1887

Abstract

Adherence capacity is one of the principal virulence factors of , and adhesion virulence factors are controlled by small RNAs (sRNAs) at the post-transcriptional level in various bacteria. Here, we aimed to identify and decipher putative adhesion-related sRNAs in clinical strains of

RNA deep-sequencing was performed to identify potential sRNAs under different adhesion conditions. The expression of sRNAs was analysed by quantitative real-time PCR (qRT-PCR), and bioinformatic methods were used to predict the functional characteristics of sRNAs.

A total of 736 differentially expressed candidate sRNAs were predicted, and these included 352 sRNAs located on the antisense to mRNA (AM) and 384 sRNAs in intergenic regions (IGRs). The top 7 differentially expressed sRNAs were successfully validated by qRT-PCR in UA159, and 2 of these were further confirmed in 100 clinical isolates. Moreover, the sequences of two sRNAs were conserved in other species, indicating a conserved role in such closely related species. A good correlation between the expression of sRNAs and the adhesion of 100 clinical strains was observed, which, combined with GO and KEGG, provides a perspective for the comprehension of sRNA function annotation.

This study revealed a multitude of novel putative adhesion-related sRNAs in and contributed to a better understanding of information concerning the transcriptional regulation of adhesion in .

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2018-05-01
2020-09-24
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References

  1. Selwitz RH, Ismail AI, Pitts NB. Dental caries. Lancet 2007;369:51–59 [CrossRef][PubMed]
    [Google Scholar]
  2. Marchisio O, Esposito MR, Genovesi A. Salivary pH level and bacterial plaque evaluation in orthodontic patients treated with Recaldent products. Int J Dent Hyg 2010;8:232–236 [CrossRef][PubMed]
    [Google Scholar]
  3. Bagramian RA, Garcia-Godoy F, Volpe AR. The global increase in dental caries. A pending public health crisis. Am J Dent 2009;22:3–8[PubMed]
    [Google Scholar]
  4. Loesche WJ. Role of Streptococcus mutans in human dental decay. Microbiol Rev 1986;50:353–380[PubMed]
    [Google Scholar]
  5. Cvitkovitch DG, Li YH, Ellen RP. Quorum sensing and biofilm formation in Streptococcal infections. J Clin Invest 2003;112:1626–1632 [CrossRef][PubMed]
    [Google Scholar]
  6. Koga T, Asakawa H, Okahashi N, Hamada S. Sucrose-dependent cell adherence and cariogenicity of serotype c Streptococcus mutans. J Gen Microbiol 1986;132:2873–2883 [CrossRef][PubMed]
    [Google Scholar]
  7. Massé E, Majdalani N, Gottesman S. Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol 2003;6:120–124 [CrossRef][PubMed]
    [Google Scholar]
  8. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011;43:880–891 [CrossRef][PubMed]
    [Google Scholar]
  9. Jørgensen MG, Nielsen JS, Boysen A, Franch T, Møller-Jensen J et al. Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli. Mol Microbiol 2012;84:36–50 [CrossRef][PubMed]
    [Google Scholar]
  10. Lease RA, Cusick ME, Belfort M. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci USA 1998;95:12456–12461 [CrossRef][PubMed]
    [Google Scholar]
  11. Barth M, Marschall C, Muffler A, Fischer D, Hengge-Aronis R. Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli. J Bacteriol 1995;177:3455–3464 [CrossRef][PubMed]
    [Google Scholar]
  12. Ko M, Park C. Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. J Mol Biol 2000;303:371–382 [CrossRef][PubMed]
    [Google Scholar]
  13. Liu Z, Treviño J, Ramirez-Peña E, Sumby P. The small regulatory RNA FasX controls pilus expression and adherence in the human bacterial pathogen group A Streptococcus. Mol Microbiol 2012;86:140–154 [CrossRef][PubMed]
    [Google Scholar]
  14. Lee HJ, Hong SH. Analysis of microRNA-size, small RNAs in Streptococcus mutans by deep sequencing. FEMS Microbiol Lett 2012;326:131–136 [CrossRef][PubMed]
    [Google Scholar]
  15. Liu S, Tao Y, Yu L, Zhuang P, Zhi Q et al. Analysis of Small RNAs in Streptococcus mutans under acid stress-a new insight for caries research. Int J Mol Sci 2016;17:1529 [CrossRef][PubMed]
    [Google Scholar]
  16. Costerton JW, Cheng KJ, Geesey GG, Ladd TI, Nickel JC et al. Bacterial biofilms in nature and disease. Annu Rev Microbiol 1987;41:435–464 [CrossRef][PubMed]
    [Google Scholar]
  17. Fletcher M. The physiological activity of bacteria attached to solid surfaces. Adv Microb Physiol 1991;32:53–85[PubMed][Crossref]
    [Google Scholar]
  18. Yu LX, Tao Y, Qiu RM, Zhou Y, Zhi QH et al. Genetic polymorphisms of the sortase A gene and social-behavioural factors associated with caries in children: a case-control study. BMC Oral Health 2015;15:54 [CrossRef][PubMed]
    [Google Scholar]
  19. Chen C, Khaleel SS, Huang H, Wu CH. Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol Med 2014;9:8 [CrossRef][PubMed]
    [Google Scholar]
  20. Solovyev VV, Tatarinova TV. Towards the integration of genomics, epidemiological and clinical data. Genome Med 2011;3:48 [CrossRef][PubMed]
    [Google Scholar]
  21. Barquist L, Burge SW, Gardner PP. Studying RNA homology and conservation with infernal: from single sequences to RNA families. Curr Protoc Bioinformatics 2016;54:12.13.11–12.13.12 [CrossRef][PubMed]
    [Google Scholar]
  22. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550 [CrossRef][PubMed]
    [Google Scholar]
  23. Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008;24:2849–2856 [CrossRef][PubMed]
    [Google Scholar]
  24. Christensen GD, Simpson WA, Younger JJ, Baddour LM, Barrett FF et al. Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices. J Clin Microbiol 1985;22:996–1006[PubMed]
    [Google Scholar]
  25. Mao MY, Yang YM, Li KZ, Lei L, Li M et al. The rnc gene promotes exopolysaccharide synthesis and represses the vicRKX gene expressions via microRNA-size small RNAs in Streptococcus mutans. Front Microbiol 2016;7:687 [CrossRef][PubMed]
    [Google Scholar]
  26. Koo H, Xiao J, Klein MI, Jeon JG. Exopolysaccharides produced by Streptococcus mutans glucosyltransferases modulate the establishment of microcolonies within multispecies biofilms. J Bacteriol 2010;192:3024–3032 [CrossRef][PubMed]
    [Google Scholar]
  27. Krzyściak W, Jurczak A, Kościelniak D, Bystrowska B, Skalniak A. The virulence of Streptococcus mutans and the ability to form biofilms. Eur J Clin Microbiol Infect Dis 2014;33:499–515 [CrossRef][PubMed]
    [Google Scholar]
  28. Daryani H, Nagarajappa R, Sharda AJ, Asawa K, Tak M et al. Cariogram model in assessment of dental caries among mentally challenged and visually impaired individuals of Udaipur, India. J Clin Diagn Res 2014;8:206–210 [CrossRef][PubMed]
    [Google Scholar]
  29. Schilling KM, Bowen WH. Glucans synthesized in situ in experimental salivary pellicle function as specific binding sites for Streptococcus mutans. Infect Immun 1992;60:284–295[PubMed]
    [Google Scholar]
  30. Li YH, Bowden GH. Characteristics of accumulation of oral gram-positive bacteria on mucin-conditioned glass surfaces in a model system. Oral Microbiol Immunol 1994;9:1–11[PubMed][Crossref]
    [Google Scholar]
  31. Wen ZT, Burne RA. Functional genomics approach to identifying genes required for biofilm development by Streptococcus mutans. Appl Environ Microbiol 2002;68:1196–1203 [CrossRef][PubMed]
    [Google Scholar]
  32. Marsh PD, Devine DA. How is the development of dental biofilms influenced by the host?. J Clin Periodontol 2011;38:28–35 [CrossRef][PubMed]
    [Google Scholar]
  33. Rivers AR, Burns AS, Chan LK, Moran MA. Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3. Front Microbiol 2016;7:380 [CrossRef][PubMed]
    [Google Scholar]
  34. Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 2008;24:2807–2813 [CrossRef][PubMed]
    [Google Scholar]
  35. Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011;3:a003798 [CrossRef][PubMed]
    [Google Scholar]
  36. Tsai CH, Liao R, Chou B, Palumbo M, Contreras LM. Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions. J Bacteriol 2015;197:40–50 [CrossRef][PubMed]
    [Google Scholar]
  37. Song J, Lays C, Vandenesch F, Benito Y, Bes M et al. The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection. PLoS One 2012;7:e37294 [CrossRef][PubMed]
    [Google Scholar]
  38. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 2002;9:11–22 [CrossRef][PubMed]
    [Google Scholar]
  39. Fröhlich KS, Vogel J. Activation of gene expression by small RNA. Curr Opin Microbiol 2009;12:674–682 [CrossRef][PubMed]
    [Google Scholar]
  40. Papenfort K, Vogel J. Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level. Res Microbiol 2009;160:278–287 [CrossRef][PubMed]
    [Google Scholar]
  41. Massé E, Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 2002;99:4620–4625 [CrossRef][PubMed]
    [Google Scholar]
  42. Massé E, Vanderpool CK, Gottesman S. Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 2005;187:6962–6971 [CrossRef][PubMed]
    [Google Scholar]
  43. Pain A, Ott A, Amine H, Rochat T, Bouloc P et al. An assessment of bacterial small RNA target prediction programs. RNA Biol 2015;12:509–513 [CrossRef][PubMed]
    [Google Scholar]
  44. Stauffer LT, Stauffer GV. Multiple roles for the sRNA GcvB in the regulation of Slp levels in Escherichia coli. ISRN Bacteriology 2013;2013:1–8 [CrossRef]
    [Google Scholar]
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