Hfq affects mRNA levels independently of degradation

<p>Abstract</p> <p>Background</p> <p>The bacterial Lsm protein, Hfq, is an RNA chaperone involved in many reactions related to RNA metabolism, such as replication and stability, control of small RNA activity and polyadenylation. Despite this wide spectrum of known functions, the global role of Hfq is almost certainly undervalued; its capacity to bind DNA and to interact with many other proteins are only now beginning to be taken into account.</p> <p>Results</p> <p>The role of Hfq in the maturation and degradation of the <it>rpsO </it>mRNA of <it>E. coli </it>was investigated <it>in vivo</it>. The data revealed a decrease in <it>rpsO </it>mRNA abundance concomitant to an increase in its stability when Hfq is absent. This indicates that the change in mRNA levels in <it>hfq </it>mutants does not result from its modification of RNA stability. Moreover, a series of independent experiments have revealed that the decrease in mRNA level is not a consequence of a reduction of translation efficiency and that Hfq is not directly implicated in translational control of <it>rpsO </it>expression. Reduced steady-state mRNA levels in the absence of Hfq were also shown for <it>rpsT, rpsB </it>and <it>rpsB-tsf</it>, but not for <it>lpp, pnp </it>or tRNA transcripts. The abundance of chimeric transcripts <it>rpsO-lacZ </it>and <it>rpsB-lacZ</it>, whose expression was driven by <it>rpsO </it>and <it>rpsB </it>promoters, respectively, was also lower in the <it>hfq </it>null-mutants, while the β-galactosidase yield remained about the same as in the parent wild-type strain.</p> <p>Conclusions</p> <p>The data obtained suggest that alteration of <it>rpsO, rpsT </it>and <it>rpsB-tsf </it>transcript levels observed under conditions of Hfq deficiency is not caused by the post-transcriptional events, such as mRNA destabilization or changes in translation control, and may rather result from changes in transcriptional activity. So far, how Hfq affects transcription remains unclear. We propose that one of the likely mechanisms of Hfq-mediated modulation of transcription might operate early in the elongation step, when interaction of Hfq with a nascent transcript would help to overcome transcription pauses and to prevent preliminary transcript release.</p

Landscape of RNA polyadenylation in E-coli

Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5 '-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A) polymerase deleted Mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A) polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A) polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3 '-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.Peer reviewe

Polyadenylation of a functional mRNA controls gene expression in Escherichia coli

Although usually implicated in the stabilization of mRNAs in eukaryotes, polyadenylation was initially shown to destabilize RNA in bacteria. All the data are consistent with polyadenylation being part of a quality control process targeting folded RNA fragments and non-functional RNA molecules to degradation. We report here an example in Escherichia coli, where polyadenylation directly controls the level of expression of a gene by modulating the stability of a functional transcript. Inactivation of poly(A)polymerase I causes overexpression of glucosamine–6-phosphate synthase (GlmS) and both the accumulation and stabilization of the glmS transcript. Moreover, we show that the glmS mRNA results from the processing of the glmU-glmS cotranscript by RNase E. Interestingly, the glmU-glmS cotranscript and the mRNA fragment encoding GlmU only slightly accumulated in the absence of poly(A)polymerase, suggesting that the endonucleolytically generated glmS mRNA harbouring a 5′ monophosphate and a 3′ stable hairpin is highly susceptible to poly(A)-dependent degradation

Un nouvel agent pontant : le 4-thiouracile, utilisation dans l'etude de la structure tertiaire de la sous-unite 30S du ribosome de E. coli

SIGLECNRS T 59858 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

RNase III Participates in the Adaptation to Temperature Shock and Oxidative Stress in <i>Escherichia coli</i>

Bacteria thrive in ever-changing environments by quickly remodeling their transcriptome and proteome via complex regulatory circuits. Regulation occurs at multiple steps, from the transcription of genes to the post-translational modification of proteins, via both protein and RNA regulators. At the post-transcriptional level, the RNA fate is balanced through the binding of ribosomes, chaperones and ribonucleases. We aim to decipher the role of the double-stranded-RNA-specific endoribonuclease RNase III and to evaluate its biological importance in the adaptation to modifications of the environment. The inactivation of RNase III affects a large number of genes and leads to several phenotypical defects, such as reduced thermotolerance in Escherichia coli. In this study, we reveal that RNase III inactivation leads to an increased sensitivity to temperature shock and oxidative stress. We further show that RNase III is important for the induction of the heat shock sigma factor RpoH and for the expression of the superoxide dismutase SodA

Rôle et mécanismes de la polyadénylation dans l'expression génétique chez Escherichia coli

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

RNA polyadenylation and its consequences in prokaryotes

International audienc

RNase III, Ribosome Biogenesis and Beyond

International audienceThe ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III