References SRD Sept 2014

S.aureus sRNA discoveries

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.

Novick RP, Ross HF, Projan SJ, Kornblum J, Kreiswirth B, et al. (1993) Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. Embo J. 12: 3967-3975.

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 USA. 102: 14249-14254.

Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, et al. (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.

Roberts C, Anderson KL, Murphy E, Projan SJ, Mounts W, Hurlburt B, Smeltzer M, Overbeek R, Disz T, Dunman PM. Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives. J Bacteriol. 2006 Apr;188(7):2593-603.

Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, et al. (2009) A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res. 37: 7239-7257.

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.

Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J, et al. (2010) Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med. 88: 565-575.

Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, et al. (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res. 38: 6620-6636.

Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, et al. (2010) Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One. 5: e10725.

Nielsen JS, Christiansen MH, Bonde M, Gottschalk S, Frees D, et al. (2010) Searching for small sigma(B)-regulated genes in Staphylococcus aureus. Arch Microbiol. 193(1):23-34.

Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, et al. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A. 108: 20172-20177.

Howden BP, Beaume M, Harrison PF, Hernandez D, Schrenzel J, Seemann T, Francois P, Stinear TP. (2013) Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure. Antimicrob Agents Chemother. 57(8):3864-74.

Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN. (2016). Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus. MBio. 9;7(1):e01990-15.

Mäder U, Nicolas P, Depke M, Pané-Farré J, Debarbouille M, van der Kooi-Pol MM et al. (2016). Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PLoS Genet.1;12(4):e1005962.

Bronsard J, Pascreau G, Sassi M, Mauro T, Augagneur Y, Felden B. (2017). sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide. Sci Rep. Jul 4;7(1):4565.

S. aureus sRNA functions

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.

Benito Y, Kolb FA, Romby P, Lina G, Etienne J, et al. (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.

Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, et al. (2005) Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. Embo J. 24: 824-835.

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

Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, et al. (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.

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 Pathog. 6: e1000927.

Chevalier C, Boisset S, Romilly C, Masquida B, Fechter P, et al. (2010) Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog. 6: e1000809.

Liu Y, Wu N, Dong J, Gao Y, Zhang X, Shao N, Yang G. (2010) SsrA (tmRNA) acts as an antisense RNA to regulate Staphylococcus aureus pigment synthesis by base pairing with crtMN mRNA FEBS Lett. 584(20):4325-4329.

Liu Y, Mu C, Ying X, Li W, Wu N, et al. (2011) RNAIII activates map expression by forming an RNA-RNA complex in Staphylococcus aureus. FEBS Lett. 585: 899–905.

Sayed N, Jousselin A, Felden B. (2011) A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol. 25;19(1):105-112.

Morrison JM, Miller EW, Benson MA, Alonzo F 3rd, Yoong P, Torres VJ, Hinrichs SH, Dunman PM. (2012) Characterization of SSR42, a novel virulence factor regulatory RNA that contributes to the pathogenesis of a Staphylococcus aureus USA300 representative. J Bacteriol. 194(11):2924-2938.

Romilly C, Chevalier C, Marzi S, Masquida B, Geissmann T, et al. (2012) Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus. RNA Biol. 9: 1461–1472.

Song J, Lays C, Vandenesch F, Benito Y, Bes M, et al. (2012) The expression of small regulatory RNAs in clinical samples reflects the different life styles of Staphylococcus aureus in colonization vs. infection. PLoS One 7: e37294.

Chunhua M, Yu L, Yaping G, Jie D, Qiang L, Xiaorong T, Guang Y. The expression of LytM is down-regulated by RNAIII in Staphylococcus aureus. J Basic Microbiol. 2012 Dec;52(6):636-41.

Kaito C, Saito Y, Ikuo M, Omae Y, Mao H, et al. (2013) Mobile Genetic Element SCCmec-encoded psm-mec RNA Suppresses Translation of agrA and Attenuates MRSA Virulence. PLoS Pathog. 9: e1003269.

Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, et al. (2013) In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III. Methods 63: 135-143.

Chabelskaya S, Bordeau V, Felden B. (2014) Dual RNA regulatory control of a Staphylococcus aureus virulence factor. Nucleic Acids Res. 42(8):4847-4858.

Eyraud A, Tattevin P, Chabelskaya S and Felden B. (2014) A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res. 42(8): 4892-4905.

Hammann P, Parmentier D, Cerciat M, Reimegård J, Helfer AC, Boisset S, Guillier M, Vandenesch F, Wagner EG, Romby P, Fechter P. (2014) A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus. Biochimie. pii: S0300-9084(14)00202-8.

Kim S, Reyes D, Beaume M, Francois P, Cheung A. (2014) Contribution of teg49 Small RNA in the 5' Upstream Transcriptional Region of sarA to Virulence in Staphylococcus aureus. Infect Immun. 82(10):4369-4379.

Pinel-Marie ML, Brielle R, Felden B. (2014) Dual toxic-peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally. Cell Rep. 7(2):424-435.

Romilly C, Lays C, Tomasini A, Caldelari I, Benito Y, Hammann P, Geissmann T, Boisset S, Romby P, Vandenesch F. (2014) A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus. PLoS Pathog. 10(3):e1003979.

Tomasini A, François P, Howden BP, Fechter P, Romby P, Caldelari I. (2014) The importance of regulatory RNAs in Staphylococcus aureus. Infect Genet Evol. 21:616-626.

Xue T, Zhang X, Sun H, Sun B (2014) ArtR, a novel sRNA of Staphylococcus aureus, regulates alpha-toxin expression by targeting the 5′ UTR of sarT mRNA. Med Microbiol Immunol. 203(1):1-12.

Yan J, Liu Y, Gao Y, Dong J, Mu C, Li D, Yang G. RNAIII suppresses the expression of LtaS via acting as an antisense RNA in Staphylococcus aureus. J Basic Microbiol. 2014 Oct 3.

S. aureus sRNA reviews

Romby P, Charpentier E. (2010) An overview of RNAs with regulatory functions in Gram-positive bacteria. Cell Mol Life Sci. 67(2):217-237.

Felden B, Vandenesch F, Bouloc P, Romby P. (2011) The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog. 7(3):e1002006.

Romilly C, Caldelari I, Parmentier D, Lioliou E, Romby P, et al. (2012) Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus. RNA Biol. 9: 402–413.

Guillet J, Hallier M, Felden B. (2013) Emerging functions for the Staphylococcus aureus RNome. PLoS Pathog. 9(12):e1003767.

Fechter P, Caldelari I, Lioliou E, Romby P. (2014) Novel aspects of RNA regulation in Staphylococcus aureus. FEBS Lett. 1;588(15):2523-2529

Lalaouna D, Eyraud A, Chabelskaya S, Felden B, Massé E. (2014) Regulatory RNAs Involved in Bacterial Antibiotic Resistance. PLoS Pathog. 10(8):e1004299

sRNA tools

Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-3415.

Busch A, Richter AS, and Backofen R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics. 24 no. 24 pp. 2849-2856.

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