Emerging features of mRNA decay in bacteria

Abstract

The problem of mRNA decay in E. coli has recently seen exciting progress, with the discoveries that key degradation enzymes are associated together in a high molecular weight degradosome and that polyadenylation promotes decay. Recent advances make it clear that mRNA decay in bacteria is far more interesting enzymatically than might have been predicted. In-depth study of specific mRNAs has revealed multiple pathways for degradation. Which pathway a given mRNA follows appears to depend in large part on the location of the initiating endonucleolytic cleavage within the mRNA. During the steps of mRNA decay, stable RNA structures pose formidable barriers to the 3' --> 5' exonucleases. However, polyadenylation is now emerging as a process that plays an important role in maintaining the momentum of exonucleolytic degradation by adding single-stranded extensions to the 3' ends of mRNAs and their decay intermediates, thereby facilitating further exonuclease digestion.

The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

“…Polyadenylation occurs in all three kingdoms of life, although it only affects a subset of mRNAs in bacteria, and actually stimulates mRNA breakdown in prokaryotes (Steege 2000). Thus, certain components of the polyadenylation machinery predated the evolution of eukaryotes, and it appears that poly(A) simply acquired new functions in eukaryotes.…”

“…Recent work on the degradation of bacterial mRNAs has elucidated the basic molecular mechanisms, which are quite different from the eukaryotic mechanism (Table 1). In summary, eubacteria like E. coli degrade their RNAs through the combined effects of multiple endonucleases and 3Ј exonucleases; many of the relevant activities are organized in degradosomes (Steege 2000). One of the well-studied endonucleases, RNAse E, nicks unstructured RNA regions adjacent to structured regions.…”

cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor

“…Degradation is initiated by endonucleases, primarily RNase E, and to a lesser extent by RNase G and RNase III (reviewed by Steege, 2000). RNase E cleaves at specific AU-rich, singlestranded sites in both mRNA and rRNA (Bessarab et al, 1998).…”

“…RNase E cleaves at specific AU-rich, singlestranded sites in both mRNA and rRNA (Bessarab et al, 1998). Endonucleolytic cleavage is followed by polyadenylation and digestion of poly(A) tails by exonucleases such as RNase II and polynucleotide phosphorylase (PNPase) (Steege, 2000). Poly(A) polymerase I (PAP I) is the enzyme primarily responsible for addition of poly(A) tails (Cao & Sarkar, 1992).…”

Transcripts of the genes sacB, amyE, sacC and csn expressed in Bacillus subtilis under the control of the 5′ untranslated sacR region display different stabilities that can be modulated

“…gnier & Arraiano, 2000 ;Steege, 2000). Three RNases involved in mRNA processing in B. subtilis have been identified : an endonuclease, RNase III (Wang & Bechhofer, 1997), and two 3h-5h exonucleases, polynucleotide phosphorylase and the yvaJ gene product (Wang & Bechhofer, 1996 ;Bechhofer & Wang, 1998 ;Oussenko & Bechhofer, 2000).…”