Function, mechanism and regulation of bacterial ribonucleases

Abstract

The maturation and degradation of RNA molecules are essential features of the mechanism of gene expression, and provide the two main points for post-transcriptional regulation. Cells employ a functionally diverse array of nucleases to carry out RNA maturation and turnover. Viruses also employ cellular ribonucleases, or even use their own in their reproductive cycles. Studies on bacterial ribonucleases, and in particular those from Escherichia coli, are providing insight into ribonuclease structure, mechanism, and regulation. Ongoing biochemical and genetic analyses are revealing that many ribonucleases are phylogenetically conserved, and exhibit overlapping functional roles and perhaps common catalytic mechanisms. This article reviews the salient features of bacterial ribonucleases, with a focus on those of E. coli, and in particular, ribonuclease III. RNase III participates in a number of RNA maturation and RNA decay pathways, and is regulated by phosphorylation in the T7 phage-infected cell. Plasmid and phage RNAs, in addition to cellular transcripts, are RNase III targets. RNase III orthologues occur in eukaryotic cells, and play key functional roles. As such, RNase III provides an important model with which to understand mechanisms of RNA maturation, RNA decay, and gene regulation.

Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively.

“…Although we identified putative RNase III cleavage sites in the 16S rRNA processing stem of Synechococcus PCC 6301 and in region D5 of the latter and of the cyanelle of C. paradoxa, we were unable to locate such sites in the sequences of Nostoc PCC 7120 and Synechocystis PCC 6803. Since a gene encoding RNase III exists in the latter organism (Kaneko et al, 1996), our sequence data indicate that, as in other bacteria (see Nicholson, 1999), this enzyme is most probably a sequence-nonspecific nuclease. In other bacteria, the antiterminator box B-box A regions are involved in maintaining the correct stoichiometry of transcription of the rRNA genes (Berg et al, 1989 ;Condon et al, 1995).…”

Two Exoribonucleases Act Sequentially to Process Mature 3′-Ends of atp9 mRNAs in Arabidopsis Mitochondria

“…30 -32). These data plus additional experiments with other RNA substrates including polyadenylated ones (data not shown) indicate that AtmtRNaseII is able to digest any unstructured regions of a RNA substrate but is stopped by a secondary structure, similarly to its bacterial counterpart (1).…”

“…The nature of these processes can vary depending on the organism or cellular compartment considered and may include maturation of 5Ј and 3Ј termini, splicing of introns, capping, editing, base modifications, or addition of nongenomically-encoded nucleotides such as polyadenylation. Processing of mRNAs is well documented for bacterial and eukaryotic nuclear mRNAs (1,2). Our knowledge of maturation of plastid transcripts is also extensive for both Chlamydomonas and higher plants (3).…”

“…1, 8, and 9). Among the eight characterized exoribonucleases in E. coli, polynucleotide phosphorylase (PNPase) 1 and RNaseII are the main exoribonucleases involved in degrading mRNAs in a 3Ј to 5Ј direction but participate also in processing events. PNPase-like proteins are also present in human mitochondria (10) and in chloroplasts.…”

T7 phage display: A novel genetic selection system for cloning RNA-binding proteins from cDNA libraries

“…We therefore investigated whether RNA degradation in T7 phage lysates could be prevented by genetically inactivating one or more ribonucleases of the host strain. RNase I was chosen as an initial target because it is a major, yet nonessential, ribonuclease activity in E. coli (30). The RNase I gene (rna) of strain BLT5615 was disrupted by P1 transduction to generate a new E. coli host strain (RNA5615) lacking this ribonuclease.…”