1887

Abstract

is the causative agent of gonorrhoea, the second most common bacterial sexually transmitted disease. Riboregulation mediated by small regulatory RNAs (sRNAs) is increasingly recognized as an important means of gene expression control in this human-restricted pathogen. sRNAs act at the post-transcriptional level by base-pairing with their target mRNAs which affects translation initiation and/or mRNA stability. In this study we initiated the characterization of a pair of highly conserved sRNAs of which exhibit redundant functions in the control of a common set of target genes. The identified targets of the sibling sRNAs NgncR_162 and NgncR_163 participate in basic metabolic processes including the methylcitrate and citrate cycle, aa uptake and degradation, and also in transcription regulation. Our data indicate that the sibling sRNAs control their targets via direct base-pairing between the same single-stranded domain(s) of the sRNA and the ribosome binding site in the 5′-untranslated region of the mRNA.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000548
2017-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/163/11/1720.html?itemId=/content/journal/micro/10.1099/mic.0.000548&mimeType=html&fmt=ahah

References

  1. Hook EW, Hansfield HH. Gonococcal infection in the adult. In Holmes KK. (editor) Sexually Transmitted Diseases New York: McGraw-Hill; 2008 pp. 627–645
    [Google Scholar]
  2. Jarvis GA, Chang TL. Modulation of HIV transmission by Neisseria gonorrhoeae: molecular and immunological aspects. Curr HIV Res 2012; 10:211–217 [View Article][PubMed]
    [Google Scholar]
  3. Jerse AE, Deal CD. Vaccine research for gonococcal infections: where are we?. Sex Transm Infect 2013; 89:iv63–iv68 [View Article][PubMed]
    [Google Scholar]
  4. Lewis DA. Global resistance of Neisseria gonorrhoeae: when theory becomes reality. Curr Opin Infect Dis 2014; 27:62–67 [View Article][PubMed]
    [Google Scholar]
  5. Gunesekere IC, Kahler CM, Ryan CS, Snyder LA, Saunders NJ et al. Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrB, which encodes methionine sulfoxide reductase. J Bacteriol 2006; 188:3463–3469 [View Article][PubMed]
    [Google Scholar]
  6. Laskos L, Dillard JP, Seifert HS, Fyfe JA, Davies JK. The pathogenic neisseriae contain an inactive rpoN gene and do not utilize the pilE σ54 promoter. Gene 1998; 208:95–102 [View Article][PubMed]
    [Google Scholar]
  7. Doucleff M, Malak LT, Pelton JG, Wemmer DE. The C-terminal RpoN domain of σ54 forms an unpredicted helix-turn-helix motif similar to domains of σ70 . J Biol Chem 2005; 280:41530–41536 [View Article][PubMed]
    [Google Scholar]
  8. Mcclure R, Tjaden B, Genco C. Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions. Front Microbiol 2014; 5:456 [View Article][PubMed]
    [Google Scholar]
  9. Remmele CW, Xian Y, Albrecht M, Faulstich M, Fraunholz M et al. Transcriptional landscape and essential genes of Neisseria gonorrhoeae . Nucleic Acids Res 2014; 42:10579–10595 [View Article][PubMed]
    [Google Scholar]
  10. Wachter J, Hill SA. Small transcriptome analysis indicates that the enzyme RppH influences both the quality and quantity of sRNAs in Neisseria gonorrhoeae . FEMS Microbiol Lett 2015; 362:1–7 [View Article]
    [Google Scholar]
  11. del Tordello E, Bottini S, Muzzi A, Serruto D. Analysis of the regulated transcriptome of Neisseria meningitidis in human blood using a tiling array. J Bacteriol 2012; 194:6217–6232 [View Article][PubMed]
    [Google Scholar]
  12. Fagnocchi L, Bottini S, Golfieri G, Fantappiè L, Ferlicca F et al. Global transcriptome analysis reveals small RNAs affecting Neisseria meningitidis bacteremia. PLoS One 2015; 10:e0126325 [View Article][PubMed]
    [Google Scholar]
  13. Capel E, Zomer AL, Nussbaumer T, Bole C, Izac B et al. Comprehensive identification of meningococcal genes and small noncoding RNAs required for host cell colonization. MBio 2016; 7:e01173-16 [View Article][PubMed]
    [Google Scholar]
  14. Papenfort K, Vogel J. Regulatory RNA in bacterial pathogens. Cell Host Microbe 2010; 8:116–127 [View Article][PubMed]
    [Google Scholar]
  15. Caldelari I, Chao Y, Romby P, Vogel J. RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med 2013; 3:a010298 [View Article][PubMed]
    [Google Scholar]
  16. Oliva G, Sahr T, Buchrieser C. Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev 2015; 39:331–349 [View Article][PubMed]
    [Google Scholar]
  17. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880–891 [View Article][PubMed]
    [Google Scholar]
  18. Saramago M, Bárria C, dos Santos RF, Silva IJ, Pobre V et al. The role of RNases in the regulation of small RNAs. Curr Opin Microbiol 2014; 18:105–115 [View Article][PubMed]
    [Google Scholar]
  19. Vogel J, Luisi BF. Hfq and its constellation of RNA. Nat Rev Microbiol 2011; 9:578–589 [View Article][PubMed]
    [Google Scholar]
  20. Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011; 75:286–300 [Crossref]
    [Google Scholar]
  21. Cahoon LA, Seifert HS. Transcription of a cis-acting, noncoding, small RNA is required for pilin antigenic variation in Neisseria gonorrhoeae . PLoS Pathog 2013; 9:e1003074 [View Article][PubMed]
    [Google Scholar]
  22. Cahoon LA, Seifert HS. An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae . Science 2009; 325:764–767 [View Article][PubMed]
    [Google Scholar]
  23. Tan FY, Wörmann ME, Loh E, Tang CM, Exley RM. Characterization of a novel antisense RNA in the major pilin locus of Neisseria meningitidis influencing antigenic variation. J Bacteriol 2015; 197:1757–1768 [View Article][PubMed]
    [Google Scholar]
  24. Mellin JR, Goswami S, Grogan S, Tjaden B, Genco CA. A novel fur- and iron-regulated small RNA, NrrF, is required for indirect fur-mediated regulation of the sdhA and sdhC genes in Neisseria meningitidis . J Bacteriol 2007; 189:3686–3694 [View Article][PubMed]
    [Google Scholar]
  25. Metruccio MM, Fantappiè L, Serruto D, Muzzi A, Roncarati D et al. The Hfq-dependent small noncoding RNA NrrF directly mediates Fur-dependent positive regulation of succinate dehydrogenase in Neisseria meningitidis . J Bacteriol 2009; 191:1330–1342 [View Article][PubMed]
    [Google Scholar]
  26. Ducey TF, Jackson L, Orvis J, Dyer DW. Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae . Microb Pathog 2009; 46:166–170 [View Article][PubMed]
    [Google Scholar]
  27. Jackson LA, Pan JC, Day MW, Dyer DW. Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae . J Bacteriol 2013; 195:5166–5173 [View Article][PubMed]
    [Google Scholar]
  28. Jackson LA, Day M, Allen J, Scott E, Dyer DW. Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth. BMC Genomics 2017; 18:317 [View Article][PubMed]
    [Google Scholar]
  29. Fantappiè L, Oriente F, Muzzi A, Serruto D, Scarlato V et al. A novel Hfq-dependent sRNA that is under FNR control and is synthesized in oxygen limitation in Neisseria meningitidis . Mol Microbiol 2011; 80:507–523 [View Article][PubMed]
    [Google Scholar]
  30. Isabella VM, Clark VL. Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae . BMC Genomics 2011; 12:51 [View Article][PubMed]
    [Google Scholar]
  31. Tanwer P, Bauer S, Heinrichs E, Panda G, Saluja D et al. Post-transcriptional regulation of target genes by the sRNA FnrS in Neisseria gonorrhoeae . Microbiology 2017; 163:1081–1092 [View Article][PubMed]
    [Google Scholar]
  32. Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C et al. The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res 2017; 45:6147–6167 [View Article][PubMed]
    [Google Scholar]
  33. Pannekoek Y, Huis In 't Veld RA, Schipper K, Bovenkerk S, Kramer G et al. Neisseria meningitidis uses sibling small regulatory RNAs to switch from cataplerotic to anaplerotic metabolism. MBio 2017; 8:e02293-16 [View Article][PubMed]
    [Google Scholar]
  34. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol 1983; 166:557–580 [View Article][PubMed]
    [Google Scholar]
  35. Ramsey ME, Hackett KT, Kotha C, Dillard JP. New complementation constructs for inducible and constitutive gene expression in Neisseria gonorrhoeae and Neisseria meningitidis . Appl Environ Microbiol 2012; 78:3068–3078 [View Article][PubMed]
    [Google Scholar]
  36. Cormack BP, Valdivia RH, Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 1996; 173:33–38 [View Article][PubMed]
    [Google Scholar]
  37. Brosius J. Superpolylinkers in cloning and expression vectors. DNA 1989; 8:759–777 [View Article][PubMed]
    [Google Scholar]
  38. Elkins C, Thomas CE, Seifert HS, Sparling PF. Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence. J Bacteriol 1991; 173:3911–3913 [View Article][PubMed]
    [Google Scholar]
  39. Urban JH, Vogel J. Translational control and target recognition by Escherichia coli small RNAs in vivo . Nucleic Acids Res 2007; 35:1018–1037 [View Article][PubMed]
    [Google Scholar]
  40. Sittka A, Pfeiffer V, Tedin K, Vogel J. The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium . Mol Microbiol 2007; 63:193–217 [View Article][PubMed]
    [Google Scholar]
  41. Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JC et al. Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 2012; 84:428–445 [View Article][PubMed]
    [Google Scholar]
  42. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675 [View Article][PubMed]
    [Google Scholar]
  43. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001; 25:402–408 [View Article][PubMed]
    [Google Scholar]
  44. Tjaden B. TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 2008; 36:W109–W113 [View Article][PubMed]
    [Google Scholar]
  45. Rouquette-Loughlin CE, Zalucki YM, Dhulipala VL, Balthazar JT, Doyle RG et al. Control of gdhR expression in Neisseria gonorrhoeae via autoregulation and a master repressor (MtrR) of a drug efflux pump operon. MBio 2017; 8:e00449-17 [View Article][PubMed]
    [Google Scholar]
  46. Catenazzi MC, Jones H, Wallace I, Clifton J, Chong JP et al. A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx. Mol Microbiol 2014; 93:346–355 [View Article][PubMed]
    [Google Scholar]
  47. Jain D. Allosteric control of transcription in GntR family of transcription regulators: a structural overview. IUBMB Life 2015; 67:556–563 [View Article][PubMed]
    [Google Scholar]
  48. Dietrich M, Munke R, Gottschald M, Ziska E, Boettcher JP et al. The effect of hfq on global gene expression and virulence in Neisseria gonorrhoeae . FEBS J 2009; 276:5507–5520 [View Article][PubMed]
    [Google Scholar]
  49. Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci USA 2011; 108:15522–15527 [View Article][PubMed]
    [Google Scholar]
  50. Holmqvist E, Unoson C, Reimegård J, Wagner EG. A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp . Mol Microbiol 2012; 84:414–427 [View Article][PubMed]
    [Google Scholar]
  51. Lee HJ, Gottesman S. sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 2016; 44:6907–6923 [View Article][PubMed]
    [Google Scholar]
  52. McClure R, Nudel K, Massari P, Tjaden B, Su X et al. The gonococcal transcriptome during infection of the lower genital tract in women. PLoS One 2015; 10:e0133982 [View Article][PubMed]
    [Google Scholar]
  53. Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J. Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci USA 2010; 107:20435–20440 [View Article]
    [Google Scholar]
  54. Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P et al. Two novel members of the LhrC family of small RNAs in Listeria monocytogenes with overlapping regulatory functions but distinctive expression profiles. RNA Biol 2016; 13:895–915 [View Article][PubMed]
    [Google Scholar]
  55. Caswell CC, Oglesby-Sherrouse AG, Murphy ER. Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles. Front Cell Infect Microbiol 2014; 4:151 [View Article][PubMed]
    [Google Scholar]
  56. Fris ME, Broach WH, Klim SE, Coschigano PW, Carroll RK et al. Sibling sRNA RyfA1 influences Shigella dysenteriae pathogenesis. Genes 2017; 8:e50 [View Article][PubMed]
    [Google Scholar]
  57. Sievers S, Lund A, Menendez-Gil P, Nielsen A, Storm Mollerup M et al. The multicopy sRNA LhrC controls expression of the oligopeptide-binding protein OppA in Listeria monocytogenes . RNA Biol 2015; 12:985–997 [View Article][PubMed]
    [Google Scholar]
  58. Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I et al. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic Acids Res 2008; 36:1913–1927 [View Article][PubMed]
    [Google Scholar]
  59. Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK et al. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe 2013; 14:683–695 [View Article][PubMed]
    [Google Scholar]
  60. Torres-Quesada O, Millán V, Nisa-Martínez R, Bardou F, Crespi M et al. Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti . PLoS One 2013; 8:e68147 [View Article][PubMed]
    [Google Scholar]
  61. Dalebroux ZD, Swanson MS. ppGpp: magic beyond RNA polymerase. Nat Rev Microbiol 2012; 10:203–212 [View Article][PubMed]
    [Google Scholar]
  62. Fisher SD, Reger AD, Baum A, Hill SA. RelA alone appears essential for (p)ppGpp production when Neisseria gonorrhoeae encounters nutritional stress. FEMS Microbiol Lett 2005; 248:1–8 [View Article][PubMed]
    [Google Scholar]
  63. Darty K, Denise A, Ponty Y. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25:1974–1975 [View Article][PubMed]
    [Google Scholar]
  64. Wright PR, Georg J, Mann M, Sorescu DA, Richter AS et al. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res 2014; 42:W119–W123 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000548
Loading
/content/journal/micro/10.1099/mic.0.000548
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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