RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y | Semantic Scholar (2024)

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 and confirm already known RNase Y substrates.

A model, based on recent published data, of RNA degradation in B. subtilis mRNAs is presented, which shows that degradation is initiated by RNase Y‐dependent endonucleolytic cleavage, followed by processive exoribon nucleolysis of the generated fragments both in 3‐to‐5′ and in 5‐to-3′ directions.

It is concluded that RNase Y is a pleiotropic regulator required for mRNA stability, mRNA processing, and removal of read-through transcripts in S. pyogenes.

The role of RNase Y in the Gram-positive anaerobic pathogen Clostridium perfringens, which until now has not been well understood, is studied to imply an important role forRNase Y-mediated RNA degradation and processing in virulence gene expression and the physiological development of the organism.

Novel evidence is provided for the idea that RNase Y is the functional equivalent of RNase E, even though the two enzymes do not share any sequence similarity.

RNase Y in S. aureus influences mRNA expression in a tightly controlled regulatory manner and is essential for coordinated activation of virulence genes.

The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.

RNase Y diffuses rapidly at the membrane in the form of dynamic short-lived foci, and the Y-complex shifts the assembly status of RNase Y toward fewer and smaller complexes, thereby increasing cleavage efficiency of complex substrates like polycistronic mRNAs.

Although the abundance of a large number of transcripts was altered by depletion of RNase III, this appears to result primarily from indirect transcriptional effects, RNase depletion led to the stabilization of many low-abundance potential regulatory RNAs, both in intergenic regions and in the antisense orientation to known transcripts.

...

...

RNase Y might be not only important for riboswitch RNA turnover but also as a key player in the initiation of mRNA decay in B. subtilis.

It is shown that the maturation of Bacillus subtilis 16S rRNA is also a two‐step process and that the enzyme responsible for the generation of the mature 5′ end is the widely distributed essential ribonuclease YkqC/RNase J1.

RNA degradosome-like complexes appear to be conserved throughout the Proteobacteria, but there is a surprising variability in composition that might contribute to the adaptation of these bacteria to the enormously wide variety of niches in which they live.

This is the first report of a specific mRNA whose stability is determined by RNase Y, and provides strong evidence that endonuclease cleavage in the body of the message, rather than degradation from the native 3' end, is the rate-determining step for mRNA decay.

Half‐life measurements of individual mRNAs show that RNases J1/J2 can alter gene expression by modulating transcript stability, suggesting a complex role of these ribonucleases in both degradative and regulatory processing events that have an important impact on gene expression.

Unexpectedly, many coding sequences showed decreased abundance in the RNase E mutant, while more than half of the annotated sRNAs showed changes in abundance, and the steady-state levels of many transcripts showed overlapping effects of both ribonucleases.

The results, which provide evidence that decay of mature rRNAs occurs in growing Escherichia coli cells in the RNA degradosome, implicate RNase E in de gradosome-mediated decay.

The results suggest that CshA is the functional equivalent of the RhlB helicase of the Escherichia coli RNA degradosome.

Transcriptome analysis of a B. subtilis strain lacking polynucleotide phosphorylase (PNPase; a 3'-to-5' exoribonuclease) revealed a striking overexpression of trp operon structural genes when the strain was grown in the presence of abundant tryptophan.

The results demonstrate that the carboxy-terminal half of ribonuclease E (RNase E) contains the binding sites for the three other major degradosomal components, the DEAD-box RNA helicase RhlB, enolase, and polynucleotide phosphorylase (PNPase).

...

...