Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

Abstract

Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this chapter we discuss the various enzymes that control transcription, translation and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5′ and 3′ termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript, are matured to individual 16S, 23S and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and non-translated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase as well as proteins that regulate the catalytic activity of particular ribonucleases. Under certain stress conditions an additional group of specialized endonucleases facilitate the cell’s ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I participate in multiple RNA processing and decay pathways.

Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli

“…RNase E is an essential endoribonuclease with major roles in maturation of stable RNA, degradation of mRNA, and posttranscriptional regulation of gene expression ( 1 – 6 ). Instability of mRNA is important for regulation of gene expression because it permits rapid remodeling of the transcriptome.…”

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“…RNAse III is a Mg +2 dependent phosphodiesterase and cleaves two phosphodiesters bonds of double-stranded RNA and generates two nucleotides, 5' phosphoryl, 3' overhangs and 3' hydroxyl ends in the products (Filippov et al, 2000;Nicholson 1999;Robertson 1982). RNAse III from bacterial cells perform their function in two ways either as double-stranded RNA processing enzymes and cleave dsRNA and RNA hairpins into small duplexes or as double-stranded RNA binding proteins and bind with ds RNA without their cleavage (Mohanty and Kushner 2018;Nicholson 1999;Dasgupta et al, 1998). The bacterial RNAse III proteins are composed of a single endonuclease domain (endoND) followed by a dsRNAbinding domain (Robertson 1982).…”

Transcriptional Organization of the Stability Module of Broad-Host-Range Plasmid RA3, from the IncU Group

“…First, it was assumed that the prokaryotic transcripts are processed only by 3=-to-5= exonucleases, leading to an abundance of transcripts for the 5= part of the multicistronic operons (polarity expression). Discovery of the endoribonucleases and their role in mRNA decay in combination with regulatory functions of RNA binding proteins and noncoding RNAs (ncRNAs) revealed a complex regulatory network responsible for differential transcript abundance even in the operons (72)(73)(74)(75)(76).…”