative Elements (ICEs): what they do and how they work. Annu Rev Genet 2015; 49:577–601 [View Article]
     [Google Scholar]
  41. Wright LD, Johnson CM, Grossman AD. Identification of a single strand origin of replication in the integrative and conjugative element ICEBs1 of Bacillus subtilis. PLOS Genet 2015; 11:e1005556 [View Article]
     [Google Scholar]
  42. Casjens SR, Hendrix RW. Bacteriophage lambda: early pioneer and still relevant. Virology 2015; 479–480:310–330 [View Article]
     [Google Scholar]
  43. Beaber JW, Hochhut B, Waldor MK. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 2004; 427:72–74 [View Article] [PubMed]
     [Google Scholar]
  44. Auchtung JM, Lee CA, Monson RE, Lehman AP, Grossman AD. Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci USA 2005; 102:12554–12559 [View Article]
     [Google Scholar]
  45. Lemme A, Sztajer H, Wagner-Döbler I. Characterization of mleR, a positive regulator of malolactic fermentation and part of the acid tolerance response in Streptococcus mutans. BMC Microbiol 2010; 10:58 [View Article]
     [Google Scholar]
  46. Walker AR, Shields RC. Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans. Front Genet 2022; 13:997341 [View Article]
     [Google Scholar]
  47. McLellan LK, Anderson ME, Grossman AD. Tn Smu1 is a functional integrative and conjugative element in Streptococcus mutans that when expressed causes growth arrest of host bacteria. bioRxiv 2022:505017 [View Article]
     [Google Scholar]
  48. Haag AF, Podkowik M, Ibarra-Chávez R, Gallego Del Sol F, Ram G et al. A regulatory cascade controls Staphylococcus aureus pathogenicity island activation. Nat Microbiol 2021; 6:1300–1308 [View Article] [PubMed]
     [Google Scholar]
  49. Lau RK, Enustun E, Gu Y, Nguyen JV, Corbett KD. A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage. bioRxiv 2022:489752 [View Article]
     [Google Scholar]
  50. Devigne A, Ithurbide S, Bouthier de la Tour C, Passot F, Mathieu M et al. DdrO is an essential protein that regulates the radiation desiccation response and the apoptotic-like cell death in the radioresistant Deinococcus radiodurans bacterium. Mol Microbiol 2015; 96:1069–1084 [View Article]
     [Google Scholar]
  51. Delavat F, Mitri S, Pelet S, van der Meer JR. Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element. Proc Natl Acad Sci USA 2016; 113:E3375–E3383 [View Article]
     [Google Scholar]
  52. Bean EL, McLellan LK, Grossman AD. Activation of the integrative and conjugative element Tn916 causes growth arrest and death of host bacteria. bioRxiv 2022:486793 [View Article]
     [Google Scholar]
  53. Prudhomme M, Attaiech L, Sanchez G, Martin B, Claverys J-P. Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science 2006; 313:89–92 [View Article] [PubMed]
     [Google Scholar]
  54. Boutry C, Delplace B, Clippe A, Fontaine L, Hols P. SOS response activation and competence development are antagonistic mechanisms in Streptococcus thermophilus. J Bacteriol 2013; 195:696–707 [View Article]
     [Google Scholar]
  55. Marx P, Sang Y, Qin H, Wang Q, Guo R et al. Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms. NPJ Biofilms Microbiomes 2020; 6:17 [View Article] [PubMed]
     [Google Scholar]
  56. Khan R, Rukke HV, Høvik H, Åmdal HA, Chen T et al. Comprehensive transcriptome profiles of Streptococcus mutans UA159 map core streptococcal competence genes. mSystems 2016; 1:e00038-15 [View Article]
     [Google Scholar]
  57. Dmitriev A, Mohapatra SS, Chong P, Neely M, Biswas S et al. CovR-controlled global regulation of gene expression in Streptococcus mutans. PLoS One 2011; 6:e20127 [View Article]
     [Google Scholar]
  58. Chattoraj P, Banerjee A, Biswas S, Biswas I. ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance. J Bacteriol 2010; 192:1312–1323 [View Article] [PubMed]
     [Google Scholar]
  59. Kaspar J, Shields RC, Burne RA. Competence inhibition by the XrpA peptide encoded within the comX gene of Streptococcus mutans. Mol Microbiol 2018; 109:345–364 [View Article] [PubMed]
     [Google Scholar]
  60. Kajfasz JK, Katrak C, Ganguly T, Vargas J, Wright L et al. Manganese uptake, mediated by SloABC and MntH, is essential for the fitness of Streptococcus mutans. mSphere 2020; 5:e00764-19 [View Article]
     [Google Scholar]
  61. Ahn S-J, Rice KC. Understanding the Streptococcus mutans Cid/Lrg system through CidB function. Appl Environ Microbiol 2016; 82:6189–6203 [View Article]
     [Google Scholar]
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Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans
Microbiology 168, 001254 (2022); https://doi.org/10.1099/mic.0.001254
/content/journal/micro/10.1099/mic.0.001254
/content/journal/micro/10.1099/mic.0.001254
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