Degradation of RNA in bacteria: comparison of mRNA and stable RNA

Degradation of RNA plays a central role in RNA metabolism. In recent years, our knowledge of the mechanisms of RNA degradation has increased considerably with discovery of the participating RNases and analysis of mutants affected in the various degradative pathways. Among these processes, mRNA decay and stable RNA degradation generally have been considered distinct, and also separate from RNA maturation. In this review, each of these processes is described, as it is currently understood in bacteria. The picture that emerges is that decay of mRNA and degradation of stable RNA share many common features, and that their initial steps also overlap with those of RNA maturation. Thus, bacterial cells do not contain dedicated machinery for degradation of different classes of RNA or for different processes. Rather, only the specificity of the RNase and the accessibility of the substrate determine whether or not a particular RNA will be acted upon

Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-Stranded RNA

3\u27 repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1

The Transcriptome of the Nosocomial Pathogen Enterococcus faecalis V583 Reveals Adaptive Responses to Growth in Blood

gains access to the bloodstream and establishes a persistent infection is not well understood.. infections

Reactions at the 3′ Terminus of Transfer Ribonucleic Acid

Rabbit liver tRNA nucleotidyltransferase was purified 25,000-fold to apparent homogeneity and a specific activity under optimal conditions of 2,000 µmoles of AMP incorporated into tRNA per hour per mg of protein. At the final step of purification the enzyme was fractionated into two species, both of which incorporated AMP, CMP, and UMP into tRNA, although with different relative rates. Both proteins had molecular weights of about 48,000 and s20,w values of about 4. Acrylamide gel electrophoresis in sodium dodecyl sulfate suggested that both proteins were single polypeptide chains. The purified enzymes were found to aggregate at elevated protein levels, but this could be prevented by high concentrations of phosphate. The amino acid compositions of both proteins were similar except for a difference in the half-cystine content. Furthermore, the species with the greater number of half-cystine residues was also more sensitive to a variety of sulfhydryl reagents. Neither protein contained any nucleotide material as determined by the ultraviolet absorption spectrum. Both enzymes were inhibited by dithiothreitol, and the AMP-, CMP-, and UMP-incorporating activities of both proteins were sensitive to incubation at temperatures between 42° and 50°. The molecular weight of tRNA nucleotidyltransferase changed during purification from about 80,000 in cruder fractions to about 48,000 after chromatography on DEAEcellulose. Evidence is presented which suggests that the molecular weight change was due to removal of bound tRNA. The formation of a tight complex between the purified enzyme and tRNA was also demonstrated

How bacterial cells keep ribonucleases under control

Ribonucleases (RNases) play an essential role in essentially every aspect of RNA metabolism, but they also can be destructive enzymes that need to be regulated to avoid unwanted degradation of RNA molecules. As a consequence, cells have evolved multiple strategies to protect RNAs against RNase action. They also utilize a variety of mechanisms to regulate the RNases themselves. These include post-transcriptional regulation, post-translational modification, trans-acting inhibitors, cellular localization, as well as others that are less well studied. In this review, I will briefly discuss how RNA molecules are protected and then examine in detail our current understanding of the mechanisms known to regulate individual RNases

Reactions at the 3′ Terminus of Transfer Ribonucleic Acid

The specificity and properties of anomalous AMP incorporation catalyzed by rabbit liver tRNA nucleotidyltransferase were studied. A single AMP residue could be added to the 3′ terminus of a variety of RNA molecules, including rRNA and 5 S RNA. In addition, tRNA molecules containing 1 or 3 terminal CMP residues, tRNA-C and tRNA-C-C-C, were also active as acceptors. The rate of AMP incorporation into these anomalous substrates was considerably more rapid if the RNA acceptor contained a terminal CMP residue. Thus, the rate of AMP incorporation into tRNA-C-C was about 20-fold more rapid than into tRNA-C-A and tRNA-C-U. Nevertheless, at high levels of enzyme it was possible to convert almost completely the latter molecules to tRNA-C-A-A and tRNA-C-U-A. All the anomalous reactions were stimulated by the presence of Mn2+, as much as 10-fold in the case of 5 S RNA, whereas normal AMP incorporation was inhibited. Under optimal conditions, wheat germ 5 S RNA was as active a substrate as tRNA-C-C. Furthermore, the two RNA acceptors had similar apparent Km values. These results are discussed in terms of the recognition site on the RNA acceptors and the importance of the 3′-terminal residue. Evidence is also presented that the 3′-terminal moiety of wheat germ 5 S RNA is predominantly CMP. In addition, an improved method for determining the location of nucleotide residues incorporated into RNA is described

Regulation of Bacterial Ribonucleases

Ribonucleases (RNases) are essential for almost every aspect of RNA metabolism. However, despite their important metabolic roles, RNases can also be destructive enzymes. As a consequence, cells must carefully regulate the amount, the activity, and the localization of RNases to avoid the inappropriate degradation of essential RNA molecules. In addition, bacterial cells often must adjust RNase levels as environmental situations demand, also requiring careful regulation of these critical enzymes. As the need for strict control of RNases has become more evident, multiple mechanisms for this regulation have been identified and studied, and these are described in this review. The major conclusion that emerges is that no common regulatory mechanism applies to all RNases, or even to a family of RNases; rather, a wide variety of processes have evolved that act on these enzymes, and in some cases, multiple regulatory mechanisms can even act on a single RNase. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates