Initiation of decay of Bacillus subtilis trp leader RNA
Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA.Journal of Biological Chemistry (Impact Factor: 4.57). 08/2007; 282(28):20238-44. DOI: 10.1074/jbc.M702747200
Transcription termination in the leader region of the Bacillus subtilis trp operon is regulated by binding of the 11-mer TRAP complex to nascent trp RNA, which results in formation of a terminator structure. Rapid decay of trp leader RNA, which is required to release the TRAP complex and maintain a sufficient supply of free TRAP, is mediated by polynucleotide phosphorylase (PNPase). Using purified B. subtilis PNPase, we showed that, when TRAP was present, PNPase binding to the 3' end of trp leader RNA and PNPase digestion of trp leader RNA from the 3' end were inefficient. These results suggested that initiation of trp leader RNA may begin with an endonuclease cleavage upstream of the transcription terminator structure. Such cleavage was observed in vivo. Mutagenesis of nucleotides at the cleavage site abolished processing and resulted in a 4-fold increase in trp leader RNA half-life. This is the first mapping of a decay-initiating endonuclease cleavage site on a native B. subtilis RNA.
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- "If the initial destabilizing cleavage by RNase Y occurred in the 3 -UTR, the lack of degradation by PNPase might stabilize the cleaved RNA sufficiently to yield a protein product. As in E. coli, PNPase from B. subtilis is sensitive to RNA secondary structure (Deikus and Bechhofer 2007). Bacillus subtilis has at least three more 3 -5 exoribonucleases that help to degrade mRNAs: RNase PH acts by phosphorolysis like PNPase, while RNase R and YhaM are hydrolytic enzymes. "
ABSTRACT: It is widely recognized that RNA degradation plays a critical role in gene regulation when fast adaptation of cell growth is required to respond to stress and changing environmental conditions. Bacterial ribonucleases acting alone or in concert with various trans-acting regulatory factors are important mediators of RNA degradation. Here, we will give an overview of what is known about ribonucleases in several Gram-positive bacteria, their specificities and mechanisms of action. In addition, we will illustrate how sRNAs act in a coordinated manner with ribonucleases to regulate the turnover of particular mRNA targets, and the complex interplay existing between the ribosome, the ribonucleases and RNAs. © FEMS 2015. All rights reserved. For permissions, please e-mail: firstname.lastname@example.org.
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- "We reasoned that, if RNase J1 cleavage at this site was constitutive and was involved in initiating decay, then altering the site such that RNase J1 would no longer recognize it might result in a longer DermC mRNA half-life. A similar sequence change at an RNase J1 target site in trp leader RNA resulted in a fourfold increase in RNA stability (Deikus and Bechhofer 2007). The effect of the GC-rich sequence on RNase J1 recognition was confirmed by in vitro analysis of RNase J1 cleavage of 59-end- labeled DermC mRNA (data not shown). "
ABSTRACT: RNase J1, a ribonuclease with 5' exonuclease and endonuclease activities, is an important factor in Bacillus subtilis mRNA decay. A model for RNase J1 endonuclease activity in mRNA turnover has RNase J1 binding to the 5' end and tracking to a target site downstream, where it makes a decay-initiating cleavage. The upstream fragment from this cleavage is degraded by 3' exonucleases; the downstream fragment is degraded by RNase J1 5' exonuclease activity. Previously, DeltaermC mRNA was used to show 5'-end dependence of mRNA turnover. Here we used DeltaermC mRNA to probe RNase J1-dependent degradation, and the results were consistent with aspects of the model. DeltaermC mRNA showed increased stability in a mutant strain that contained a reduced level of RNase J1. In agreement with the tracking concept, insertion of a strong stem-loop structure at +65 resulted in increased stability. Weakening this stem-loop structure resulted in reversion to wild-type stability. RNA fragments containing the 3' end were detected in a strain with reduced RNase J1 expression, but were undetectable in the wild type. The 5' ends of these fragments mapped to the upstream side of predicted stem-loop structures, consistent with an impediment to RNase J1 5' exonuclease processivity. A DeltaermC mRNA deletion analysis suggested that decay-initiating endonuclease cleavage could occur at several sites near the 3' end. However, even in the absence of these sites, stability was further increased in a strain with reduced RNase J1, suggesting alternate pathways for decay that could include exonucleolytic decay from the 5' end.
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ABSTRACT: Meroplankton was sampled at 11 stations in the southern Kara Sea and the Yenisei Estuaryin September 2000. Larvae of 29 benthic taxa representing 10 higher groups were identified. Meroplankton was present at almost all stations and most depth levels. The two most abundant groups were Echinodermata (68%) and Polychaeta (26%). Echinoderms dominated total meroplankton locally due to mass occurrences of Ophiopluteus larvae. The relative group composition was highly variable and seemed to depend mainly on the local hydrographic pattern. Comparison of meroplanktonic data with the distribution of the adults revealed for Spionida and Bivalvia a ‘downstream’ transport of the larvae whereas for other polychaete species and Ophiuroida ‘upstream’ transport into the estuary occurred. The distribution and concentration of the larvae within the estuary is explained by physical barriers established by hydrographic gradients, the prevailing mixing processes and the presence of a near-bottom counter current.
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