1887

Abstract

In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000045
2016-03-02
2019-12-15
Loading full text...

Full text loading...

/deliver/fulltext/mgen/2/3/mgen000045.html?itemId=/content/journal/mgen/10.1099/mgen.0.000045&mimeType=html&fmt=ahah

References

  1. Andrade J. M., Pobre V., Arraiano C. M.. 2013; Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One8:e52866 [CrossRef][PubMed]
    [Google Scholar]
  2. Andrews S. J., Rothnagel J. A.. 2014; Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet15:193–204 [CrossRef][PubMed]
    [Google Scholar]
  3. Backofen R., Hess W. R.. 2010; Computational prediction of sRNAs and their targets in bacteria. RNA Biol7:33–42 [CrossRef][PubMed]
    [Google Scholar]
  4. Balasubramanian D., Vanderpool C. K.. 2013; Deciphering the interplay between two independent functions of the small RNA regulator SgrS in Salmonella. J Bacteriol195:4620–4630 [CrossRef][PubMed]
    [Google Scholar]
  5. Barbe V., Vallenet D., Fonknechten N., Kreimeyer A., Oztas S., Labarre L., Cruveiller S., Robert C., Duprat S., other authors. 2004; Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res32:5766–5779 [CrossRef][PubMed]
    [Google Scholar]
  6. Carroll R. K., Weiss A., Shaw L. N.. 2016; RNA-sequencing of Staphylococcus aureus messenger RNA. Methods Mol Biol1373:131–141[PubMed][CrossRef]
    [Google Scholar]
  7. Caswell C. C., Gaines J. M., Ciborowski P., Smith D., Borchers C. H., Roux C. M., Sayood K., Dunman P. M., Roop R. M. II. 2012; Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol85:345–360 [CrossRef][PubMed]
    [Google Scholar]
  8. Citron M., Schuster H.. 1990; The c4 repressors of bacteriophages P1 and P7 are antisense RNAs. Cell62:591–598 [CrossRef][PubMed]
    [Google Scholar]
  9. Citron M., Schuster H.. 1992; The c4 repressor of bacteriophage P1 is a processed 77 base antisense RNA. Nucleic Acids Res20:3085–3090 [CrossRef][PubMed]
    [Google Scholar]
  10. Davis K. A., Moran K. A., McAllister C. K., Gray P. J.. 2005; Multidrug-resistant Acinetobacter extremity infections in soldiers. Emerg Infect Dis11:1218–1224 [CrossRef][PubMed]
    [Google Scholar]
  11. Gales A. C., Jones R. N., Sader H. S.. 2006; Global assessment of the antimicrobial activity of polymyxin B against 54 731 clinical isolates of Gram-negative bacilli: report from the SENTRY antimicrobial surveillance programme (2001-2004). Clin Microbiol Infect12:315–321 [CrossRef][PubMed]
    [Google Scholar]
  12. Gimpel M., Heidrich N., Mäder U., Krügel H., Brantl S.. 2010; A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol76:990–1009 [CrossRef][PubMed]
    [Google Scholar]
  13. Gottesman S., Storz G.. 2011; Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol3:a003798 [CrossRef][PubMed]
    [Google Scholar]
  14. Gripenland J., Netterling S., Loh E., Tiensuu T., Toledo-Arana A., Johansson J.. 2010; RNAs: regulators of bacterial virulence. Nat Rev Microbiol8:857–866 [CrossRef][PubMed]
    [Google Scholar]
  15. Hartmann R. K., Heinrich J., Schlegl J., Schuster H.. 1995; Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Proc Natl Acad Sci U S A92:5822–5826 [CrossRef][PubMed]
    [Google Scholar]
  16. Heinrich J., Velleman M., Schuster H.. 1995; The tripartite immunity system of phages P1 and P7.FEMS Microbiol Rev17:121–126 [CrossRef][PubMed]
    [Google Scholar]
  17. Hobbs E. C., Fontaine F., Yin X., Storz G.. 2011; An expanding universe of small proteins. Curr Opin Microbiol14:167–173 [CrossRef][PubMed]
    [Google Scholar]
  18. Hofacker I. L.. 2003; Vienna RNA secondary structure server. Nucleic Acids Res31:3429–3431 [CrossRef][PubMed]
    [Google Scholar]
  19. Hujer K. M., Hujer A. M., Hulten E. A., Bajaksouzian S., Adams J. M., Donskey C. J., Ecker D. J., Massire C., Eshoo M. W., other authors. 2006; Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the Walter Reed Army Medical Center. Antimicrob Agents Chemother50:4114–4123 [CrossRef][PubMed]
    [Google Scholar]
  20. Imperi F., Antunes L. C., Blom J., Villa L., Iacono M., Visca P., Carattoli A.. 2011; The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB Life63:1068–1074 [CrossRef][PubMed]
    [Google Scholar]
  21. Jacobs A. C., Thompson M. G., Black C. C., Kessler J. L., Clark L. P., McQueary C. N., Gancz H. Y., Corey B. W., Moon J. K., other authors. 2014; AB5075, a highly virulent isolate of Acinetobacter baumannii, as a model strain for the evaluation of pathogenesis and antimicrobial treatments. MBio5:e01076–e01014 [CrossRef][PubMed]
    [Google Scholar]
  22. Jawad A., Seifert H., Snelling A. M., Heritage J., Hawkey P. M.. 1998; Survival of Acinetobacter baumannii on dry surfaces: comparison of outbreak and sporadic isolates. J Clin Microbiol36:1938–1941[PubMed]
    [Google Scholar]
  23. Juni E., Janik A.. 1969; Transformation of Acinetobacter calco-aceticus (Bacterium anitratum). J Bacteriol98:281–288[PubMed]
    [Google Scholar]
  24. Ko K. S., Suh J. Y., Kwon K. T., Jung S. I., Park K. H., Kang C. I., Chung D. R., Peck K. R., Song J. H.. 2007; High rates of resistance to colistin and polymyxin B in subgroups of Acinetobacter baumannii isolates from Korea. J Antimicrob Chemother60:1163–1167 [CrossRef][PubMed]
    [Google Scholar]
  25. Kramer A., Schwebke I., Kampf G.. 2006; How long do nosocomial pathogens persist on inanimate surfaces?. A systematic review. BMC Infect Dis6:130 [CrossRef][PubMed]
    [Google Scholar]
  26. Lesho E., Yoon E. J., McGann P., Snesrud E., Kwak Y., Milillo M., Onmus-Leone F., Preston L., St Clair K., other authors. 2013; Emergence of colistin-resistance in extremely drug-resistant Acinetobacter baumannii containing a novel pmrCAB operon during colistin therapy of wound infections. J Infect Dis208:1142–1151 [CrossRef][PubMed]
    [Google Scholar]
  27. Li J., Rayner C. R., Nation R. L., Owen R. J., Spelman D., Tan K. E., Liolios L.. 2006; Heteroresistance to colistin in multidrug-resistant Acinetobacter baumannii. Antimicrob Agents Chemother50:2946–2950 [CrossRef][PubMed]
    [Google Scholar]
  28. Livny J., Waldor M. K.. 2007; Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol10:96–101 [CrossRef][PubMed]
    [Google Scholar]
  29. Navon-Venezia S., Leavitt A., Carmeli Y.. 2007; High tigecycline resistance in multidrug-resistant Acinetobacter baumannii. J Antimicrob Chemother59:772–774 [CrossRef][PubMed]
    [Google Scholar]
  30. Nawrocki E. P., Burge S. W., Bateman A., Daub J., Eberhardt R. Y., Eddy S. R., Floden E. W., Gardner P. P., Jones T. A., other authors. 2015; Rfam 12.0: updates to the RNA families database. Nucleic Acids Res43:(D1)D130–D137 [CrossRef][PubMed]
    [Google Scholar]
  31. Peleg A. Y., Seifert H., Paterson D. L.. 2008; Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev21:538–582 [CrossRef][PubMed]
    [Google Scholar]
  32. Pendleton J. N., Gorman S. P., Gilmore B. F.. 2013; Clinical relevance of the ESKAPE pathogens. Expert Rev Anti Infect Ther11:297–308 [CrossRef][PubMed]
    [Google Scholar]
  33. Peterman N., Lavi-Itzkovitz A., Levine E.. 2014; Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity. Nucleic Acids Res42:12177–12188 [CrossRef][PubMed]
    [Google Scholar]
  34. Pichon C., Felden B.. 2008; Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics24:2807–2813 [CrossRef][PubMed]
    [Google Scholar]
  35. Queenan A. M., Bush K.. 2007; Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev20:440–458 [CrossRef][PubMed]
    [Google Scholar]
  36. Rice L. B.. 2008; Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis197:1079–1081 [CrossRef][PubMed]
    [Google Scholar]
  37. Romby P., Vandenesch F., Wagner E. G.. 2006; The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol9:229–236 [CrossRef][PubMed]
    [Google Scholar]
  38. Ruzin A., Keeney D., Bradford P. A.. 2007; AdeABC multidrug efflux pump is associated with decreased susceptibility to tigecycline in Acinetobacter calcoaceticus-Acinetobacter baumannii complex. J Antimicrob Chemother59:1001–1004 [CrossRef][PubMed]
    [Google Scholar]
  39. Schilling D., Findeiss S., Richter A. S., Taylor J. A., Gerischer U.. 2010; The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Arch Microbiol192:691–702 [CrossRef][PubMed]
    [Google Scholar]
  40. Sharma C. M., Vogel J.. 2014; Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol19:97–105 [CrossRef][PubMed]
    [Google Scholar]
  41. Sharma R., Arya S., Patil S. D., Sharma A., Jain P. K., Navani N. K., Pathania R.. 2014; Identification of novel regulatory small RNAs in Acinetobacter baumannii. PLoS One9:e93833 [CrossRef][PubMed]
    [Google Scholar]
  42. Sridhar J., Gunasekaran P.. 2013; Computational small RNA prediction in bacteria. Bioinform Biol Insights7:83–95[PubMed]
    [Google Scholar]
  43. Thomason M. K., Storz G.. 2010; Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet44:167–188 [CrossRef][PubMed]
    [Google Scholar]
  44. Vila J., Martí S., Sánchez-Céspedes J.. 2007; Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii. J Antimicrob Chemother59:1210–1215 [CrossRef][PubMed]
    [Google Scholar]
  45. Waters L. S., Storz G.. 2009; Regulatory RNAs in bacteria. Cell136:615–628 [CrossRef][PubMed]
    [Google Scholar]
  46. Weinberg Z., Wang J. X., Bogue J., Yang J., Corbino K., Moy R. H., Breaker R. R.. 2010; Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol11:R31 [CrossRef][PubMed]
    [Google Scholar]
  47. Weiss A., Ibarra J. A., Paoletti J., Carroll R. K., Shaw L. N.. 2014; The δ subunit of RNA polymerase guides promoter selectivity and virulence in Staphylococcus aureus. Infect Immun82:1424–1435 [CrossRef][PubMed]
    [Google Scholar]
  48. Wisplinghoff H., Schmitt R., Wöhrmann A., Stefanik D., Seifert H.. 2007; Resistance to disinfectants in epidemiologically defined clinical isolates of Acinetobacter baumannii. J Hosp Infect66:174–181 [CrossRef][PubMed]
    [Google Scholar]
  49. Yun H. C., Branstetter J. G., Murray C. K.. 2008; Osteomyelitis in military personnel wounded in Iraq and Afghanistan. J Trauma64:S163–S168 [CrossRef][PubMed]
    [Google Scholar]
  50. Zuker M.. 2003; Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res31:3406–3415 [CrossRef][PubMed]
    [Google Scholar]
  51. 1. Weiss, A., Broach, W. H., Lee, M. C. & Shaw, L. N. (2015). NCBI Gene Expression Omnibus GSE75708.
  52. 2. Weiss, A., Broach, W. H., Lee, M. C. & Shaw, L. N. (2015). Figshare http://dx.doi.org/10.6084/m9.figshare.1592959
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000045
Loading
/content/journal/mgen/10.1099/mgen.0.000045
Loading

Data & Media loading...

Supplements

Supplementary Data

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