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

• Published in: FEMS microbiology reviews 2010-09, Vol.34 (5), p.883-923
• Main Authors: Arraiano, Cecília M, Andrade, José M, Domingues, Susana, Guinote, Inês B, Malecki, Michal, Matos, Rute G, Moreira, Ricardo N, Pobre, Vânia, Reis, Filipa P, Saramago, Margarida, Silva, Inês J, Viegas, Sandra C
• Format: Article
• Language: English
• Subjects: Adaptations; Bacillus subtilis; Bacteria - genetics; Biodegradation; Decay; Degradation; DNA helicase; Double-stranded RNA; E coli; Endonuclease; Endoribonucleases - metabolism; Environmental conditions; Enzymes; Eukaryotes; Exonuclease; Extremities; Gene Expression; Gene Expression Regulation, Bacterial; mRNA turnover; Multienzyme Complexes - metabolism; Phosphopyruvate hydratase; Phosphorylase; Phosphorylases; Polyadenylation; Polynucleotide phosphorylase; Polyribonucleotide Nucleotidyltransferase - metabolism; Post-transcription; post-transcriptional control of gene expression; Quality control; Ribonuclease E; Ribonuclease III; Ribonucleases - metabolism; Ribonucleic acid; Ribosomes; RNA; RNA helicase; RNA Helicases - metabolism; RNA processing; RNA Processing, Post-Transcriptional; RNA Stability; RNA, Bacterial - metabolism; RNA-mediated interference; RNases
• ISSN: 0168-6445; 1574-6976; 1574-6976
• DOI: 10.1111/j.1574-6976.2010.00242.x

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.