1887

Abstract

doi: 10.1099/mgen.0.000126.001.

Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq) transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000126
2017-07-17
2019-09-20
Loading full text...

Full text loading...

/deliver/fulltext/mgen/3/9/mgen000126.html?itemId=/content/journal/mgen/10.1099/mgen.0.000126&mimeType=html&fmt=ahah

References

  1. Neville BA, O'Toole PW. Probiotic properties of Lactobacillus salivarius and closely related Lactobacillus species. Future Microbiol 2010;5:759–774 [CrossRef][PubMed]
    [Google Scholar]
  2. O'Callaghan J, Buttó LF, MacSharry J, Nally K, O'Toole PW. Influence of adhesion and bacteriocin production by Lactobacillus salivarius on the intestinal epithelial cell transcriptional response. Appl Environ Microbiol 2012;78:5196–5203 [CrossRef][PubMed]
    [Google Scholar]
  3. van Pijkeren JP, Canchaya C, Ryan KA, Li Y, Claesson MJ et al. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118. Appl Environ Microbiol 2006;72:4143–4153 [CrossRef][PubMed]
    [Google Scholar]
  4. Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP et al. Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci USA 2006;103:6718–6723 [CrossRef][PubMed]
    [Google Scholar]
  5. Harris HMB, Bourin MJB, Claesson MJ, O'Toole PW. Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal. Microb Genom 2017;;3::000115. [CrossRef]
    [Google Scholar]
  6. Li Y, Canchaya C, Fang F, Raftis E, Ryan KA et al. Distribution of megaplasmids in Lactobacillus salivarius and other lactobacilli. J Bacteriol 2007;189:6128–6139 [CrossRef][PubMed]
    [Google Scholar]
  7. Repoila F, Darfeuille F. Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol Cell 2009;101:117–131 [CrossRef][PubMed]
    [Google Scholar]
  8. Romby P, Charpentier E. An overview of RNAs with regulatory functions in Gram-positive bacteria. Cell Mol Life Sci 2010;67:217–237 [CrossRef][PubMed]
    [Google Scholar]
  9. Wagner EGH. Regulatory RNAs in bacteria: biological roles and mechanisms. J Biomol Struct Dyn 2009;26:811
    [Google Scholar]
  10. Papenfort K, Vogel J. Regulatory RNA in bacterial pathogens. Cell Host Microbe 2010;8:116–127 [CrossRef][PubMed]
    [Google Scholar]
  11. Felden B, Vandenesch F, Bouloc P, Romby P. The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog 2011;7:e1002006 [CrossRef][PubMed]
    [Google Scholar]
  12. Guillet J, Hallier M, Felden B. Emerging functions for the Staphylococcus aureus RNome. PLoS Pathog 2013;9:e1003767 [CrossRef][PubMed]
    [Google Scholar]
  13. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 2009;459:950–956 [CrossRef][PubMed]
    [Google Scholar]
  14. Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C et al. The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 2011;39:4235–4248 [CrossRef][PubMed]
    [Google Scholar]
  15. Mujahid S, Bergholz TM, Oliver HF, Boor KJ, Wiedmann M. Exploration of the role of the non-coding RNA SbrE in L. monocytogenes stress response. Int J Mol Sci 2013;14:378–393
    [Google Scholar]
  16. Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 2008;24:2807–2813 [CrossRef][PubMed]
    [Google Scholar]
  17. Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011;75:286–300 [CrossRef][PubMed]
    [Google Scholar]
  18. Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S et al. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 2012;8:583 [CrossRef][PubMed]
    [Google Scholar]
  19. Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009;136:615–628 [CrossRef][PubMed]
    [Google Scholar]
  20. Moody MJ, Young RA, Jones SE, Elliot MA. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. BMC Genomics 2013;14:558 [CrossRef][PubMed]
    [Google Scholar]
  21. Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR. Identification of a large noncoding RNA in extremophilic eubacteria. Proc Natl Acad Sci USA 2006;103:19490–19495 [CrossRef][PubMed]
    [Google Scholar]
  22. Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature 2009;462:656–659 [CrossRef][PubMed]
    [Google Scholar]
  23. Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR. Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol 2011;79:21–34 [CrossRef][PubMed]
    [Google Scholar]
  24. Wallace JG, Zhou Z, Breaker RR. OLE RNA protects extremophilic bacteria from alcohol toxicity. Nucleic Acids Res 2012;40:6898–6907 [CrossRef][PubMed]
    [Google Scholar]
  25. Wehner S, Mannala GK, Qing X, Madhugiri R, Chakraborty T et al. Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology. PLoS One 2014;9:e108639 [CrossRef][PubMed]
    [Google Scholar]
  26. Wels M, Bongers RS, Boekhorst J, Molenaar D, Sturme M et al. Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome. J Bacteriol 2009;191:3420–3423 [CrossRef][PubMed]
    [Google Scholar]
  27. Gillet R, Felden B. Emerging views on tmRNA-mediated protein tagging and ribosome rescue. Mol Microbiol 2001;42:879–885 [CrossRef][PubMed]
    [Google Scholar]
  28. Muto A, Ushida C, Himeno H. A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem Sci 1998;23:25–29 [CrossRef][PubMed]
    [Google Scholar]
  29. Saguy M, Gillet R, Metzinger L, Felden B. tmRNA and associated ligands: a puzzling relationship. Biochimie 2005;87:897–903 [CrossRef][PubMed]
    [Google Scholar]
  30. Janssen BD, Hayes CS. The tmRNA ribosome-rescue system. Adv Protein Chem Struct Biol 2012;86:151–191 [CrossRef][PubMed]
    [Google Scholar]
  31. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  32. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21 [CrossRef][PubMed]
    [Google Scholar]
  33. Anders S, Pyl PT, Huber W. HTSeq – a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–169 [CrossRef][PubMed]
    [Google Scholar]
  34. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621–628 [CrossRef][PubMed]
    [Google Scholar]
  35. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:402 [CrossRef][PubMed]
    [Google Scholar]
  36. McGrath PT. Characterizing cDNA ends by circular RACE. Methods Mol Biol 2011;772:257–265 [CrossRef][PubMed]
    [Google Scholar]
  37. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 2008;9:474 [CrossRef][PubMed]
    [Google Scholar]
  38. Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J et al. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 2009;68:351–362 [CrossRef][PubMed]
    [Google Scholar]
  39. Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C et al. Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum. BMC Genomics 2014;15:150 [CrossRef][PubMed]
    [Google Scholar]
  40. Lloréns-Rico V, Serrano L, Lluch-Senar M. Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?. BMC Genomics 2014;15:633 [CrossRef][PubMed]
    [Google Scholar]
  41. Barends S, Kraal B, van Wezel GP. The tmRNA-tagging mechanism and the control of gene expression: a review. Wiley Interdiscip Rev RNA 2011;2:233–246 [CrossRef][PubMed]
    [Google Scholar]
  42. Mellin JR, Cossart P. The non-coding RNA world of the bacterial pathogen Listeria monocytogenes. RNA Biol 2012;9:372–378 [CrossRef][PubMed]
    [Google Scholar]
  43. Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME et al. Structure and complexity of a bacterial transcriptome. J Bacteriol 2009;191:3203–3211 [CrossRef][PubMed]
    [Google Scholar]
  44. Zheng H, Liu E, Shi T, Ye L, Konno T et al. Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome. Mol Biosyst 2016;12:508–519 [CrossRef][PubMed]
    [Google Scholar]
  45. Macklaim JM, Fernandes AD, di Bella JM, Hammond JA, Reid G et al. Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis. Microbiome 2013;1:12 [CrossRef][PubMed]
    [Google Scholar]
  46. Eikmeyer FG, Heinl S, Marx H, Pühler A, Grabherr R et al. Identification of oxygen-responsive transcripts in the silage inoculant Lactobacillus buchneri CD034 by RNA sequencing. PLoS One 2015;10:e0134149 [CrossRef][PubMed]
    [Google Scholar]
  47. Lawley B, Sims IM, Tannock GW. Whole-transcriptome shotgun sequencing (RNA-seq) screen reveals upregulation of cellobiose and motility operons of Lactobacillus ruminis L5 during growth on tetrasaccharides derived from barley β-glucan. Appl Environ Microbiol 2013;79:5661–5669 [CrossRef][PubMed]
    [Google Scholar]
  48. Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG et al. Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol 2012;78:4141–4148 [CrossRef][PubMed]
    [Google Scholar]
  49. Golomb BL, Hirao LA, Dandekar S, Marco ML. Gene expression of Lactobacillus plantarum and the commensal microbiota in the ileum of healthy and early SIV-infected rhesus macaques. Sci Rep 2016;6:24723 [CrossRef][PubMed]
    [Google Scholar]
  50. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010;11:R31 [CrossRef][PubMed]
    [Google Scholar]
  51. Ham JS, Kim HW, Seol KH, Jang A, Jeong SG et al. Genome sequence of Lactobacillus salivarius NIAS840, isolated from chicken intestine. J Bacteriol 2011;193:5551–5552 [CrossRef][PubMed]
    [Google Scholar]
  52. Sun Z, Harris HM, McCann A, Guo C, Argimón S et al. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 2015;6:8322 [CrossRef][PubMed]
    [Google Scholar]
  53. Zhang M, Qiao X, Zhao L, Jiang L, Ren F. Lactobacillus salivarius REN counteracted unfavorable 4-nitroquinoline-1-oxide-induced changes in colonic microflora of rats. J Microbiol 2011;49:877–883 [CrossRef][PubMed]
    [Google Scholar]
  54. Jiménez E, Martín R, Maldonado A, Martín V, Gómez de Segura A et al. Complete genome sequence of Lactobacillus salivarius CECT 5713, a probiotic strain isolated from human milk and infant feces. J Bacteriol 2010;192:5266–5267 [CrossRef][PubMed]
    [Google Scholar]
  55. Zhang W, Wong KK, Magliozzo RS, Kozarich JW. Inactivation of pyruvate formate-lyase by dioxygen: defining the mechanistic interplay of glycine 734 and cysteine 419 by rapid freeze-quench EPR. Biochemistry 2001;40:4123–4130 [CrossRef][PubMed]
    [Google Scholar]
  56. Kahala M, Savijoki K, Palva A. In vivo expression of the Lactobacillus brevis S-layer gene. J Bacteriol 1997;179:284–286 [CrossRef][PubMed]
    [Google Scholar]
  57. Chamary JV, Hurst LD. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 2005;6:R75 [CrossRef][PubMed]
    [Google Scholar]
  58. Gaimster H, Summers D. Plasmids in the driving seat: the regulatory RNA Rcd gives plasmid ColE1 control over division and growth of its E. coli host. Plasmid 2015;78:59–64 [CrossRef][PubMed]
    [Google Scholar]
  59. Weaver KE. Emerging plasmid-encoded antisense RNA regulated systems. Curr Opin Microbiol 2007;10:110–116 [CrossRef][PubMed]
    [Google Scholar]
  60. van Melderen L. Toxin-antitoxin systems: why so many, what for?. Curr Opin Microbiol 2010;13:781–785 [CrossRef][PubMed]
    [Google Scholar]
  61. Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP et al. Characterization of endogenous plasmids from Lactobacillus salivarius UCC118. Appl Environ Microbiol 2008;74:3216–3228 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000126
Loading
/content/journal/mgen/10.1099/mgen.0.000126
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error