Regulation of mRNA Stability During Bacterial Stress Responses

Abstract

Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5 ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.

Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

“…Indeed most of these genes remain expressed at high level ('CAT-3' or 'CAT_4') but below a threshold classically associated with boundaries (a string of genes with above 20 normalized reads per kb, Supplementary Table 5). Moreover, we cannot exclude the possibility that some of these transcripts are stable RNAs produced in exponential rather than stationary phase 43 . This loss of boundaries in the central compartment is reminiscent of the phenomena observed in eukaryotes during G1-to-mitosis transition 44 and could reflect a more general phenomenon of genome compaction during the cell cycle.…”

Dynamics of the compartmentalizedStreptomyceschromosome during metabolic differentiation

“…These are generally located within the terminal arms, Supplementary Table 5). Moreover, we cannot exclude the possibility that some of these transcripts are stable RNAs produced in exponential rather than stationary phase 43 . This loss of boundaries in the central compartment is reminiscent of the phenomena observed in eukaryotes during G1-to-mitosis transition 44 and could reflect a more general phenomenon of genome compaction during the cell cycle.…”

Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo

“…Since the putative regulatory transcriptional sequences of the wild type and mutant genes are the same, this suggests that the increase in wild type transcript was not due to transcriptional up-regulation. It has been proposed that recognition of a nonsense mRNA could depend on translation [ 52 ] and that mRNA depletion is a consequence of the appearance of long tracts of mRNA that are unprotected by scanning ribosomes [ 28 ], which, by binding to the mRNA, have a protective effect on its stability [ 53 ]. Thus, we explain the higher amounts of fucA mRNA with an increment of translating ribosomes, which stabilize fucA mRNA and lead to the increased transcript level revealed by Real-time PCR.…”

“…The increasing demand of α- l -fucosidase in the presence of xyloglucan oligosaccharides was not surprising. Several α- l -fucosidases belonging to glycoside hydrolases family GH29 in the Carbohydrate Active enZYmes database ( (accessed on 4 March 2021)) [ 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ]. In addition, we have previously reported that in S. solfataricus the α-xylosidase XylS and the β-glycosidase Ssβ-gly, hydrolyzed tamarind seed xyloglucan oligosaccharides in vitro [ 48 ].…”