All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay

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Abstract
Bacterial and eukaryotic mRNAs differ markedly in their structure and organization and in the means by which they recruit ribosomes for translation. Early evidence led to the conclusion that the principal mechanisms of mRNA degradation in these organisms are also different, as mRNA lifetimes seemed to be controlled primarily by internal events (endonucleolytic cleavage) in bacteria and by 3′- and 5′-terminal events (deadenylation, decapping and exonucleolytic digestion) in eukaryotic cells. Subsequent discoveries have identified several striking parallels between the mechanisms by which mRNA is degraded in bacteria and eukaryotes. These include the triggering of bacterial mRNA degradation by a 5′-terminal event (pyrophosphate removal) that resembles eukaryotic decapping, roles for 3′ polyadenylation and 5′ exonucleolytic digestion in both bacterial and eukaryotic RNA turnover, and the importance of internal cleavage for the decay of certain eukaryotic mRNAs. Furthermore, some key degradative enzymes in these two kingdoms seem to have evolved from a common ancestor, suggesting that they have an ancient role in RNA degradation. All organisms seem to have quality control pathways for rapidly destroying defective mRNAs that cannot be translated properly. Despite similar outcomes, the mechanisms of mRNA degradation through these pathways differ substantially between bacteria and eukaryotes. Both bacteria and eukaryotes use short non-coding RNAs (sRNAs in bacteria and microRNAs or small interfering RNAs in eukaryotes) to regulate gene expression. In each cell type, base pairing of the non-coding RNA to a partially or fully complementary mRNA generally leads to translational repression and accelerated mRNA decay. The principal mechanisms by which non-coding RNAs cause these effects in bacteria and eukaryotes seem to differ in several ways. Nevertheless, recent evidence suggests that a distinct class of non-coding RNAs (CRISPR RNAs) may trigger mRNA degradation in some bacterial species by a mechanism reminiscent of RNA interference in eukaryotes. Despite growing recognition of the similarities between mRNA degradation in bacteria and eukaryotic cells, some fundamental differences remain. Foremost among these is the widespread importance of low-specificity endonucleases in bacterial mRNA decay and their much more limited role in eukaryotes, where mRNA degradation is dominated by events at the 3′ and 5′ termini. This difference may be an evolutionary consequence of the distinct mechanisms by which bacteria and eukaryotes control translation initiation.

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