151
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Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880-91. [PMID: 21925377 PMCID: PMC3176440 DOI: 10.1016/j.molcel.2011.08.022] [Citation(s) in RCA: 866] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/23/2011] [Accepted: 08/23/2011] [Indexed: 11/24/2022]
Abstract
Research on the discovery and characterization of small, regulatory RNAs in bacteria has exploded in recent years. These sRNAs act by base pairing with target mRNAs with which they share limited or extended complementarity, or by modulating protein activity, in some cases by mimicking other nucleic acids. Mechanistic insights into how sRNAs bind mRNAs and proteins, how they compete with each other, and how they interface with ribonucleases are active areas of discovery. Current work also has begun to illuminate how sRNAs modulate expression of distinct regulons and key transcription factors, thus integrating sRNA activity into extensive regulatory networks. In addition, the application of RNA deep sequencing has led to reports of hundreds of additional sRNA candidates in a wide swath of bacterial species. Most importantly, recent studies have served to clarify the abundance of remaining questions about how, when, and why sRNA-mediated regulation is of such importance to bacterial lifestyles.
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Affiliation(s)
- Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 18 Library Drive, Bethesda, MD 20892-5430, USA.
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152
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Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci U S A 2011; 108:E709-17. [PMID: 21876162 DOI: 10.1073/pnas.1101655108] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A major class of bacterial small, noncoding RNAs (sRNAs) acts by base-pairing with mRNAs to alter the translation from and/or stability of the transcript. Our laboratory has shown that Hfq, the chaperone that mediates the interaction of many sRNAs with their targets, is required for the virulence of the enteropathogen Yersinia pseudotuberculosis. This finding suggests that sRNAs play a critical role in the regulation of virulence in this pathogen, but these sRNAs are not known. Using a deep sequencing approach, we identified the global set of sRNAs expressed in vitro by Y. pseudotuberculosis. Sequencing of RNA libraries from bacteria grown at 26 °C and 37 °C resulted in the identification of 150 unannotated sRNAs. The majority of these sRNAs are Yersinia specific, without orthologs in either Escherichia coli or Salmonella typhimurium. Six sRNAs are Y. pseudotuberculosis specific and are absent from the genome of the closely related species Yersinia pestis. We found that the expression of many sRNAs conserved between Y. pseudotuberculosis and Y. pestis differs in both timing and dependence on Hfq, suggesting evolutionary changes in posttranscriptional regulation between these species. Deletion of multiple sRNAs in Y. pseudotuberculosis leads to attenuation of the pathogen in a mouse model of yersiniosis, as does the inactivation in Y. pestis of a conserved, Yersinia-specific sRNA in a mouse model of pneumonic plague. Finally, we determined the regulon controlled by one of these sRNAs, revealing potential virulence determinants in Y. pseudotuberculosis that are regulated in a posttranscriptional manner.
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153
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Kloc M, Foreman V, Reddy SA. Binary function of mRNA. Biochimie 2011; 93:1955-61. [PMID: 21784124 DOI: 10.1016/j.biochi.2011.07.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 07/08/2011] [Indexed: 12/21/2022]
Abstract
Since the discovery of messenger RNA (mRNA) over half a century ago, the assumption has always been that the only function of mRNA is to make a protein. However, recent studies of prokaryotic and eukaryotic organisms unexpectedly show that some mRNAs may be functionally binary and have additional structural functions that are unrelated to their translation product. These findings imply that some of the phenotypic features of cells and organisms can also be binary, that is, they depend both on the function of a protein and the independent structural function of its mRNA. In this review, we will discuss this concept within the framework of multifunctional RNA molecules and the RNA World Hypothesis.
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Affiliation(s)
- Malgorzata Kloc
- Department of Surgery, The Methodist Hospital and The Methodist Hospital Research Institute, 6565 Fannin St., Houston, TX 77030, USA.
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154
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Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JCD, Vogel J. Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 2011; 81:1144-65. [PMID: 21696468 DOI: 10.1111/j.1365-2958.2011.07751.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
GcvB is one of the most highly conserved Hfq-associated small RNAs in Gram-negative bacteria and was previously reported to repress several ABC transporters for amino acids. To determine the full extent of GcvB-mediated regulation in Salmonella, we combined a genome-wide experimental approach with biocomputational target prediction. Comparative pulse expression of wild-type versus mutant sRNA variants revealed that GcvB governs a large post-transcriptional regulon, impacting ~1% of all Salmonella genes via its conserved G/U-rich domain R1. Complementary predictions of C/A-rich binding sites in mRNAs and gfp reporter fusion experiments increased the number of validated GcvB targets to more than 20, and doubled the number of regulated amino acid transporters. Unlike the previously described targeting via the single R1 domain, GcvB represses the glycine transporter CycA by exceptionally redundant base-pairing. This novel ability of GcvB is focused upon the one target that could feedback-regulate the glycine-responsive synthesis of GcvB. Several newly discovered mRNA targets involved in amino acid metabolism, including the global regulator Lrp, question the previous assumption that GcvB simply acts to limit unnecessary amino acid uptake. Rather, GcvB rewires primary transcriptional control circuits and seems to act as a distinct regulatory node in amino acid metabolism.
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Affiliation(s)
- Cynthia M Sharma
- Institute for Molecular Infection Biology, Research Centre of Infectious Diseases, University of Würzburg, Germany
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155
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Vanderpool CK, Balasubramanian D, Lloyd CR. Dual-function RNA regulators in bacteria. Biochimie 2011; 93:1943-9. [PMID: 21816203 DOI: 10.1016/j.biochi.2011.07.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 07/08/2011] [Indexed: 12/18/2022]
Abstract
The importance of small RNA (sRNA) regulators has been recognized across all domains of life. In bacteria, sRNAs typically control the expression of virulence and stress response genes via antisense base pairing with mRNA targets. Originally dubbed "non-coding RNAs," a number of bacterial antisense sRNAs have been found to encode functional proteins. Although very few of these dual-function sRNAs have been characterized, they have been found in both gram-negative and gram-positive organisms. Among the few known examples, the functions and mechanisms of regulation by dual-function sRNAs are variable. Some dual-function sRNAs depend on the RNA chaperone Hfq for base pairing-dependent regulation (riboregulation); this feature appears so far exclusive to gram-negative bacterial sRNAs. Other variations can be found in the spatial organization of the coding region with respect to the riboregulation determinants. How the functions of encoded proteins relate to riboregulation is for the most part not understood. However, in one case it appears that there is physiological redundancy between protein and riboregulation functions. This mini-review focuses on the two best-studied bacterial dual-function sRNAs: RNAIII from Staphylococcus aureus and SgrS from Escherichia coli and includes a discussion of what is known about the structure, function and physiological roles of these sRNAs as well as what questions remain outstanding.
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Affiliation(s)
- Carin K Vanderpool
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.
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156
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Liu Y, Dong J, Wu N, Gao Y, Zhang X, Mu C, Shao N, Fan M, Yang G. The production of extracellular proteins is regulated by ribonuclease III via two different pathways in Staphylococcus aureus. PLoS One 2011; 6:e20554. [PMID: 21655230 PMCID: PMC3105085 DOI: 10.1371/journal.pone.0020554] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/05/2011] [Indexed: 01/11/2023] Open
Abstract
Staphylococcus aureus ribonuclease III belongs to the enzyme family known to degrade double-stranded RNAs. It has previously been reported that RNase III cannot influence cell growth but regulates virulence gene expression in S. aureus. Here we constructed an RNase III inactivation mutant (Δrnc) from S. aureus 8325-4. It was found that the extracellular proteins of Δrnc were decreased. Furthermore, we explored how RNase III regulated the production of the extracellular proteins in S. aureus. We found during the lag phase of the bacterial growth cycle RNase III could influence the extracellular protein secretion via regulating the expression of secY2, one component of accessory secretory (sec) pathway. After S. aureus cells grew to exponential phase, RNase III can regulate the expression of extracellular proteins by affecting the level of RNAIII. Further investigation showed that the mRNA stability of secY2 and RNAIII was affected by RNase III. Our results suggest that RNase III could regulate the pathogenicity of S. aureus by influencing the level of extracellular proteins via two different ways respectively at different growth phases.
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Affiliation(s)
- Yu Liu
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Jie Dong
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Na Wu
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Yaping Gao
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Xin Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Chunhua Mu
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Ming Fan
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
| | - Guang Yang
- Beijing Institute of Basic Medical Sciences, Beijing, People's Republic of China
- * E-mail:
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157
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Mraheil MA, Billion A, Kuenne C, Pischimarov J, Kreikemeyer B, Engelmann S, Hartke A, Giard JC, Rupnik M, Vorwerk S, Beier M, Retey J, Hartsch T, Jacob A, Cemič F, Hemberger J, Chakraborty T, Hain T. Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application. Microb Biotechnol 2011; 3:658-76. [PMID: 21255362 PMCID: PMC3815340 DOI: 10.1111/j.1751-7915.2010.00171.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the recent years, the number of drug- and multi-drug-resistant microbial strains has increased rapidly. Therefore, the need to identify innovative approaches for development of novel anti-infectives and new therapeutic targets is of high priority in global health care. The detection of small RNAs (sRNAs) in bacteria has attracted considerable attention as an emerging class of new gene expression regulators. Several experimental technologies to predict sRNA have been established for the Gram-negative model organism Escherichia coli. In many respects, sRNA screens in this model system have set a blueprint for the global and functional identification of sRNAs for Gram-positive microbes, but the functional role of sRNAs in colonization and pathogenicity for Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis and Clostridium difficile is almost completely unknown. Here, we report the current knowledge about the sRNAs of these socioeconomically relevant Gram-positive pathogens, overview the state-of-the-art high-throughput sRNA screening methods and summarize bioinformatics approaches for genome-wide sRNA identification and target prediction. Finally, we discuss the use of modified peptide nucleic acids (PNAs) as a novel tool to inactivate potential sRNA and their applications in rapid and specific detection of pathogenic bacteria.
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Affiliation(s)
- Mobarak A Mraheil
- Institute of Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, 35392 Giessen, Germany
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158
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Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011; 471:602-7. [PMID: 21455174 PMCID: PMC3070239 DOI: 10.1038/nature09886] [Citation(s) in RCA: 1667] [Impact Index Per Article: 128.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 01/28/2011] [Indexed: 12/12/2022]
Abstract
CRISPR/Cas systems constitute a widespread class of immunity systems that protect bacteria and archaea against phages and plasmids, and commonly use repeat/spacer-derived short crRNAs to silence foreign nucleic acids in a sequence-specific manner. Although the maturation of crRNAs represents a key event in CRISPR activation, the responsible endoribonucleases (CasE, Cas6, Csy4) are missing in many CRISPR/Cas subtypes. Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans-encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts. We show that tracrRNA directs the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein; all these components are essential to protect S. pyogenes against prophage-derived DNA. Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders.
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Affiliation(s)
- Elitza Deltcheva
- The Laboratory for Molecular Infection Medicine Sweden, Umeå, Sweden
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159
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Bonde M, Højland DH, Kolmos HJ, Kallipolitis BH, Klitgaard JK. Thioridazine affects transcription of genes involved in cell wall biosynthesis in methicillin-resistant Staphylococcus aureus. FEMS Microbiol Lett 2011; 318:168-76. [PMID: 21375577 DOI: 10.1111/j.1574-6968.2011.02255.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The antipsychotic drug thioridazine is a candidate drug for an alternative treatment of infections caused by methicillin-resistant Staphylococcus aureus (MRSA) in combination with the β-lactam antibiotic oxacillin. The drug has been shown to have the capability to resensitize MRSA to oxacillin. We have previously shown that the expression of some resistance genes is abolished after treatment with thioridazine and oxacillin. To further understand the mechanism underlying the reversal of resistance, we tested the expression of genes involved in antibiotic resistance and cell wall biosynthesis in response to thioridazine in combination with oxacillin. We observed that the oxacillin-induced expression of genes belonging to the VraSR regulon is reduced by the addition of thioridazine. The exclusion of such key factors involved in cell wall biosynthesis will most likely lead to a weakened cell wall and affect the ability of the bacteria to sustain oxacillin treatment. Furthermore, we found that thioridazine itself reduces the expression level of selected virulence genes and that selected toxin genes are not induced by thioridazine. In the present study, we find indications that the mechanism underlying reversal of resistance by thioridazine relies on decreased expression of specific genes involved in cell wall biosynthesis.
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Affiliation(s)
- Mette Bonde
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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160
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Abstract
Staphylococcus aureus is a major human pathogen causing a wide spectrum of nosocomial and community-associated infections with high morbidity and mortality. S. aureus generates a large number of virulence factors whose timing and expression levels are precisely tuned by regulatory proteins and RNAs. The aptitude of bacteria to use RNAs to rapidly modify gene expression, including virulence factors in response to stress or environmental changes, and to survive in a host is an evolving concept. Here, we focus on the recently inventoried S. aureus regulatory RNAs, with emphasis on those with identified functions, two of which are directly involved in pathogenicity.
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161
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Matsuo M, Oogai Y, Kato F, Sugai M, Komatsuzawa H. Growth-phase dependence of susceptibility to antimicrobial peptides in Staphylococcus aureus. MICROBIOLOGY-SGM 2011; 157:1786-1797. [PMID: 21393369 DOI: 10.1099/mic.0.044727-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cell surface charge is responsible for susceptibility to cationic antimicrobial peptides. Previously, Staphylococcus aureus dlt and mprF were identified as factors conferring a positive charge upon cell surfaces. In this study, we investigated the regulation of cell surface charge during growth. Using a group of S. aureus MW2 mutants, which are gene-inactivated in 15 types of two-component systems (TCSs), we tested dltC and mprF expression and found that two TCSs, aps and agr, were associated with dltC and mprF expression in a growth phase-dependent manner. The first of these, aps, which had already been identified as a sensor of antimicrobial peptides and a positive regulator of dlt and mprF expression, was expressed strongly in the exponential phase, while its expression was significantly suppressed by agr in the stationary phase, resulting in higher expression of dltC and mprF in the exponential phase and lower expression in the stationary phase. Since both types of expression affected the cell surface charge, the susceptibility to antimicrobial peptides and cationic antibiotics was changed during growth. Furthermore, we found that the ability to sense antimicrobial peptides only functioned in the exponential phase. These results suggest that cell surface charge is tightly regulated during growth in S. aureus.
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Affiliation(s)
- Miki Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
| | - Fuminori Kato
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima 734-8553, Japan
| | - Motoyuki Sugai
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima 734-8553, Japan
| | - Hitoshi Komatsuzawa
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Japan
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162
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Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F. Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein. Mol Microbiol 2011; 80:492-506. [PMID: 21320185 DOI: 10.1111/j.1365-2958.2011.07589.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wounded plants activate a complex defence programme in response to Agrobacterium tumefaciens. They synthesize the non-proteinogenic amino acid γ-aminobutyric acid (GABA), which stimulates degradation of the quorum sensing signal N-(3-oxo-octanoyl) homoserine lactone. GABA is transported into A. tumefaciens via an ABC transporter dependent on the periplasmic binding protein Atu2422. We demonstrate that expression of atu2422 and two other ABC transporter genes is downregulated by the conserved small RNA (sRNA) AbcR1 (for ABC regulator). AbcR1 is encoded in tandem with another sRNA, which is similar in sequence and structure. Both sRNAs accumulate during stationary phase but only the absence of AbcR1 resulted in significant accumulation of Atu2422 and increased GABA import. AbcR1 inhibits initiation of atu2422 translation by masking its Shine-Dalgarno sequence and thereby reduces stability of the atu2422 transcript. It is the first described bacterial sRNA that controls uptake of a plant-generated signalling molecule. Given that similar sRNAs and ABC transporter genes are present in various Rhizobiaceae and in Brucella, it is likely that such sRNA-mediated control impacts a number of host-microbe interactions.
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Affiliation(s)
- Ina Wilms
- Lehrstuhl für Biologie der Mikroorganismen Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44780 Bochum, Germany
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163
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RNAIII activates map expression by forming an RNA-RNA complex in Staphylococcus aureus. FEBS Lett 2011; 585:899-905. [PMID: 21349272 DOI: 10.1016/j.febslet.2011.02.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 02/16/2011] [Accepted: 02/16/2011] [Indexed: 12/30/2022]
Abstract
Staphylococcus aureus is a gram-positive pathogen responsible for a wide variety of diseases. RNAIII is the key effector of the accessory gene regulator (agr) system. It is a regulatory RNA (514 nucleotides long) that acts at both transcription and translation level to regulate the production of numerous toxins, enzymes and cell surface proteins. Here, we reveal that map (major histocompatibility complex class II analogous protein) is positively regulated by RNAIII. Our further study indicates that the 108-135nt fragment of RNAIII acts as an antisense RNA and anneals to map mRNA, forming RNA duplexes. The interaction between RNAIII and map mRNA may activate translation initiation. This may be helpful for understanding the regulation of virulence in S. aureus.
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164
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Olson PD, Kuechenmeister LJ, Anderson KL, Daily S, Beenken KE, Roux CM, Reniere ML, Lewis TL, Weiss WJ, Pulse M, Nguyen P, Simecka JW, Morrison JM, Sayood K, Asojo OA, Smeltzer MS, Skaar EP, Dunman PM. Small molecule inhibitors of Staphylococcus aureus RnpA alter cellular mRNA turnover, exhibit antimicrobial activity, and attenuate pathogenesis. PLoS Pathog 2011; 7:e1001287. [PMID: 21347352 PMCID: PMC3037362 DOI: 10.1371/journal.ppat.1001287] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 01/10/2011] [Indexed: 11/23/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus is estimated to cause more U.S. deaths annually than HIV/AIDS. The emergence of hypervirulent and multidrug-resistant strains has further amplified public health concern and accentuated the need for new classes of antibiotics. RNA degradation is a required cellular process that could be exploited for novel antimicrobial drug development. However, such discovery efforts have been hindered because components of the Gram-positive RNA turnover machinery are incompletely defined. In the current study we found that the essential S. aureus protein, RnpA, catalyzes rRNA and mRNA digestion in vitro. Exploiting this activity, high through-put and secondary screening assays identified a small molecule inhibitor of RnpA-mediated in vitro RNA degradation. This agent was shown to limit cellular mRNA degradation and exhibited antimicrobial activity against predominant methicillin-resistant S. aureus (MRSA) lineages circulating throughout the U.S., vancomycin intermediate susceptible S. aureus (VISA), vancomycin resistant S. aureus (VRSA) and other Gram-positive bacterial pathogens with high RnpA amino acid conservation. We also found that this RnpA-inhibitor ameliorates disease in a systemic mouse infection model and has antimicrobial activity against biofilm-associated S. aureus. Taken together, these findings indicate that RnpA, either alone, as a component of the RNase P holoenzyme, and/or as a member of a more elaborate complex, may play a role in S. aureus RNA degradation and provide proof of principle for RNA catabolism-based antimicrobial therapy. The last decade has witnessed a mass downsizing in pharmaceutical antibiotic drug discovery initiatives. This has posed a major healthcare issue that will likely worsen with time; antibiotic resistant bacteria continue to emerge while advances in new therapeutic options languish. In the current body of work, we show that agents that limit bacterial RNA turnover have potential as a new class of antibiotics. More specifically, our findings indicate the essential bacterial protein, RnpA, exhibits in vitro ribonuclease activity and either alone and/or as a member of the RNase P holoenzyme, may contribute to the RNA degradation properties of Staphylococcus aureus, a predominant cause of hospital and community bacterial infections. Accordingly, using high throughput screening we identified small molecule inhibitors of RnpA's in vitro RNA degradation activity. One of these agents, RNPA1000, was shown to limit S. aureus mRNA turnover and growth. RNPA1000 also limited growth of other important Gram-positive bacterial pathogens, exhibited antimicrobial efficacy against biofilm associated S. aureus and protected against the S. aureus pathogenesis in an animal model of infection. When taken together, our results illustrate that components of the bacterial RNA degradation machinery have utility as antibiotic drug-discovery targets and that RNPA1000 may represent a progenitor of this new class of antibiotics.
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Affiliation(s)
- Patrick D. Olson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lisa J. Kuechenmeister
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kelsi L. Anderson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sonja Daily
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Christelle M. Roux
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Michelle L. Reniere
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Tami L. Lewis
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - William J. Weiss
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Mark Pulse
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Phung Nguyen
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Jerry W. Simecka
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - John M. Morrison
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Khalid Sayood
- Department of Electrical Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Oluwatoyin A. Asojo
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mark S. Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Eric P. Skaar
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Paul M. Dunman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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165
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Thoendel M, Kavanaugh JS, Flack CE, Horswill AR. Peptide signaling in the staphylococci. Chem Rev 2010; 111:117-51. [PMID: 21174435 DOI: 10.1021/cr100370n] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Matthew Thoendel
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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166
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Shi Z, Nicholson RH, Jaggi R, Nicholson AW. Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates. Nucleic Acids Res 2010; 39:2756-68. [PMID: 21138964 PMCID: PMC3074117 DOI: 10.1093/nar/gkq1030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ribonuclease III cleaves double-stranded (ds) structures in bacterial RNAs and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, the biochemical properties of A. aeolicus (Aa)-RNase III and the reactivity epitopes of its substrates are not known. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of ∼70–85°C, with either Mg2+ or Mn2+ supporting efficient catalysis. Small hairpins based on the stem structures associated with the Aquifex 16S and 23S rRNA precursors are cleaved at sites that are consistent with production of the immediate precursors to the mature rRNAs. Substrate reactivity is independent of the distal box sequence, but is strongly dependent on the proximal box sequence. Structural studies have shown that a conserved glutamine (Q157) in the Aa-RNase III dsRNA-binding domain (dsRBD) directly interacts with a proximal box base pair. Aa-RNase III cleavage of the pre-16S substrate is blocked by the Q157A mutation, which reflects a loss of substrate binding affinity. Thus, a highly conserved dsRBD-substrate interaction plays an important role in substrate recognition by bacterial RNase III.
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MESH Headings
- Amino Acid Sequence
- Bacteria/enzymology
- Base Pairing
- Base Sequence
- Biocatalysis
- Cations, Divalent/chemistry
- Enzyme Stability
- Glutamine/chemistry
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- RNA Precursors/chemistry
- RNA Precursors/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Double-Stranded/metabolism
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- Ribonuclease III/chemistry
- Ribonuclease III/metabolism
- Salts/chemistry
- Temperature
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Affiliation(s)
- Zhongjie Shi
- Department of Chemistry and Department of Biology, Temple University, Philadelphia, PA, USA
| | - Rhonda H. Nicholson
- Department of Chemistry and Department of Biology, Temple University, Philadelphia, PA, USA
| | - Ritu Jaggi
- Department of Chemistry and Department of Biology, Temple University, Philadelphia, PA, USA
| | - Allen W. Nicholson
- Department of Chemistry and Department of Biology, Temple University, Philadelphia, PA, USA
- *To whom correspondence should be addressed. Tel: +1 215 204 9048; Fax: +1 215 204 1532;
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167
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Viegas SC, Silva IJ, Saramago M, Domingues S, Arraiano CM. Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway. Nucleic Acids Res 2010; 39:2918-30. [PMID: 21138960 PMCID: PMC3074148 DOI: 10.1093/nar/gkq1239] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the control of free MicA levels in the cell. We purified both Salmonella enzymes and demonstrated that in vitro RNase III is only active over MicA when in complex with its targets (whether ompA or lamB mRNAs). In vivo, MicA is demonstrated to be cleaved by RNase III in a coupled way with ompA mRNA. On the other hand, RNase E is able to cleave unpaired MicA and does not show a marked dependence on its 5′ phosphorylation state. The main conclusion of this work is the existence of two independent pathways for MicA turnover. Each pathway involves a distinct endoribonuclease, having a different role in the context of the fine-tuned regulation of porin levels. Cleavage of MicA by RNase III in a target-dependent fashion, with the concomitant decay of the mRNA target, strongly resembles the eukaryotic RNAi system, where RNase III-like enzymes play a pivotal role.
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Affiliation(s)
- Sandra C Viegas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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168
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Abstract
RNA-based pathways that regulate protein expression are much more widespread than previously thought. Regulatory RNAs, including 5' and 3' untranslated regions next to the coding sequence, cis-acting antisense RNAs and trans-acting small non-coding RNAs, are effective regulatory molecules that can influence protein expression and function in response to external cues such as temperature, pH and levels of metabolites. This Review discusses the mechanisms by which these regulatory RNAs, together with accessory proteins such as RNases, control the fate of mRNAs and proteins and how this regulation influences virulence in pathogenic bacteria.
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169
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When one is better than two: RNA with dual functions. Biochimie 2010; 93:633-44. [PMID: 21111023 DOI: 10.1016/j.biochi.2010.11.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/17/2010] [Indexed: 11/23/2022]
Abstract
The central dogma of biology, until not long ago, held that genetic information stored on DNA molecules was translated into the final protein products through RNA as intermediate molecules. Then, an additional level of complexity in the regulation of genome expression was added, implicating new classes of RNA molecules called non-coding RNA (ncRNA). These ncRNA are also often referred to as functional RNA in that, although they do not contain the capacity to encode proteins, do have a function as RNA molecules. They have been thus far considered as truly non-coding RNA since no ORF long enough to be considered, nor protein, have been associated with them. However, the recent identification and characterization of bifunctional RNA, i.e. RNA for which both coding capacity and activity as functional RNA have been reported, suggests that a definite categorization of some RNA molecules is far from being straightforward. Indeed, several RNA primarily classified as non-protein-coding RNA has been showed to hold coding capacities and associated peptides. Conversely, mRNA, usually regarded as strictly protein-coding, may act as functional RNA molecules. Here, we describe several examples of these bifunctional RNA that have been already characterized from bacteria to mammals. We also extend this concept to fortuitous acquisition of dual function in pathological conditions and to the recently highlighted duality between information carried by a gene and its pseudogenes counterparts.
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170
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Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL. Identification of small RNAs in Francisella tularensis. BMC Genomics 2010; 11:625. [PMID: 21067590 PMCID: PMC3091763 DOI: 10.1186/1471-2164-11-625] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 11/10/2010] [Indexed: 12/29/2022] Open
Abstract
Background Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far. Results We have used a combination of experimental assays and in silico prediction to identify sRNAs in F. tularensis strain LVS. Using a cDNA cloning and sequencing approach we have shown that F. tularensis expresses homologues of several sRNAs that are well-conserved among diverse bacteria. We have also discovered two abundant putative sRNAs that share no sequence similarity or conserved genomic context with any previously annotated regulatory transcripts. Deletion of either of these two loci led to significant changes in the expression of several mRNAs that likely include the cognate target(s) of these sRNAs. Deletion of these sRNAs did not, however, significantly alter F. tularensis growth under various stress conditions in vitro, its replication in murine cells, or its ability to induce disease in a mouse model of F. tularensis infection. We also conducted a genome-wide in silico search for intergenic loci that suggests F. tularensis encodes several other sRNAs in addition to the sRNAs found in our experimental screen. Conclusion Our findings suggest that F. tularensis encodes a significant number of non-coding regulatory RNAs, including members of well conserved families of structural and housekeeping RNAs and other poorly conserved transcripts that may have evolved more recently to help F. tularensis deal with the unique and diverse set of environments with which it must contend.
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171
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A cis-encoded antisense small RNA regulated by the HP0165-HP0166 two-component system controls expression of ureB in Helicobacter pylori. J Bacteriol 2010; 193:40-51. [PMID: 20971914 DOI: 10.1128/jb.00800-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Expression of urease is essential for gastric colonization by Helicobacter pylori. The increased level of urease in gastric acidity is due, in part, to acid activation of the two-component system (TCS) consisting of the membrane sensor HP0165 and its response regulator, HP0166, which regulates transcription of the seven genes of the urease gene cluster. We now find that there are two major ureAB transcripts: a 2.7-kb full-length ureAB transcript and a 1.4-kb truncated transcript lacking 3' ureB. Acidic pH (pH 4.5) results in a significant increase in transcription of ureAB, while neutral pH (pH 7.4) increases the truncated 1.4-kb transcript. Northern blot analysis with sense RNA and strand-specific oligonucleotide probes followed by 5' rapid amplification of cDNA ends detects an antisense small RNA (sRNA) encoded by the 5' ureB noncoding strand consisting of ∼290 nucleotides (5'ureB-sRNA). Deletion of HP0165 elevates the level of the truncated 1.4-kb transcript along with that of the 5'ureB-sRNA at both pH 7.4 and pH 4.5. Overexpression of 5'ureB-sRNA increases the 1.4-kb transcript, decreases the 2.7-kb transcript, and decreases urease activity. Electrophoretic mobility shift assay shows that unphosphorylated HP0166 binds specifically to the 5'ureB-sRNA promoter. The ability of the HP0165-HP0166 TCS to both increase and decrease ureB expression at low and high pHs, respectively, facilitates gastric habitation and colonization over the wide range of intragastric pHs experienced by the organism.
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172
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Abstract
Bacterial stress responses provide them the opportunity to survive hostile environments, proliferate and potentially cause diseases in humans and animals. The way in which pathogenic bacteria interact with host immune cells triggers a complicated series of events that include rapid genetic re‐programming in response to the various host conditions encountered. Viewed in this light, the bacterial host‐cell induced stress response (HCISR) is similar to any other well‐characterized environmental stress to which bacteria must respond by upregulating a group of specific stress‐responsive genes. Post stress, bacteria must resume their pre‐stress genetic program, and, as a consequence, must degrade unnecessary stress responsive transcripts through RNA decay mechanisms. Further, there is a well‐established role for several ribonucleases in the cold shock response whereby they modulate the changing transcript landscape in response to the stress, and during acclimation and subsequent genetic re‐programming post stress. Recently, ribonucleases have been implicated as virulence‐associated factors in several notable Gram‐negative pathogens including, the yersiniae, the salmonellae, Helicobacter pylori, Shigella flexneri and Aeromonas hydrophila. This review will focus on the roles played by ribonucleases in bacterial virulence, other bacterial stress responses, and on their novel therapeutic applications.
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Affiliation(s)
- Abidat Lawal
- Department of Biology, Center for Bionanotechnology and Environmental Research, Texas Southern University, Houston, TX, USA
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173
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Nathania L, Nicholson AW. Thermotoga maritima ribonuclease III. Characterization of thermostable biochemical behavior and analysis of conserved base pairs that function as reactivity epitopes for the Thermotoga 23S rRNA precursor. Biochemistry 2010; 49:7164-78. [PMID: 20677811 DOI: 10.1021/bi100930u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cleavage of double-stranded (ds) RNA by ribonuclease III is a conserved early step in bacterial rRNA maturation. Studies on the mechanism of dsRNA cleavage by RNase III have focused mainly on the enzymes from mesophiles such as Escherichia coli. In contrast, neither the catalytic properties of extremophile RNases III nor the structures and reactivities of their cognate substrates have been described. The biochemical behavior of RNase III of the hyperthermophilic bacterium Thermotoga maritima was analyzed using purified recombinant enzyme. T. maritima (Tm) RNase III catalytic activity exhibits a broad optimal temperature range of approximately 40-70 degrees C, with significant activity at 95 degrees C. Tm-RNase III cleavage of substrate is optimally supported by Mg(2+) at >or=1 mM concentrations. Mn(2+), Co(2+), and Ni(2+) also support activity but with reduced efficiencies. The enzyme functions optimally at pH 8 and approximately 50-80 mM salt concentrations. Small RNA hairpins that incorporate the 16S and 23S pre-rRNA stem sequences are efficiently cleaved by Tm-RNase III at sites that are consistent with production in vivo of the immediate precursors to the mature rRNAs. Analysis of pre-23S substrate variants reveals a dependence of reactivity on the base-pair (bp) sequence in the proximal box (pb), a site of protein contact that functions as a positive recognition determinant for Escherichia coli (Ec) RNase III substrates. The dependence of reactivity on the pb sequence is similar to that observed with Ec-RNase III substrates. In fact, Tm-RNase III cleaves an Ec-RNase III substrate with identical specificity and is inhibited by antideterminant bp that also inhibit Ec-RNase III. These results indicate the conservation, across a broad phylogenetic distance, of positive and negative determinants of reactivity of bacterial RNase III substrates.
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Affiliation(s)
- Lilian Nathania
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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174
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Hfq is a global regulator that controls the pathogenicity of Staphylococcus aureus. PLoS One 2010; 5. [PMID: 20927372 PMCID: PMC2947504 DOI: 10.1371/journal.pone.0013069] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 08/27/2010] [Indexed: 01/21/2023] Open
Abstract
The Hfq protein is reported to be an RNA chaperone, which is involved in the stress response and the virulence of several pathogens. In E. coli, Hfq can mediate the interaction between some sRNAs and their target mRNAs. But it is controversial whether Hfq plays an important role in S. aureus. In this study, we found that the deletion of hfq gene in S. aureus 8325-4 can increase the surface carotenoid pigments. The hfq mutant was more resistant to oxidative stress but the pathogenicity of the mutant was reduced. We reveal that the Hfq protein can be detected only in some S. aureus strains. Using microarray and qRT-PCR, we identified 116 genes in the hfq mutant which had differential expression from the wild type, most of which are related to the phenotype and virulence of S. aureus. Among the 116 genes, 49 mRNAs can specifically bind Hfq protein, which indicates that Hfq also acts as an RNA binding protein in S. aureus. Our data suggest that Hfq protein of S. aureus is a multifunctional regulator involved in stress and virulence.
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175
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Liu Y, Wu N, Dong J, Gao Y, Zhang X, Shao N, Yang G. SsrA (tmRNA) acts as an antisense RNA to regulate Staphylococcus aureus pigment synthesis by base pairing with crtMN mRNA. FEBS Lett 2010; 584:4325-9. [PMID: 20854817 DOI: 10.1016/j.febslet.2010.09.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/13/2010] [Accepted: 09/13/2010] [Indexed: 12/20/2022]
Abstract
SsrA RNA (small stable RNA A), also known as tmRNA and 10Sa RNA, functions both as tRNA and mRNA through its unique structure. The carotenoid pigment is the eponymous feature of human pathogen Staphylococcus aureus. Here, we found that the pigment of the mutant strain with ssrA deletion was increased. Furthermore, it was demonstrated that ssrA could act as an antisense RNA aside from its well-known biological function, and crtMN, encoding two essential enzymes for the pigment synthesis, was identified as target of ssrA. Further investigation showed ssrA could specifically base pair with the RBS (ribosomal binding site) region of the crtMN mRNA. Our results revealed a new mechanism by which ssrA regulated the biosynthesis of pigment in S. aureus.
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Affiliation(s)
- Yu Liu
- Beijing Institute of Basic Medical Sciences, Beijing, China
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176
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The chaperone ClpX stimulates expression of Staphylococcus aureus protein A by Rot dependent and independent pathways. PLoS One 2010; 5:e12752. [PMID: 20856878 PMCID: PMC2939077 DOI: 10.1371/journal.pone.0012752] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 08/20/2010] [Indexed: 12/26/2022] Open
Abstract
The Clp ATPases (Hsp100) constitute a family of closely related proteins that have protein reactivating and remodelling activities typical of molecular chaperones. In Staphylococcus aureus the ClpX chaperone is essential for virulence and for transcription of spa encoding Protein A. The present study was undertaken to elucidate the mechanism by which ClpX stimulates expression of Protein A. For this purpose, we prepared antibodies directed against Rot, an activator of spa transcription, and demonstrated that cells devoid of ClpX contain three-fold less Rot than wild-type cells. By varying Rot expression from an inducible promoter we showed that expression of Protein A requires a threshold level of Rot. In the absence of ClpX the Rot content is reduced below this threshold level, hence, explaining the substantially reduced Protein A expression in the clpX mutant. Experiments addressed at pinpointing the role of ClpX in Rot synthesis revealed that ClpX is required for translation of Rot. Interestingly, translation of the spa mRNA was, like the rot mRNA, enhanced by ClpX. These data demonstrate that ClpX performs dual roles in regulating Protein A expression, as ClpX stimulates transcription of spa by enhancing translation of Rot, and that ClpX additionally is required for full translation of the spa mRNA. The current findings emphasize that ClpX has a central role in fine-tuning virulence regulation in S. aureus.
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177
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Obana N, Shirahama Y, Abe K, Nakamura K. Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5′ leader sequence. Mol Microbiol 2010; 77:1416-28. [DOI: 10.1111/j.1365-2958.2010.07258.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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178
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Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J Bacteriol 2010; 192:5559-71. [PMID: 20802038 DOI: 10.1128/jb.00464-10] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small noncoding RNAs (sRNAs) regulate gene expression in Escherichia coli by base pairing with mRNAs and modulating translation and mRNA stability. The sRNAs DsrA and RprA stimulate the translation of the stress response transcription factor RpoS by base pairing with the 5' untranslated region of the rpoS mRNA. In the present study, we found that the rpoS mRNA was unstable in the absence of DsrA and RprA and that expression of these sRNAs increased both the accumulation and the half-life of the rpoS mRNA. Mutations in dsrA, rprA, or rpoS that disrupt the predicted pairing sequences and reduce translation of RpoS also destabilize the rpoS mRNA. We found that the rpoS mRNA accumulates in an RNase E mutant strain in the absence of sRNA expression and, therefore, is degraded by an RNase E-mediated mechanism. DsrA expression is required, however, for maximal translation even when rpoS mRNA is abundant. This suggests that DsrA protects rpoS mRNA from degradation by RNase E and that DsrA has a further activity in stimulating RpoS protein synthesis. rpoS mRNA is subject to degradation by an additional pathway, mediated by RNase III, which, in contrast to the RNase E-mediated pathway, occurs in the presence and absence of DsrA or RprA. rpoS mRNA and RpoS protein levels are increased in an RNase III mutant strain with or without the sRNAs, suggesting that the role of RNase III in this context is to reduce the translation of RpoS even when the sRNAs are acting to stimulate translation.
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179
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Transcriptional profiling of XdrA, a new regulator of spa transcription in Staphylococcus aureus. J Bacteriol 2010; 192:5151-64. [PMID: 20675497 DOI: 10.1128/jb.00491-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of spa, encoding the virulence factor protein A in Staphylococcus aureus, is tightly controlled by a complex regulatory network, ensuring its temporal expression over growth and at appropriate stages of the infection process. Transcriptomic profiling of XdrA, a DNA-binding protein that is conserved in all S. aureus genomes and shares similarity with the XRE family of helix-turn-helix, antitoxin-like proteins, revealed it to be a previously unidentified activator of spa transcription. To assess how XdrA fits into the complex web of spa regulation, a series of regulatory mutants were constructed; consisting of single, double, triple, and quadruple mutants lacking XdrA and/or the three key regulators previously shown to influence spa transcription directly (SarS, SarA, and RNAIII). A series of lacZ reporter gene fusions containing nested deletions of the spa promoter identified regions influenced by XdrA and the other three regulators. XdrA had almost as strong an activating effect on spa as SarS and acted on the same spa operator regions as SarS, or closely overlapping regions. All data from microarrays, Northern and Western blot analyses, and reporter gene fusion experiments indicated that XdrA is a major activator of spa expression that appears to act directly on the spa promoter and not through previously characterized regulators.
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180
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Belasco JG. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 2010; 11:467-78. [PMID: 20520623 PMCID: PMC3145457 DOI: 10.1038/nrm2917] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite its universal importance for controlling gene expression, mRNA degradation was initially thought to occur by disparate mechanisms in eukaryotes and bacteria. This conclusion was based on differences in the structures used by these organisms to protect mRNA termini and in the RNases and modifying enzymes originally implicated in mRNA decay. Subsequent discoveries have identified several striking parallels between the cellular factors and molecular events that govern mRNA degradation in these two kingdoms of life. Nevertheless, some key distinctions remain, the most fundamental of which may be related to the different mechanisms by which eukaryotes and bacteria control translation initiation.
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Affiliation(s)
- Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, 10016, USA.
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181
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Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883-923. [PMID: 20659169 DOI: 10.1111/j.1574-6976.2010.00242.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.
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Affiliation(s)
- Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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182
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Chabelskaya S, Gaillot O, Felden B. A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PLoS Pathog 2010; 6:e1000927. [PMID: 20532214 PMCID: PMC2880579 DOI: 10.1371/journal.ppat.1000927] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 04/26/2010] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus, a pathogen responsible for hospital and community-acquired infections, expresses many virulence factors under the control of numerous regulatory systems. Here we show that one of the small pathogenicity island RNAs, named SprD, contributes significantly to causing disease in an animal model of infection. We have identified one of the targets of SprD and our in vivo data demonstrate that SprD negatively regulates the expression of the Sbi immune-evasion molecule, impairing both the adaptive and innate host immune responses. SprD interacts with the 5′ part of the sbi mRNA and structural mapping of SprD, its mRNA target, and the ‘SprD-mRNA’ duplex, in combination with mutational analysis, reveals the molecular details of the regulation. It demonstrates that the accessible SprD central region interacts with the sbi mRNA translational start site. We show by toeprint experiments that SprD prevents translation initiation of sbi mRNA by an antisense mechanism. SprD is a small regulatory RNA required for S. aureus pathogenicity with an identified function, although the mechanism of virulence control by the RNA is yet to be elucidated. Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including small RNAs (sRNAs). Here we show that one sRNA is essential for a major human bacterial pathogen, Staphylococcus aureus, to cause a disease in an animal model of infection. Our study provides evidence that this RNA regulates the expression of an immune evasion molecule secreted by the bacterium to impair the host immune responses, and we have solved the mechanism of the RNA-based regulation at molecular level. So far, the mechanism of bacterial virulence controlled by SprD is unrevealed, but that small RNA has a huge impact in the course of a bacterial infection. It implies possible new strategies in fighting against that major human and animal bacterial pathogen in preventing the expression of this regulatory RNA.
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MESH Headings
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Blotting, Northern
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Electrophoretic Mobility Shift Assay
- Female
- Gene Expression Regulation, Bacterial/genetics
- Genomic Islands/genetics
- Humans
- Immune Evasion
- Immunoblotting
- Mice
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Antisense/genetics
- RNA, Bacterial/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sequence Homology, Nucleic Acid
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Staphylococcal Infections/genetics
- Staphylococcal Infections/metabolism
- Staphylococcal Infections/microbiology
- Staphylococcus aureus/genetics
- Staphylococcus aureus/pathogenicity
- Virulence
- Virulence Factors/genetics
- Virulence Factors/metabolism
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Affiliation(s)
- Svetlana Chabelskaya
- Université de Rennes I, Inserm U835, Upres EA2311, Biochimie Pharmaceutique, Rennes, France
| | - Olivier Gaillot
- Université de Rennes I, Inserm U835, Upres EA2311, Biochimie Pharmaceutique, Rennes, France
| | - Brice Felden
- Université de Rennes I, Inserm U835, Upres EA2311, Biochimie Pharmaceutique, Rennes, France
- * E-mail:
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183
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Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 2010; 38:6620-36. [PMID: 20511587 PMCID: PMC2965222 DOI: 10.1093/nar/gkq462] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Using an experimental approach, we investigated the RNome of the pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among the latter, 10 are encoded in intergenic regions, three are generated by premature transcription termination associated with riboswitch activities, and one is expressed from the complementary strand of a transposase gene. The expression of four sRNAs increases during the transition from exponential to stationary phase. We focused our study on RsaE, an sRNA that is highly conserved in the bacillales order and is deleterious when over-expressed. We show that RsaE interacts in vitro with the 5' region of opp3A mRNA, encoding an ABC transporter component, to prevent formation of the ribosomal initiation complex. A previous report showed that RsaE targets opp3B which is co-transcribed with opp3A. Thus, our results identify an unusual case of riboregulation where the same sRNA controls an operon mRNA by targeting two of its cistrons. A combination of biocomputational and transcriptional analyses revealed a remarkably coordinated RsaE-dependent downregulation of numerous metabolic enzymes involved in the citrate cycle and the folate-dependent one-carbon metabolism. As we observed that RsaE accumulates transiently in late exponential growth, we propose that RsaE functions to ensure a coordinate downregulation of the central metabolism when carbon sources become scarce.
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Affiliation(s)
- Chantal Bohn
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Centre scientifique d'Orsay, Université Paris-Sud, bâtiment 400, 91405 Orsay Cedex, France
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184
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Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol 2010; 76:990-1009. [PMID: 20444087 DOI: 10.1111/j.1365-2958.2010.07158.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Small non-coding RNAs (sRNAs) have been found to regulate gene expression in all three kingdoms of life. So far, relatively little is known about sRNAs from Gram-positive bacteria. SR1 is a regulatory sRNA from the Bacillus subtilis chromosome that inhibits by base-pairing translation initiation of ahrC mRNA encoding a transcriptional activator of the arginine catabolic operons. Here we present a novel target of SR1, the glycolytic gapA operon. Both microarray and Northern blot analyses show that the amount of gapA operon mRNA is significantly higher in the presence of SR1 when cells were grown in complex medium until stationary phase. Translational lacZ fusions and toeprinting analyses demonstrate that SR1 does not promote translation of gapA mRNA. By contrast, the half-life of gapA operon mRNA is strongly reduced in the sr1 knockout strain. SR1 does not act as a base-pairing sRNA on gapA operon mRNA. Instead, we demonstrate that the 39 aa peptide encoded by SR1, SR1P, is responsible for the effect of SR1 on the gapA operon. We show that SR1P binds GapA, thereby stabilizing the gapA operon mRNA by a hitherto unknown mechanism. SR1 is the first dual-function sRNA found in B. subtilis.
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Affiliation(s)
- Matthias Gimpel
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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185
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Chevalier C, Boisset S, Romilly C, Masquida B, Fechter P, Geissmann T, Vandenesch F, Romby P. Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog 2010; 6:e1000809. [PMID: 20300607 PMCID: PMC2837412 DOI: 10.1371/journal.ppat.1000809] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 02/05/2010] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus RNAIII is the intracellular effector of the quorum sensing system that temporally controls a large number of virulence factors including exoproteins and cell-wall-associated proteins. Staphylocoagulase is one major virulence factor, which promotes clotting of human plasma. Like the major cell surface protein A, the expression of staphylocoagulase is strongly repressed by the quorum sensing system at the post-exponential growth phase. Here we used a combination of approaches in vivo and in vitro to analyze the mechanism used by RNAIII to regulate the expression of staphylocoagulase. Our data show that RNAIII represses the synthesis of the protein through a direct binding with the mRNA. Structure mapping shows that two distant regions of RNAIII interact with coa mRNA and that the mRNA harbors a conserved signature as found in other RNAIII-target mRNAs. The resulting complex is composed of an imperfect duplex masking the Shine-Dalgarno sequence of coa mRNA and of a loop-loop interaction occurring downstream in the coding region. The imperfect duplex is sufficient to prevent the formation of the ribosomal initiation complex and to repress the expression of a reporter gene in vivo. In addition, the double-strand-specific endoribonuclease III cleaves the two regions of the mRNA bound to RNAIII that may contribute to the degradation of the repressed mRNA. This study validates another direct target of RNAIII that plays a role in virulence. It also illustrates the diversity of RNAIII-mRNA topologies and how these multiple RNAIII-mRNA interactions would mediate virulence regulation.
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Affiliation(s)
- Clément Chevalier
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Sandrine Boisset
- INSERM U851, Centre National de Référence des Staphylocoques, Lyon, France; Université de Lyon, Lyon, France
| | - Cédric Romilly
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Benoit Masquida
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Pierre Fechter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Thomas Geissmann
- INSERM U851, Centre National de Référence des Staphylocoques, Lyon, France; Université de Lyon, Lyon, France
| | - François Vandenesch
- INSERM U851, Centre National de Référence des Staphylocoques, Lyon, France; Université de Lyon, Lyon, France
- * E-mail: (FV); (PR)
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (FV); (PR)
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186
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Lioliou E, Romilly C, Romby P, Fechter P. RNA-mediated regulation in bacteria: from natural to artificial systems. N Biotechnol 2010; 27:222-35. [PMID: 20211281 DOI: 10.1016/j.nbt.2010.03.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bacteria use various means of RNA-mediated gene regulation. Regulatory RNAs include mRNA leaders that affect expression in cis or in trans, non-coding RNAs that trap regulatory proteins or interact with one or multiple target mRNAs, and RNAs that protect the bacteria against foreign and invasive DNA. The aim of this review is to outline the basic principles of bacterial RNA-mediated regulation, with a special focus on both cis-acting regulatory regions of mRNAs and antisense RNAs (asRNAs), and to give a brief overview of selected examples of RNA-based technology that have paved the way for biotechnological applications.
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Affiliation(s)
- Efthimia Lioliou
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, Strasbourg cedex, France
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187
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Reduced vancomycin susceptibility in Staphylococcus aureus, including vancomycin-intermediate and heterogeneous vancomycin-intermediate strains: resistance mechanisms, laboratory detection, and clinical implications. Clin Microbiol Rev 2010; 23:99-139. [PMID: 20065327 DOI: 10.1128/cmr.00042-09] [Citation(s) in RCA: 656] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The emergence of vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) over the past decade has provided a challenge to diagnostic microbiologists to detect these strains, clinicians treating patients with infections due to these strains, and researchers attempting to understand the resistance mechanisms. Recent data show that these strains have been detected globally and in many cases are associated with glycopeptide treatment failure; however, more rigorous clinical studies are required to clearly define the contribution of hVISA to glycopeptide treatment outcomes. It is now becoming clear that sequential point mutations in key global regulatory genes contribute to the hVISA and VISA phenotypes, which are associated predominately with cell wall thickening and restricted vancomycin access to its site of activity in the division septum; however, the phenotypic features of these strains can vary because the mutations leading to resistance can vary. Interestingly, changes in the staphylococcal surface and expression of agr are likely to impact host-pathogen interactions in hVISA and VISA infections. Given the subtleties of vancomycin susceptibility testing against S. aureus, it is imperative that diagnostic laboratories use well-standardized methods and have a framework for detecting reduced vancomycin susceptibility in S. aureus.
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188
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ten Broeke-Smits NJP, Pronk TE, Jongerius I, Bruning O, Wittink FR, Breit TM, van Strijp JAG, Fluit AC, Boel CHE. Operon structure of Staphylococcus aureus. Nucleic Acids Res 2010; 38:3263-74. [PMID: 20150412 PMCID: PMC2879529 DOI: 10.1093/nar/gkq058] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In bacteria, gene regulation is one of the fundamental characteristics of survival, colonization and pathogenesis. Operons play a key role in regulating expression of diverse genes involved in metabolism and virulence. However, operon structures in pathogenic bacteria have been determined only by in silico approaches that are dependent on factors such as intergenic distances and terminator/promoter sequences. Knowledge of operon structures is crucial to fully understand the pathophysiology of infections. Presently, transcriptome data obtained from growth curves in a defined medium were used to predict operons in Staphylococcus aureus. This unbiased approach and the use of five highly reproducible biological replicates resulted in 93.5% significantly regulated genes. These data, combined with Pearson's correlation coefficients of the transcriptional profiles, enabled us to accurately compile 93% of the genome in operon structures. A total of 1640 genes of different functional classes were identified in operons. Interestingly, we found several operons containing virulence genes and showed synergistic effects for two complement convertase inhibitors transcribed in one operon. This is the first experimental approach to fully identify operon structures in S. aureus. It forms the basis for further in vitro regulation studies that will profoundly advance the understanding of bacterial pathophysiology in vivo.
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189
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Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 2010; 37:7239-57. [PMID: 19786493 PMCID: PMC2790875 DOI: 10.1093/nar/gkp668] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.
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Affiliation(s)
- Thomas Geissmann
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France
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190
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Romby P, Charpentier E. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 2010; 67:217-37. [PMID: 19859665 PMCID: PMC11115938 DOI: 10.1007/s00018-009-0162-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/07/2009] [Accepted: 09/23/2009] [Indexed: 11/26/2022]
Abstract
During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest. In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10-20% of all genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria.
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Affiliation(s)
- Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| | - Emmanuelle Charpentier
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
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191
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Activation of gene expression by small RNA. Curr Opin Microbiol 2009; 12:674-82. [DOI: 10.1016/j.mib.2009.09.009] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 09/20/2009] [Indexed: 11/22/2022]
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192
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Nielsen JS, Lei LK, Ebersbach T, Olsen AS, Klitgaard JK, Valentin-Hansen P, Kallipolitis BH. Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes. Nucleic Acids Res 2009; 38:907-19. [PMID: 19942685 PMCID: PMC2817478 DOI: 10.1093/nar/gkp1081] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Small trans-encoded RNAs (sRNAs) modulate the translation and decay of mRNAs in bacteria. In Gram-negative species, antisense regulation by trans-encoded sRNAs relies on the Sm-like protein Hfq. In contrast to this, Hfq is dispensable for sRNA-mediated riboregulation in the Gram-positive species studied thus far. Here, we provide evidence for Hfq-dependent translational repression in the Gram-positive human pathogen Listeria monocytogenes, which is known to encode at least 50 sRNAs. We show that the Hfq-binding sRNA LhrA controls the translation and degradation of its target mRNA by an antisense mechanism, and that Hfq facilitates the binding of LhrA to its target. The work presented here provides the first experimental evidence for Hfq-dependent riboregulation in a Gram-positive bacterium. Our findings indicate that modulation of translation by trans-encoded sRNAs may occur by both Hfq-dependent and -independent mechanisms, thus adding another layer of complexity to sRNA-mediated riboregulation in Gram-positive species.
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Affiliation(s)
- Jesper Sejrup Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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193
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Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G. Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides. Mol Microbiol 2009; 74:1497-512. [PMID: 19906181 DOI: 10.1111/j.1365-2958.2009.06949.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen ((1)O(2)) in Rhodobacter sphaeroides. Our study reports the genome-wide search for small RNAs (sRNAs) involved in the regulatory response to (1)O(2). By using 454 pyrosequencing and Northern blot analysis, we identified 20 sRNAs from R. sphaeroides aerobic cultures or following treatment with (1)O(2) or superoxide (O(-)(2)). One sRNA was specifically induced by (1)O(2) and its expression depends on the extracytoplasmic function sigma factor RpoE. Two sRNAs induced by (1)O(2) and O(-)(2) were cotranscribed with upstream genes preceded by promoters with target sequences for the alternative sigma factors RpoH(I) and RpoH(II). The most abundant sRNA was processed in the presence of (1)O(2) but not by O(-)(2). From this and a second sRNA a conserved 3'-segment accumulated from a larger precursor. Absence of the RNA chaperone Hfq changed the half-lives, abundance and processing of (1)O(2)-affected sRNAs. Orthologues of three sRNA genes are present in different alpha-proteobacteria, but the majority was unique to R. sphaeroides or Rhodobacterales species. Our discovery that abundant sRNAs are affected by (1)O(2) exposure extends the knowledge on the role of sRNAs and Hfq in the regulatory response to oxidative stress.
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Affiliation(s)
- Bork A Berghoff
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
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194
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Perez N, Treviño J, Liu Z, Ho SCM, Babitzke P, Sumby P. A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PLoS One 2009; 4:e7668. [PMID: 19888332 PMCID: PMC2765633 DOI: 10.1371/journal.pone.0007668] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 10/12/2009] [Indexed: 12/25/2022] Open
Abstract
The coordinated regulation of gene expression is essential for pathogens to infect and cause disease. A recently appreciated mechanism of regulation is that afforded by small regulatory RNA (sRNA) molecules. Here, we set out to assess the prevalence of sRNAs in the human bacterial pathogen group A Streptococcus (GAS). Genome-wide identification of candidate GAS sRNAs was performed through a tiling Affymetrix microarray approach and identified 40 candidate sRNAs within the M1T1 GAS strain MGAS2221. Together with a previous bioinformatic approach this brings the number of novel candidate sRNAs in GAS to 75, a number that approximates the number of GAS transcription factors. Transcripts were confirmed by Northern blot analysis for 16 of 32 candidate sRNAs tested, and the abundance of several of these sRNAs were shown to be temporally regulated. Six sRNAs were selected for further study and the promoter, transcriptional start site, and Rho-independent terminator identified for each. Significant variation was observed between the six sRNAs with respect to their stability during growth, and with respect to their inter- and/or intra-serotype-specific levels of abundance. To start to assess the contribution of sRNAs to gene regulation in M1T1 GAS we deleted the previously described sRNA PEL from four clinical isolates. Data from genome-wide expression microarray, quantitative RT-PCR, and Western blot analyses are consistent with PEL having no regulatory function in M1T1 GAS. The finding that candidate sRNA molecules are prevalent throughout the GAS genome provides significant impetus to the study of this fundamental gene-regulatory mechanism in an important human pathogen.
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Affiliation(s)
- Nataly Perez
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Jeanette Treviño
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Zhuyun Liu
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Siu Chun Michael Ho
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Paul Sumby
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- * E-mail:
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195
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Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD, Vogel J. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74:139-158. [PMID: 19732340 DOI: 10.1111/j.1365-2958.2009.06857.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome-wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial 'core' small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post-transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl-accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady-state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non-motile. Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post-transcriptional regulation.
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Affiliation(s)
- Kai Papenfort
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Nelly Said
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Tim Welsink
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Sacha Lucchini
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Jay C D Hinton
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
| | - Jörg Vogel
- Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
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196
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On the facultative requirement of the bacterial RNA chaperone, Hfq. Trends Microbiol 2009; 17:399-405. [PMID: 19733080 DOI: 10.1016/j.tim.2009.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 06/04/2009] [Accepted: 06/12/2009] [Indexed: 12/29/2022]
Abstract
The pleiotropic post-transcriptional regulator Hfq is an RNA chaperone that facilitates pairing interactions between small regulatory RNAs (sRNAs) and their mRNA targets in several bacteria. However, this classical pattern, derived from the Escherichia coli model, is not applicable to the whole bacterial kingdom. In this article we discuss the facultative requirement for Hfq for sRNA-mRNA duplex formation among bacteria and the specific features of the Hfq protein and RNA duplexes that might account for the dispensability or requirement of the chaperone. Apparent links between the need for Hfq, the GC content of bacterial genomes and the free energy of experimentally validated sRNA-mRNA pairing interactions are presented.
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197
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Pfeiffer V, Papenfort K, Lucchini S, Hinton JCD, Vogel J. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 2009; 16:840-6. [PMID: 19620966 DOI: 10.1038/nsmb.1631] [Citation(s) in RCA: 223] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 06/04/2009] [Indexed: 02/03/2023]
Abstract
Bacterial small noncoding RNAs (sRNAs) generally recognize target mRNAs in the 5' region to prevent 30S ribosomes from initiating translation. It was thought that the mRNA coding sequence (CDS) was refractory to sRNA-mediated repression, because elongating 70S ribosomes have an efficient RNA helicase activity that prevents stable target pairing. We report that the Hfq-associated MicC sRNA silences Salmonella typhimurium ompD mRNA via a <or=12-bp RNA duplex within the CDS (codons 23-26) that is essential and sufficient for repression. MicC does not inhibit translational initiation at this downstream position but instead acts by accelerating RNase E-dependent ompD mRNA decay. We propose an alternative gene-silencing pathway within bacterial CDS wherein sRNAs repress targets by endonucleolytic mRNA destabilization rather than by the prototypical inhibition of translational initiation. The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria.
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Affiliation(s)
- Verena Pfeiffer
- Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
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198
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Microbial quorum sensing: a tool or a target for antimicrobial therapy? Biotechnol Appl Biochem 2009; 54:65-84. [PMID: 19594442 DOI: 10.1042/ba20090072] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inter-cell communication aided by released chemical signals when cell density reaches a critical concentration has been investigated for over 30 years as quorum sensing. Originally discovered in Gram-negative bacteria, quorum-sensing systems have also been studied extensively in Gram-positive bacteria and dimorphic fungi. Microbial communities communicating via quorum sensing employ various chemical signals to supervise their surrounding environment, alter genetic expression and gain advantage over their competitors. These signals vary from acylhomoserine lactones to small modified or unmodified peptides to complex gamma-butyrolactone molecules. The scope of this review is to give an insight into some of the quorum-sensing systems now known and to explore their role in microbial physiology and development of pathogenesis. Particular attention will be dedicated to the signalling molecules involved in quorum-sensing-mediated processes and the potential shown by some of their natural and synthetic analogues in the treatment of infections triggered by quorum sensing.
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At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci. Microbiol Mol Biol Rev 2009; 73:233-48. [PMID: 19487727 DOI: 10.1128/mmbr.00005-09] [Citation(s) in RCA: 281] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacteria live in environments that are subject to rapid changes in the availability of the nutrients that are necessary to provide energy and biosynthetic intermediates for the synthesis of macromolecules. Consequently, bacterial survival depends on the ability of bacteria to regulate the expression of genes coding for enzymes required for growth in the altered environment. In pathogenic bacteria, adaptation to an altered environment often includes activating the transcription of virulence genes; hence, many virulence genes are regulated by environmental and nutritional signals. Consistent with this observation, the regulation of most, if not all, virulence determinants in staphylococci is mediated by environmental and nutritional signals. Some of these external signals can be directly transduced into a regulatory response by two-component regulators such as SrrAB; however, other external signals require transduction into intracellular signals. Many of the external environmental and nutritional signals that regulate virulence determinant expression can also alter bacterial metabolic status (e.g., iron limitation). Altering the metabolic status results in the transduction of external signals into intracellular metabolic signals that can be "sensed" by regulatory proteins (e.g., CodY, Rex, and GlnR). This review uses information derived primarily using Bacillus subtilis and Escherichia coli to articulate how gram-positive pathogens, with emphasis on Staphylococcus aureus and Staphylococcus epidermidis, regulate virulence determinant expression in response to a changing environment.
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Identification and gene disruption of small noncoding RNAs in Streptomyces griseus. J Bacteriol 2009; 191:4896-904. [PMID: 19465662 DOI: 10.1128/jb.00087-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small noncoding RNAs (sRNAs) have been shown to control diverse cellular processes in prokaryotes. To identify and characterize novel bacterial sRNAs, a gram-positive, soil-inhabiting, filamentous bacterium, Streptomyces griseus, was examined, on the assumption that Streptomyces should express sRNAs as important regulators of morphological and physiological differentiation. By bioinformatics investigation, 54 sRNA candidates, which were encoded on intergenic regions of the S. griseus chromosome and were highly conserved in those of both Streptomyces coelicolor A3(2) and Streptomyces avermitilis, were selected. Of these 54 sRNA candidates, 17 transcripts were detected by Northern blot analysis of the total RNAs isolated from cells grown on solid medium. Then, the direction of transcription of each sRNA candidate gene was determined by S1 nuclease mapping, followed by exclusion of four sRNA candidates that were considered riboswitches of their downstream open reading frames (ORFs). Finally, a further sRNA candidate was excluded because it was cotranscribed with the upstream ORF determined by reverse transcription-PCR. Thus, 12 sRNAs ranging in size from 40 to 300 nucleotides were identified in S. griseus. Seven of them were apparently transcribed in a growth phase-dependent manner. Furthermore, of the 12 sRNAs, the expression profiles of 7 were significantly influenced by a mutation of adpA, which encodes the central transcriptional regulator of the A-factor regulatory cascade involved in both morphological differentiation and secondary metabolism in S. griseus. However, disruption of all 12 sRNA genes showed no detectable phenotypic changes; all the disruptants grew and formed aerial mycelium and spores with the same time course as the wild-type strain on various media and produced streptomycin similarly to the wild-type strain.
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