The critical role of RNA processing and degradation in the control of gene expression

Abstract

The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.

The double-stranded transcriptome of Escherichia coli

“…RNase III plays a major role in the maturation of ribosomal RNA and regulates the quantity of mRNAs and ncRNAs (10,23,24). Our data suggest that asRNAs transcribed opposite to gene junctions form dsRNA complexes with the mRNA and guide processing and/or degradation of the operon.…”

“…Ribonuclease III (RNase III) is a highly conserved endoribonuclease that specifically cleaves dsRNAs and regulates gene expression in E. coli and other bacteria (7)(8)(9)(10). Lasa et al (9) recently demonstrated that RNase III plays a central role in a type of antisense regulation specific for Gram-positive bacteria.…”

One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic–anoxic interface in a flooded paddy soil

“…The half-life of pmoA mRNA is unknown. The half-life of other mRNAs may be as short as 30 s, but could also be much longer depending on the environment and the growth state (Arraiano et al, 2010;Steglich et al, 2010). However, we are confident that we preserved the in situ mRNA content by shock freezing the soil with liquid nitrogen when still in the microcosm.…”

Pervasive transcription: detecting functional RNAs in bacteria

“…13 Because uncontrolled transcription from genome-wide promoter-like sequences are potentially dangerous, bacteria have several systems in place to control the generation of spurious transcripts: (i) The histone-like nucleoid structuring protein (H-NS) suppresses transcription initiation from intragenic promoters, 14 (ii) the termination factor Rho and its cofactor NusG function in the termination of asRNA transcription, 15,16 and (iii) multiple RNases degrade aberrant RNAs. 17 A lack of asRNA conservation among closely related bacteria might not necessarily indicate lack of function because, as shown recently in Drosophila, functional genes can arise rapidly in a lineage-specific manner. 18 Additionally, ncRNAs evolve rapidly in eukaryotes, with the rate of evolutionary turnover similar to other regulatory sequences.…”