mRNA degradation and maturation in prokaryotes: the global players

Laalami, Soumaya; Putzer, Harald

doi:10.1515/bmc.2011.042

Cited by 23 publications

(28 citation statements)

References 111 publications

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“…( C ) Mapping of the 5΄ end of the processed RNA in construct pCG394. The sae sequence is aligned with those of three different clones (1, 2 and 3). The RNA 5΄ adapter is underlined, and the mapped position for alternative cleavage site 2 (aCS2) is shown in bold.…”

Section: Resultsmentioning

confidence: 99%

Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus

Marincola

Wolz

2017

Nucleic Acids Research

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In gram-positive bacteria, RNase J1, RNase J2 and RNase Y are thought to be major contributors to mRNA degradation and maturation. In Staphylococcus aureus, RNase Y activity is restricted to regulating the mRNA decay of only certain transcripts. Here the saePQRS operon was used as a model to analyze RNase Y specificity in living cells. A RNase Y cleavage site is located in an intergenic region between saeP and saeQ. This cleavage resulted in rapid degradation of the upstream fragment and stabilization of the downstream fragment. Thereby, the expression ratio of the different components of the operon was shifted towards saeRS, emphasizing the regulatory role of RNase Y activity. To assess cleavage specificity different regions surrounding the sae CS were cloned upstream of truncated gfp, and processing was analyzed in vivo using probes up- and downstream of CS. RNase Y cleavage was not determined by the cleavage site sequence. Instead a 24-bp double-stranded recognition structure was identified that was required to initiate cleavage 6 nt upstream. The results indicate that RNase Y activity is determined by secondary structure recognition determinants, which guide cleavage from a distance.

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Section: Resultsmentioning

confidence: 99%

Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus

Marincola

Wolz

2017

Nucleic Acids Research

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“…the thrS and thrZ leaders can also be a substrate for the endonucleolytic activity of RNases J1/J2 [5]. Indeed, RNase J and RNase Y and to that matter also E. coli RNase E have very similar endonucleolytic cleavage specificities and the thrS T-box leader can actually be cut in vitro at the same position by all three nucleases [17]. The respective contributions of RNases J and Y to T-box leader cleavage in vivo remains to be analysed but the strong and broad effect of RNase Y observed here suggests that this enzyme plays a major role in the turnover of T-box leader RNAs and riboswitch RNAs in general in B. subtilis.…”

Section: Discussionmentioning

confidence: 99%

“…Initiation of mRNA decay might thus be more similar between E. coli and B. subtilis than previously assumed, with an endonucleolytic cleavage being the crucial step (for a recent review, see [17]). In this model, the 5′ exonucleolytic activity of RNase J would be mainly responsible for degrading cleavage intermediates initially generated by RNase Y and, to a lesser extent, by RNase J or another endoribonuclease.…”

Section: Introductionmentioning

confidence: 97%

Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays

et al. 2013

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RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis. Its characterization provided the first evidence that endonucleolytic cleavage plays a major role in the mRNA metabolism of this organism. RNase Y shares important functional features with the RNA decay initiating RNase E from Escherichia coli, notably a similar cleavage specificity and a preference for 5′ monophosphorylated substrates. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. The downstream cleavage products are likely to be degraded by the 5′ exonucleolytic activity of RNases J1/J2 as we show for a specific case. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% were in common in all three studies. This highlights that experimental conditions and data analysis play an important role in identifying RNase Y substrates by global transcriptional profiling. Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allow an exceptionally detailed view of the turnover of hundreds of new RNA substrates.

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“…The asterisk indicates the only RNase Y cleavage site demonstrated to occur in vivo and in vitro. Two asterisks show that this cleavage site can be cleaved by RNases J, Y, and E [24] Bs Bacillus subtilis , Sa Staphylococcus aureus , C cleavage site, scRNA small cytoplasmic RNA…”

Section: The Direct Entry Pathwaymentioning

confidence: 99%

Initiation of mRNA decay in bacteria

Laalami

Zig

Putzer

2013

Cell. Mol. Life Sci.

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115

109

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The instability of messenger RNA is fundamental to the control of gene expression. In bacteria, mRNA degradation generally follows an “all-or-none” pattern. This implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. Studies of E. coli and B. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. The early view that mRNA decay in these two model organisms is radically different has given way to new models that can be resumed by “different enzymes—similar strategies”. The recent characterization of key ribonucleases sheds light on an impressive case of convergent evolution that illustrates that the surprisingly similar functions of these totally unrelated enzymes are of general importance to RNA metabolism in bacteria. We now know that the major mRNA decay pathways initiate with an endonucleolytic cleavage in E. coli and B. subtilis and probably in many of the currently known bacteria for which these organisms are considered representative. We will discuss here the different pathways of eubacterial mRNA decay, describe the major players and summarize the events that can precede and/or favor nucleolytic inactivation of a mRNA, notably the role of the 5′ end and translation initiation. Finally, we will discuss the role of subcellular compartmentalization of transcription, translation, and the RNA degradation machinery.

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mRNA degradation and maturation in prokaryotes: the global players

Cited by 23 publications

References 111 publications

Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus

Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus

Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays

Initiation of mRNA decay in bacteria

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