Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus. Int J Microbiol 2009:525491

Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA.
International Journal of Microbiology 03/2009; 2009:525491. DOI: 10.1155/2009/525491
Source: PubMed


The regulation of mRNA turnover is a recently appreciated phenomenon by which bacteria modulate gene expression. This review outlines the mechanisms by which three major classes of bacterial trans-acting factors, ribonucleases (RNases), RNA binding proteins, and small noncoding RNAs (sRNA), regulate the transcript stability and protein production of target genes. Because the mechanisms of RNA decay and maturation are best characterized in Escherichia coli, the majority of this review will focus on how these factors modulate mRNA stability in this organism. However, we also address the effects of RNases, RNA binding proteins, sRNAs on mRNA turnover, and gene expression in Bacillus subtilis, which has served as a model for studying RNA processing in gram-positive organisms. We conclude by discussing emerging studies on the role modulating mRNA stability has on gene expression in the important human pathogen Staphylococcus aureus.

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    • "The primary regulator of mRNA stability in E. coli in non-stress conditions is the endoribonuclease RNaseE, which sits at the center of a multiprotein mRNA degradasome complex (5). Bacillus subtilis and S. aureus do not have a direct homolog of RNaseE, but they do have RNases with similar function (3). In addition to the degradasome there are at least three other mechanisms by which prokaryotic RNA stability is regulated: accessory endoribonucleases (including toxin-antitoxin modules), exoribonucleases and interactions with RNA structure-modifying molecules (including pyrophosphatase and small non-coding RNAs) (3). "
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    ABSTRACT: Mycobacterium tuberculosis (MTB) is a highly successful pathogen that infects over a billion people. As with most organisms, MTB adapts to stress by modifying its transcriptional profile. Remodeling of the transcriptome requires both altering the transcription rate and clearing away the existing mRNA through degradation, a process that can be directly regulated in response to stress. To understand better how MTB adapts to the harsh environs of the human host, we performed a global survey of the decay rates of MTB mRNA transcripts. Decay rates were measured for 2139 of the ∼4000 MTB genes, which displayed an average half-life of 9.5 min. This is nearly twice the average mRNA half-life of other prokaryotic organisms where these measurements have been made. The transcriptome was further stabilized in response to lowered temperature and hypoxic stress. The generally stable transcriptome described here, and the additional stabilization in response to physiologically relevant stresses, has far-ranging implications for how this pathogen is able to adapt in its human host.
    Nucleic Acids Research 11/2012; 41(1). DOI:10.1093/nar/gks1019 · 9.11 Impact Factor
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    • "Most RNases, including RNase J and RNase Y, which are thought to be the major RNases in B. subtilis, are shared with other Bacilli [15-17]. Indeed, the full complement of key RNases found in B. subtilis (RNase Y, RNase J1, RNase J2, RNase III, PNPase, RNase R, RNase PH, RNAse P, RNase Z, RNase HII, MazF/EndoA, YhaM, KapD, RNase HIII, RNase M5, YhcR) [18,19] are present in Bacillus cereus (GenBank and UniProt databases). RNase Bsn is also present in a range of B. cereus strains, but is, however, absent in the two B. cereus strains subject to study here. "
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    ABSTRACT: Recent years have shown a marked increase in the use of next-generation sequencing technologies for quantification of gene expression (RNA sequencing, RNA-Seq). The expression level of a gene is a function of both its rate of transcription and RNA decay, and the influence of mRNA decay rates on gene expression in genome-wide studies of Gram-positive bacteria is under-investigated. In this work, we employed RNA-Seq in a genome-wide determination of mRNA half-lives in the Gram-positive bacterium Bacillus cereus. By utilizing a newly developed normalization protocol, RNA-Seq was used successfully to determine global mRNA decay rates at the single nucleotide level. The analysis revealed positional degradation patterns, with mRNAs being degraded from both ends of the molecule, indicating that both 5' to 3' and 3' to 5' directions of RNA decay are present in B. cereus. Other operons showed segmental degradation patterns where specific ORFs within polycistrons were degraded at variable rates, underlining the importance of RNA processing in gene regulation. We determined the half-lives for more than 2,700 ORFs in B. cereus ATCC 10987, ranging from less than one minute to more than fifteen minutes, and showed that mRNA decay rate correlates globally with mRNA expression level, GC content, and functional class of the ORF. To our knowledge, this study presents the first global analysis of mRNA decay in a bacterium at single nucleotide resolution. We provide a proof of principle for using RNA-Seq in bacterial mRNA decay analysis, revealing RNA processing patterns at the single nucleotide level.
    Genome biology 04/2012; 13(4):R30. DOI:10.1186/gb-2012-13-4-r30 · 10.81 Impact Factor
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    • "A variety of posttranscriptional regulatory strategies involve RNases. The cell can directly control global RNA decay by adjusting the levels of RNases [4] [5]. "
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    ABSTRACT: It is widely acknowledged that RNA stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. Bacterial ribonucleases acting alone or in concert with regulatory RNAs or RNA binding proteins are the mediators of the regulatory outcome on RNA stability. We will give a current update of what is known about ribonucleases in the model Gram-positive organism Bacillus subtilis and will describe their established roles in virulence in several Gram-positive pathogenic bacteria that are imposing major health concerns worldwide. Implications on bacterial evolution through stabilization/transfer of genetic material (phage or plasmid DNA) as a result of ribonucleases' functions will be covered. The role of ribonucleases in emergence of antibiotic resistance and new concepts in drug design will additionally be discussed.
    International Journal of Microbiology 03/2012; 2012(8):592196. DOI:10.1155/2012/592196
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