RNA synthesis and turnover as part of the gene expression network in bacteria. Different types of RNA (mRNAs, ribosomal and transfer RNA pre-cursors and various non-coding RNAs) either can directly be involved in translation (e.g. mRNAs) or undergo further processing (pre-cursors of stable RNA) or degradation (untranslated or poorly translated mRNAs) by the RNA decay machinery. The final products of RNA turnover, mononucleotides, are used for the next cycles of RNA synthesis (recycling).

Bacterial mRNA decay machineries. (A) The RNA degradosome is a multicomponent ribonucleolytic complex that includes an endoribonuclease (RNase E), a 3'→5' exoribonuclease (polynucleotide phosphorylase (PNPase)), a DEAD-box RNA helicase (RhlB helicase), and the glycolytic enzyme enolase [31-33]). (B) In E. coli, PNPase is associated with the RhlB independently of the RNA degradosome to form an evolutionarily conserved RNA-degradation machine termed as the "bacterial exosome" [34,35]. This complex was shown to catalyze the 3'→ 5' exonucleolytic degradation of RNA using RhlB as cofactor to unwind structured RNA in an ATP-dependent manner.

The phylogenetic distribution of main ribonucleases (RNase E/G, RNase III, RNases J1/J2, RNase Y, RNase PH, PNPase, RNase R, RNase II, Oligoribonuclease) and ancillary RNA modifying enzymes (RppH, PAPI, DEAD-box helicases) involved in the disintegration and turnover of bacterial transcripts are indicated by colored filled circles (from 'a' to 'l', respectively). The percentage of organisms in each phylum/class of bacteria for which the presence of each particular enzyme has been predicted by searching the NCBI database is indicated by differentially colored circles. The data are compiled based on analysis of completely sequenced genomes (1217 complete genome sequences available by 4 November 2010). Draft assemblies of genomes and hypothetical proteins were excluded from the analysis.

Current unified model of mRNA decay pathways in Escherichia coli. (A) Schematic representation of major enzymatic steps involved in the disintegration and complete turnover of primary transcripts in E. coli. The decay of a regular transcript is usually initiated by endonucleolytic cleavage to generate primary decay intermediates that are further converted to short oligoribonucleotides by the combined action of exo- and endoribonucleases. The oligoribonucleotides are further degraded into mononucleotides by oligoribonuclease. (B) Ancillary enzymes facilitating mRNA turnover and their modes of action. Degradation of mRNA can be stimulated via pyrophosphate removal by RppH, which converts 5'-triphosporylated primary transcripts into their monophosphorylated variants, thus facilitating their endoribonucleolytic cleavage by RNase E [22,76] or by RNases J1/J2 [12] or by RNase Y [16] in B. subtilis. As the action of exoribonucleases can be inhibited by 3'-terminal stem-loop structures, two groups of ancillary RNA-modifying enzymes, PAPI and RhlB, help exonucleases to overcome this inhibitory effect. PAPI exerts its action by adding short stretches of adenosine residues, thereby facilitating exonuclease binding and subsequent cleavage of structured RNAs [10]. Enzymes of the second group, DEAD-box helicases such as E. coli RhlB, increase the efficiency of the exonuclease-dependent decay by unwinding double-stranded RNA regions in an ATP-dependent fashion.