A Current overview of regulatory RNAs in staphylococcus aureus

Regulatory RNAs in Prokaryotes

Volumn , Issue , 2012, Pages 51-76

  Caldelari, Isabelle ^a   Fechter, Pierre ^a   Lioliou, Efthimia ^a   Romilly, Cédric ^a   Chevalier, Clément ^a   Gaspin, Christine ^b   Romby, Pascale ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84957021286     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-0218-3_3     Document Type: Chapter

References (102)

1. Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J, Rozhdestvensky TS, Peters G, von Eiff C, Becker K (2010) Identification of differentially expressed small non-proteincoding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med 88: 565-575.
2. Anderson KL, Dunman PM (2009) Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus. Int J Microbiol ID 525-591.
3. Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dun-man PM (2006) Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188: 6739-6756.
4. Barrick JE, Breaker RR (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239.
5. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A 101: 6421-6426.
6. Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P (2010) Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One 5: e10725.
7. Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F (2000) Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. RNA 6: 668-679.
8. Bischoff M, Dunman P, Kormanec J., Macapagal, D., Murphy, E., Mounts, W., Berger-Bachi, B., and Projan, S. (2004) Microarray-based analysis of the Staphylococcus aureus sigmaB regulon. J Bacteriol 186: 4085-4099.
9. Blevins JS, Beenken KE, Elasri MO, Hurlburt BK, Smeltzer MS (2002) Strain-dependent differences in the regulatory roles of sarA and agr in Staphylococcus aureus. Infect Immun 70: 470-480.
10. Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR (2007) Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3: 44-49.
11. Bohn C, Rigoulay C, Bouloc, P (2007) No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus. BMC Microbiol 7: 10.
12. Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezee-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res.
13. Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P. (2007) Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21: 1353-1366.
14. Brantl S (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10: 102-109.
15. Breaker RR (2009) Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol 4: 771-773.
16. Cassat J, Dunman PM, Murphy E, Projan SJ, Beenken KE, Palm KJ, Yang SJ, Rice KC, Bayles KW, Smeltzer MS (2006) Transcriptional profiling of a Staphylococcus aureus clinical isolate and its isogenic agr and sarA mutants reveals global differences in comparison to the laboratory strain RN6390. Microbiology 152: 3075-3090.
17. Chabelskaya S, Gaillot O, Felden B (2010) A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PLoS Pat-hog 6: e1000927.
18. Chander P, Halbig KM, Miller JK, Fields CJ, Bonner HK, Grabner GK, Switzer RL, Smith JL (2005) Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides. J Bacteriol 187: 1773-1782.
19. Cheung AL, Bayer AS, Zhang G, Gresham H, Xiong YQ (2004) Regulation of virulence determinants in vitro and in vivo in Staphylococcus aureus. FEMS Immunol Med Microbiol 40: 1-9.
20. Chevalier C, Boisset S, Romilly C, Masquida B, Fechter P, Geissmann T, Vandenesch F, Romby P (2010) Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog 6: e1000809.
21. Choonee N, Even S, Zig L, Putzer H (2007) Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res 35: 1578-1588.
22. Chowdhury S, Maris C, Allain FH, Narberhaus F (2006) Molecular basis for temperature sensing by an RNA thermometer. EMBO J 25: 2487-2497.
23. Clatworthy AE, Pierson E, Hung DT (2007) Targeting virulence: a new paradigm for antimicrobial therapy. Nat Chem Biol 3: 541-548.
24. Collins JA, Irnov I, Baker S, Winkler WC (2007) Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21: 3356-3368.
25. Condon C (2007) Maturation and degradation of RNA in bacteria. Curr Opin Microbiol 10: 271-278.
26. Cramton SE, Schnell NF, Gotz F, Bruckner R (2000) Identification of a new repetitive element in Staphylococcus aureus. Infect Immun 68: 2344-2348.
27. Dunman PM, Murphy E, Haney S, Palacios D, Tucker-Kellogg G, Wu S, Brown EL, Zagursky RJ, Shlaes D, Projan SJ (2001) Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci. J Bacteriol 183: 7341-7353.
28. Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G (2010) Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res 38: 3743-3759.
29. Gefen O, Balaban NQ (2009) The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiol Rev 33: 704-717.
30. Geisinger E, Adhikari RP, Jin R, Ross HF, Novick RP (2006) Inhibition of rot translation by RNAIII, a key feature of agr function. Mol Microbiol 61: 1038-1048.
31. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P (2009a) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 37: 7239-7257.
32. Geissmann T, Marzi S, Romby P (2009b) The role of mRNA structure in translational control in bacteria. RNA Biol 6: 153-160.
33. Green NJ, Grundy FJ, Henkin TM (2010) The T box mechanism: tRNA as a regulatory molecule. FEBS Lett 584: 318-324.
34. Grissa I, Vergnaud G, Pourcel C (2008) CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 36: W145-8.
35. Grundy FJ, Haldeman MT, Hornblow GM, Ward JM, Chalker AF, Henkin TM (1997) The Staphylococcus aureus ileS gene, encoding isoleucyl-tRNA synthetase, is a member of the T-box family. J Bacteriol 179: 3767-3772.
36. Gutierrez-Preciado A, Jensen RA, Yanofsky C, Merino E (2005) New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria. Trends Genet 21: 432-436.
37. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167-170.
38. Huntzinger E, Boisset S, Saveanu C. Benito Y, Geissmann T, Namane A, Lina G, Etienne J, Ehres-mann B, Ehresmann C, Jacquier A, Vandenesch F, Romby P (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J 24: 824-835.
39. Iost I, Dreyfus M (1995) The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J 14: 3252-3261.
40. Irnov I, Sharma CM, Vogel J, Winkler WC (2010) Identification of regulatory RNAs in Bacillus su884btilis. Nucleic Acids Res, in press.
41. Jelsbak L, Hemmingsen L, Donat S, Ohlsen K, Boye K, Westh H, Ingmer H, Frees D (2010) Growth phase-dependent regulation of the global virulence regulator Rot in clinical isolates of Staphylococcus aureus. Int J Med Microbiol 300: 229-236.
42. Johansson J, Mandin P, Renzoni A, Chiaruttini C, Springer M, Cossart P (2002) An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110: 551-561.
43. Klein DJ, Ferre-D’Amare AR (2006) Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752-1756.
44. Klinkert B, Narberhaus F (2009) Microbial thermosensors. Cell Mol Life Sci 66: 2661-2676.
45. Knezevic I, Bachem S, Sickmann A, Meyer HE, Stulke J, Hengstenberg W (2000) Regulation of the glucose-specific phosphotransferase system (PTS) of Staphylococcus carnosus by the antiterminator protein GlcT. Microbiology 146: 2333-2342.
46. Lasa I (2006) Towards the identification of the common features of bacterial biofilm development. Int Microbiol 9: 21-28.
47. Lee EJ, Groisman EA (2010) An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Mol Microbiol 76: 1020-1033.
48. Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118: 69-82.
49. Livny J, Teonadi H, Livny M, Waldor MK (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 3: e3197.
50. Llopis PM, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C (2010) Spatial organization of the flow of genetic information in bacteria. Nature 466: 77-81.
51. Loh E, Dussurget O, Gripenland J, Vaitkevicius K, Tiensuu T, Mandin P, Repoila F, Buchrieser C, Cossart P, Johansson J (2009) A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes. Cell 139: 770-779.
52. Lu Y, Turner RJ, Switzer RL (1996) Function of RNA secondary structures in transcriptional attenuation of the Bacillus subtilispyr operon. Proc Natl Acad Sci U S A 93: 14462-14467.
53. Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D. (2009) Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 19: 1084-1092.
54. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-1845.
55. Marraffini LA, Sontheimer EJ (2010a) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181-190.
56. Marraffini LA, Sontheimer EJ (2010b) Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463: 568-571.
57. Marzi S, Fechter P, Chevalier C, Romby P, Geissmann T (2008) RNA switches regulate initiation of translation in bacteria. Biol Chem 389: 585-598.
58. Morfeldt E, Taylor D, von Gabain A, Arvidson S (1995) Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J 14: 4569-4577.
59. Mulhbacher J, Brouillette E, Allard M, Fortier LC, Malouin F, Lafontaine DA (2010) Novel ribo-switch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog 6: e1000865.
60. Murphy E (1985) Nucleotide sequence of ermA, a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus. J Bacteriol 162: 633-640.
61. Nagata M, Kaito C, Sekimizu K (2008) Phosphodiesterase activity of CvfA is required for virulence in Staphylococcus aureus. J Biol Chem 283: 2176-2184.
62. Narberhaus F (2010) Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs. RNA Biol 7.
63. Narberhaus F, Waldminghaus T, Chowdhury S (2006) RNA thermometers. FEMS Microbiol Rev 30: 3-16.
64. Nechooshtan G, Elgrably-Weiss M, Sheaffer A, Westhof E, Altuvia S (2009) A pH-responsive riboregulator. Genes Dev 23: 2650-2662.
65. Novick RP (2003) Autoinduction and signal transduction in the regulation of staphylococcal virulence. Mol Microbiol 48: 1429-1449.
66. Novick RP, Geisinger E (2008) Quorum sensing in staphylococci. Annu Rev Genet 42: 541-564.
67. Novick RP, Iordanescu S, Projan SJ, Kornblum J, Edelman I (1989) pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator. Cell 59: 395-404.
68. Novick RP, Ross HF, Projan SJ, Kornblum J, Kreiswirth B, Moghazeh, S (1993) Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12: 3967-3975.
69. Opdyke JA, Kang JG, Storz G (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186: 6698-6705.
70. Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16: 840-846.
71. Pichon C, Felden B (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci U S A 102: 14249-14254.
72. Proctor RA, von Eiff C, Kahl BC, Becker K, McNamara P, Herrmann M, Peters G (2006) Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections. Nat Rev Microbiol 4: 295-305.
73. Proshkin S, Rahmouni AR, Mironov A, Nudler E (2010) Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328: 504-508.
74. Queck SY, Jameson-Lee M, Villaruz AE, Bach TH, Khan BA, Sturdevant DE, Ricklefs SM, Li M, Otto M (2008) RNAIII-independent target gene control by the agr quorum-sensing system: insight into the evolution of virulence regulation in Staphylococcus aureus. Mol Cell 32: 150-158.
75. Ramesh A, Winkler WC (2010) Magnesium-sensing riboswitches in bacteria. RNA Biol 7.
76. Rasmussen S, Nielsen HB, Jarmer H (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 73: 1043-1057.
77. Roberts C, Anderson KL, Murphy E, Projan SJ, Mounts W, Hurlburt B, Smeltzer M, Overbeek R, Disz T, Dunman PM (2006) Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives. J Bacteriol 188: 2593-2603.
78. Romby P, Charpentier E (2010) An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 67: 217-237.
79. Seif E, Altman S (2008) RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis. RNA 14: 1237-1243.
80. Serganov A (2009) The long and the short of riboswitches. Curr Opin Struct Biol 19: 251-259.
81. Serganov A, Huang L, Patel DJ (2009) Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458: 233-237.
82. Shahbabian K, Jamalli A, Zig L, Putzer H (2009) RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28: 3523-3533.
83. Shimoni Y, Altuvia S, Margalit H, Biham O (2009) Stochastic analysis of the SOS response in Escherichia coli. PLoS One 4: e5363.
84. Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H (2007) Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol Syst Biol 3: 138.
85. Smith AM, Fuchs RT, Grundy FJ, Henkin TM (2010) Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal. RNA Biol 7.
86. Somerville GA, Proctor RA (2009) At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci. Microbiol Mol Biol Rev 73: 233-248.
87. Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR (2005) Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol 12: 1325-1335.
88. Toledo-Arana A, Repoila F, Cossart P (2007) Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 10: 182-188.
89. Tormo-Mas MA, Mir I, Shrestha A, Tallent SM, Campoy S, Lasa I, Barbe J, Novick RP, Christie GE, Penades JR (2010) Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands. Nature 465: 779-782.
90. Tormo MA, Ferrer MD, Maiques E, Ubeda C, Selva L, Lasa I, Calvete JJ, Novick RP, Penades JR (2008) Staphylococcus aureus pathogenicity island DNA is packaged in particles composed of phage proteins. J Bacteriol 190: 2434-2440.
91. Vandenesch F, Projan SJ, Kreiswirth B, Etienne J, Novick RP (1993) Agr-related sequences in Staphylococcus lugdunensis. FEMS Microbiol Lett 111: 115-122.
92. Vogel J (2009) A rough guide to the non-coding RNA world of Salmonella. Mol Microbiol 71: 1-11.
93. Waldminghaus T, Gaubig LC, Narberhaus F (2007) Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers. Mol Genet Genomics 278: 555-564.
94. Wang J, Henkin TM, Nikonowicz EP (2010) NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA. Nucleic Acids Res 38: 3388-3398.
95. Wassarman KM (2007) 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 10: 164-168.
96. Wassarman KM, Saecker RM (2006) Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 314: 1601-1603.
97. Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136: 615-628.
98. Winkler WC, Cohen-Chalamish S, Breaker RR (2002) An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A 99: 15908-15913.
99. Winkler WC, Nahvi A, Roth A, Collins AJ, Breaker RR (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
100. Wyatt MA, Wang W, Roux CM, Beasley FC, Heinrichs DE, Dunman PM, Magarvey NA (2010) Staphylococcus aureus Nonribosomal Peptide Secondary Metabolites Regulate Virulence. Science.
101. Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL (2007) A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 3: e126.
102. Zegans ME, Wagner JC, Cady KC, Murphy DM, Hammond JH, O’Toole GA (2009) Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J Bacteriol 191: 210-219.