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Volume 168, Issue 10

Investigating the competence regulon through a combination of transcriptome analysis and phenotypic evaluation Free

Abstract

is a recently identified member of the Mitis group of streptococci. This species has been associated with infective endocarditis; however its mechanisms of pathogenesis and virulence are not fully understood. This study aimed to investigate the influence of the competence-stimulating peptide (CSP) and the competence regulon quorum-sensing circuitry (ComABCDE) on subsequent gene transcription and expression, as well as resultant phenotypes. In this study we confirmed the native CSP identity, ascertained when endogenous CSP was produced and completed a transcriptome-wide analysis of all genes following CSP exposure. RNA sequencing analysis revealed the upregulation of genes known to be associated with competence, biofilm formation and virulence. As such, a variety of phenotypic assays were utilized to assess the correlation between increased mRNA expression and potential phenotype response, ultimately gaining insight into the effects of CSP on both gene expression and developed phenotypes. The results indicated that the addition of exogenous CSP aided in competence development and successful transformation, yielding an average transformation efficiency comparable to that of other Mitis group streptococci. Additional studies are needed to further delineate the effects of CSP exposure on biofilm formation and virulence. Overall, this study provides novel information regarding and provides a substantial foundation on which this species and its role in disease pathogenesis can be further investigated.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): competence , competence-stimulating peptide , quorum sensing and Streptococcus sinensis
Funding
This study was supported by the:
  • National Institute of General Medical Sciences (Award R35GM128651)
    • Principle Award Recipient: YftahTal-Gan
  • Directorate for Mathematical and Physical Sciences (Award CHE-1808370)
    • Principle Award Recipient: YftahTal-Gan
© 2022 The Authors
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2022-10-25
2024-05-20
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References

  1. Salvadori G, Junges R, Morrison DA, Petersen FC. Competence in Streptococcus pneumoniae and close commensal relatives: mechanisms and implications. Front Cell Infect Microbiol 2019; 9:94 [View Article]
     [Google Scholar]
  2. Hannan S, Ready D, Jasni AS, Rogers M, Pratten J et al. Transfer of antibiotic resistance by transformation with eDNA within oral biofilms. FEMS Immunol Med Microbiol 2010; 59:345–349 [View Article]
     [Google Scholar]
  3. Zhu L, Lau GW. Inhibition of competence development, horizontal gene transfer and virulence in Streptococcus pneumoniae by a modified competence stimulating peptide. PLoS Pathog 2011; 7:e1002241 [View Article]
     [Google Scholar]
  4. Gómez-Mejia A, Gámez G, Hammerschmidt S. Streptococcus pneumoniae two-component regulatory systems: the interplay of the pneumococcus with its environment. Int J Med Microbiol 2018; 308:722–737 [View Article]
     [Google Scholar]
  5. Lee MS, Morrison DA. Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J Bacteriol 1999; 181:5004–5016 [View Article]
     [Google Scholar]
  6. Lella M, Tal-Gan Y. Strategies to attenuate the competence regulon in Streptococcus pneumoniae. Pept Sci 2021; 113:e24222 [View Article]
     [Google Scholar]
  7. Jensen A, Scholz CFP, Kilian M. Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus. Int J Syst Evol Microbiol 2016; 66:4803–4820 [View Article]
     [Google Scholar]
  8. Pestova EV, Håvarstein LS, Morrison DA. Regulation of competence for genetic transformation in Streptococcus pneumoniae by an auto-induced peptide pheromone and a two-component regulatory system. Mol Microbiol 1996; 21:853–862 [View Article]
     [Google Scholar]
  9. Johnston C, Hinds J, Smith A, van der Linden M, Van Eldere J et al. Detection of large numbers of pneumococcal virulence genes in streptococci of the mitis group. J Clin Microbiol 2010; 48:2762–2769 [View Article]
     [Google Scholar]
  10. Lau GW, Haataja S, Lonetto M, Kensit SE, Marra A et al. A functional genomic analysis of type 3 Streptococcus pneumoniae virulence. Mol Microbiol 2001; 40:555–571 [View Article]
     [Google Scholar]
  11. Jack AA, Daniels DE, Jepson MA, Vickerman MM, Lamont RJ et al. Streptococcus gordonii comCDE (competence) operon modulates biofilm formation with Candida albicans. Microbiology 2015; 161:411–421 [View Article]
     [Google Scholar]
  12. Luo P, Li H, Morrison DA. ComX is a unique link between multiple quorum sensing outputs and competence in Streptococcus pneumoniae. Mol Microbiol 2003; 50:623–633 [View Article]
     [Google Scholar]
  13. McBrayer DN, Cameron CD, Tal-Gan Y. Development and utilization of peptide-based quorum sensing modulators in gram-positive bacteria. Org Biomol Chem 2020; 18:7273–7290 [View Article]
     [Google Scholar]
  14. Knutsen E, Ween O, Håvarstein LS. Two separate quorum-sensing systems upregulate transcription of the same ABC transporter in Streptococcus pneumoniae. J Bacteriol 2004; 186:3078–3085 [View Article]
     [Google Scholar]
  15. Moreno-Gámez S, Sorg RA, Domenech A, Kjos M, Weissing FJ et al. Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence. Nat Commun 2017; 8:854 [View Article]
     [Google Scholar]
  16. Zu Y, Li W, Wang Q, Chen J, Guo Q. ComDE two-component signal transduction systems in oral streptococci: structure and function. Curr Issues Mol Biol 2019; 32:201–258 [View Article]
     [Google Scholar]
  17. Luo P, Li H, Morrison DA. ComX is a unique link between multiple quorum sensing outputs and competence in Streptococcus pneumoniae. Mol Microbiol 2003; 50:623–633 [View Article]
     [Google Scholar]
  18. Sung CK, Morrison DA. Two distinct functions of ComW in stabilization and activation of the alternative sigma factor ComX in Streptococcus pneumoniae. J Bacteriol 2005; 187:3052–3061 [View Article]
     [Google Scholar]
  19. Lin J, Lau GW. DprA-dependent exit from the competent state regulates multifaceted Streptococcus pneumoniae virulence. Infect Immun 2019; 87:e00349-19 [View Article]
     [Google Scholar]
  20. Peterson SN, Sung CK, Cline R, Desai BV, Snesrud EC et al. Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Mol Microbiol 2004; 51:1051–1070 [View Article]
     [Google Scholar]
  21. Salvadori G, Junges R, Åmdal HA, Chen T, Morrison DA et al. High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 2018; 19:453 [View Article]
     [Google Scholar]
  22. Rodriguez AM, Callahan JE, Fawcett P, Ge X, Xu P et al. Physiological and molecular characterization of genetic competence in Streptococcus sanguinis. Mol Oral Microbiol 2011; 26:99–116 [View Article]
     [Google Scholar]
  23. Vickerman MM, Iobst S, Jesionowski AM, Gill SR. Genome-wide transcriptional changes in Streptococcus gordonii in response to competence signaling peptide. J Bacteriol 2007; 189:7799–7807 [View Article]
     [Google Scholar]
  24. Slager J, Aprianto R, Veening J-W. Refining the pneumococcal competence regulon by RNA sequencing. J Bacteriol 2019; 201:e00780-18 [View Article]
     [Google Scholar]
  25. Luo P, Li H, Morrison DA. Identification of ComW as a new component in the regulation of genetic transformation in Streptococcus pneumoniae. Mol Microbiol 2004; 54:172–183 [View Article]
     [Google Scholar]
  26. Prudhomme M, Berge M, Martin B, Polard P. Pneumococcal competence coordination relies on a cell-contact sensing mechanism. PLoS Genet 2016; 12:e1006113 [View Article]
     [Google Scholar]
  27. Weng L, Piotrowski A, Morrison DA. Exit from competence for genetic transformation in Streptococcus pneumoniae is regulated at multiple levels. PLoS One 2013; 8:e64197 [View Article]
     [Google Scholar]
  28. Mirouze N, Bergé MA, Soulet A-L, Mortier-Barrière I, Quentin Y et al. Direct involvement of DprA, the transformation-dedicated RecA loader, in the shut-off of pneumococcal competence. Proc Natl Acad Sci U S A 2013; 110:E1035–44 [View Article]
     [Google Scholar]
  29. Johnston C, Mortier-Barriere I, Khemici V, Polard P. Fine-tuning cellular levels of DprA ensures transformant fitness in the human pathogen Streptococcus pneumoniae. Mol Microbiol 2018; 109:663–675 [View Article]
     [Google Scholar]
  30. Weyder M, Prudhomme M, Bergé M, Polard P, Fichant G. Dynamic modeling of Streptococcus pneumoniae competence provides regulatory mechanistic insights into its tight temporal regulationCompetence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation. Front Microbiol 2018; 9:1637 [View Article]
     [Google Scholar]
  31. Lin J, Zhu L, Lau GW. Disentangling competence for genetic transformation and virulence in Streptococcus pneumoniae. Curr Genet 2016; 62:97–103 [View Article]
     [Google Scholar]
  32. Watkins RR, Bonomo RA. Overview: global and local impact of antibiotic resistance. Infect Dis Clin North Am 2016; 30:313–322 [View Article]
     [Google Scholar]
  33. Woo PCY, Tam DMW, Leung K-W, Lau SKP, Teng JLL et al. Streptococcus sinensis sp. nov., a novel species isolated from a patient with infective endocarditis. J Clin Microbiol 2002; 40:805–810 [View Article]
     [Google Scholar]
  34. Woo PC, Teng JL, Leung K-W, Lau SK, Tse H et al. Streptococcus sinensis may react with Lancefield group F antiserum. J Med Microbiol 2004; 53:1083–1088 [View Article]
     [Google Scholar]
  35. Teng JLL, Huang Y, Tse H, Chen JHK, Tang Y et al. Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus. Genome Biol Evol 2014; 6:2930–2943 [View Article]
     [Google Scholar]
  36. Tanner AC, Haffer C, Bratthall GT, Visconti RA, Socransky SS. A study of the bacteria associated with advancing periodontitis in man. J Clin Periodontol 1979; 6:278–307 [View Article]
     [Google Scholar]
  37. Drancourt M, Roux V, Fournier P-E, Raoult D. rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 2004; 42:497–504 [View Article]
     [Google Scholar]
  38. Harrington A, Tal-Gan Y. Identification of Streptococcus gallolyticus subsp. gallolyticus (Biotype I) competence-stimulating peptide pheromone. J Bacteriol 2018; 200:00709–00717 [View Article]
     [Google Scholar]
  39. Yang Y, Koirala B, Sanchez LA, Phillips NR, Hamry SR et al. Structure-activity relationships of the competence stimulating peptides (CSPs) in Streptococcus pneumoniae reveal motifs critical for intra-group and cross-group ComD receptor activation. ACS Chem Biol 2017; 12:1141–1151 [View Article]
     [Google Scholar]
  40. Chan W, White P. Fmoc Solid Phase Peptide Synthesis: A Practical Approach, vol 222 OUP Oxford; 1999 [View Article]
     [Google Scholar]
  41. Guo M, Ye L, Yu T, Han L, Li Q et al. IL-1β enhances the antiviral effect of IFN-α on HCV replication by negatively modulating ERK2 activation. ACS Infect Dis 2020; 6:1708–1718 [View Article]
     [Google Scholar]
  42. Kjos M, Miller E, Slager J, Lake FB, Gericke O et al. Expression of Streptococcus pneumoniae bacteriocins is induced by antibiotics via regulatory interplay with the competence system. PLoS Pathog 2016; 12:e1005422 [View Article]
     [Google Scholar]
  43. Sambrook J, Russell DW. Purification of nucleic acids by extraction with phenol: chloroform. CSH Protoc 2006; 2006:pdb.prot4045 [View Article]
     [Google Scholar]
  44. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article]
     [Google Scholar]
  45. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article]
     [Google Scholar]
  46. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
     [Google Scholar]
  47. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
     [Google Scholar]
  48. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article]
     [Google Scholar]
  49. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15:550 [View Article]
     [Google Scholar]
  50. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:1–8 [View Article]
     [Google Scholar]
  51. Mull RW, Tal-Gan Y. Elucidating the role and structure-activity relationships of the Streptococcus oligofermentans competence-stimulating peptide. ACS Chem Biol 2021; 16:2834–2844 [View Article]
     [Google Scholar]
  52. Kratochvil MJ, Tal-Gan Y, Yang T, Blackwell HE, Lynn DM. Nanoporous superhydrophobic coatings that promote the extended release of water-labile quorum sensing inhibitors and enable long-term modulation of quorum sensing in Staphylococcus aureus. ACS Biomater Sci Eng 2015; 1:1039–1049 [View Article]
     [Google Scholar]
  53. Ogier J-C, Pagès S, Galan M, Barret M, Gaudriault S. rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing. BMC Microbiol 2019; 19:171 [View Article]
     [Google Scholar]
  54. Håvarstein LS, Hakenbeck R, Gaustad P. Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges. J Bacteriol 1997; 179:6589–6594 [View Article]
     [Google Scholar]
  55. Denapaite D, Rieger M, Köndgen S, Brückner R, Ochigava I et al. Highly variable Streptococcus oralis strains are common among viridans streptococci isolated from primates. mSphere 2016; 1:e00041-15 [View Article]
     [Google Scholar]
  56. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–8 [View Article]
     [Google Scholar]
  57. de Saizieu A, Gardès C, Flint N, Wagner C, Kamber M et al. Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide. J Bacteriol 2000; 182:4696–4703 [View Article]
     [Google Scholar]
  58. Shanker E, Federle MJ. Quorum sensing regulation of competence and bacteriocins in Streptococcus pneumoniae and mutans. Genes (Basel) 2017; 8:E15 [View Article]
     [Google Scholar]
  59. Cassone M, Gagne AL, Spruce LA, Seeholzer SH, Sebert ME. The HtrA protease from Streptococcus pneumoniae digests both denatured proteins and the competence-stimulating peptide. J Biol Chem 2012; 287:38449–38459 [View Article]
     [Google Scholar]
  60. Ibrahim YM, Kerr AR, McCluskey J, Mitchell TJ. Role of HtrA in the virulence and competence of Streptococcus pneumoniae. Infect Immun 2004; 72:3584–3591 [View Article]
     [Google Scholar]
  61. Wang X, Cai J, Shang N, Zhu L, Shao N et al. The carbon catabolite repressor CcpA mediates optimal competence development in Streptococcus oligofermentans through post-transcriptional regulation. Mol Microbiol 2019; 112:552–568 [View Article]
     [Google Scholar]
  62. Zheng L, Chen Z, Itzek A, Herzberg MC, Kreth J. CcpA regulates biofilm formation and competence in Streptococcus gordonii. Mol Oral Microbiol 2012; 27:83–94 [View Article]
     [Google Scholar]
  63. Suntharalingam P, Cvitkovitch DG. Quorum sensing in streptococcal biofilm formation. Trends Microbiol 2005; 13:3–6 [View Article]
     [Google Scholar]
  64. Brennan AA, Mehrani M, Tal-Gan Y. Modulating streptococcal phenotypes using signal peptide analogues. Open Biol 2022; 12:220143 [View Article]
     [Google Scholar]
  65. Shanker E, Federle MJ. quorum sensing regulation of competence and bacteriocins in Streptococcus pneumoniae and mutans. Genes (Basel) 2017; 8:E15 [View Article]
     [Google Scholar]
  66. Winkler ME, Morrison DA. Competence beyond genes: filling in the details of the pneumococcal competence transcriptome by a systems approach. J Bacteriol 2019; 201:e00238-19 [View Article]
     [Google Scholar]
  67. Bikash CR, Tal-Gan Y. Identification of highly potent competence stimulating peptide-based quorum sensing activators in Streptococcus mutans through the utilization of N-methyl and reverse alanine scanning. Bioorg Med Chem Lett 2019; 29:811–814 [View Article]
     [Google Scholar]
  68. Salvadori G, Junges R, Morrison DA, Petersen FC. Overcoming the barrier of low efficiency during genetic transformation of Streptococcus mitis. Front Microbiol 2016; 7:1009 [View Article]
     [Google Scholar]
  69. Bensing BA, Rubens CE, Sullam PM. Genetic loci of Streptococcus mitis that mediate binding to human platelets. Infect Immun 2001; 69:1373–1380 [View Article]
     [Google Scholar]
  70. Rukke HV, Kalluru RS, Repnik U, Gerlini A, José RJ et al. Protective role of the capsule and impact of serotype 4 switching on Streptococcus mitis. Infect Immun 2014; 82:3790–3801 [View Article]
     [Google Scholar]
  71. Jack AA, Daniels DE, Jepson MA, Vickerman MM, Lamont RJ et al. Streptococcus gordonii comCDE (competence) operon modulates biofilm formation with Candida albicans. Microbiology 2015; 161:411–421 [View Article]
     [Google Scholar]
  72. Jedrzejas MJ. Pneumococcal virulence factors: structure and function. Microbiol Mol Biol Rev 2001; 65:187–207 [View Article]
     [Google Scholar]
  73. Berry AM, Yother J, Briles DE, Hansman D, Paton JC. Reduced virulence of a defined pneumolysin-negative mutant of Streptococcus pneumoniae. Infect Immun 1989; 57:2037–2042 [View Article]
     [Google Scholar]
  74. Tovpeko Y, Bai J, Morrison DA. Competence for genetic transformation in Streptococcus pneumoniae: mutations in σa bypass the comw requirement for late gene expression. J Bacteriol 2016; 198:2370–2378 [View Article]
     [Google Scholar]
  75. Liu Y, Zeng Y, Huang Y, Gu L, Wang S et al. HtrA-mediated selective degradation of DNA uptake apparatus accelerates termination of pneumococcal transformation. Mol Microbiol 2019; 112:1308–1325 [View Article]
     [Google Scholar]
  76. Iyer R, Baliga NS, Camilli A. Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol 2005; 187:8340–8349 [View Article]
     [Google Scholar]
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Investigating the Streptococcus sinensis competence regulon through a combination of transcriptome analysis and phenotypic evaluation
Microbiology 168, 001256 (2022); https://doi.org/10.1099/mic.0.001256
/content/journal/micro/10.1099/mic.0.001256
/content/journal/micro/10.1099/mic.0.001256
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