Composition and conservation of the mRNA-degrading machinery in bacteria

Abstract

RNA synthesis and decay counteract each other and therefore inversely regulate gene expression in pro- and eukaryotic cells by controlling the steady-state level of individual transcripts. Genetic and biochemical data together with recent in depth annotation of bacterial genomes indicate that many components of the bacterial RNA decay machinery are evolutionarily conserved and that their functional analogues exist in organisms belonging to all kingdoms of life. Here we briefly review biological functions of essential enzymes, their evolutionary conservation and multienzyme complexes that are involved in mRNA decay in Escherichia coli and discuss their conservation in evolutionarily distant bacteria.

Figure 1

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).

Figure 2

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.

Figure 3

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.

Figure 4

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.