Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus

Abstract

The regulation of mRNA turnover is a recently appreciated phenomenon by which bacteria modulate gene expression. This review outlines the mechanisms by which three major classes of bacterial trans-acting factors, ribonucleases (RNases), RNA binding proteins, and small noncoding RNAs (sRNA), regulate the transcript stability and protein production of target genes. Because the mechanisms of RNA decay and maturation are best characterized in Escherichia coli, the majority of this review will focus on how these factors modulate mRNA stability in this organism. However, we also address the effects of RNases, RNA binding proteins, sRNAs on mRNA turnover, and gene expression in Bacillus subtilis, which has served as a model for studying RNA processing in gram-positive organisms. We conclude by discussing emerging studies on the role modulating mRNA stability has on gene expression in the important human pathogen Staphylococcus aureus.

Figure 1

Degradosome-mediated RNA decay. The E. coli degradosome is composed of at least four subunits: RNase E, PNPase, RhlB helicase, and enolase. The initial RNA cleavage event is catalyzed by the 5′ → 3′ endoribonuclease RNase E (large cut-out circle) which loads onto a transcript and scans for downstream cleavage sites: A/U rich regions proceeded by stem-loop structures in 5′ monophosphorylated transcripts. The 3′ → 5′ exoribonuclease PNPase (small cut-out circle) catalyzes cleavage of RNase E-generated decay intermediates. Otherwise inhibitory secondary structures to PNPase-mediated degradation are resolved by RhlB helicase (cross). The role of enolase (hexagon) in mRNA decay is not well characterized.

Figure 2

RNA binding proteins affect mRNA stability. RNA binding proteins affect gene expression by stabilizing or destabilizing mRNA targets by altering their susceptibility to RNases. RNA binding proteins may inhibit protein production by destabilizing mRNA molecules which results in RNase-mediated degradation. Alternatively, RNases may be inhibited by RNA binding proteins which stabilizes the mRNA resulting in increased protein production.

Figure 3

Small RNAs base pair with mRNA targets to affect mRNA stability. Antisense base pairing between sRNAs and their target transcripts mediates mRNA stability by altering the susceptibility of the message to RNases and the translation machinery. Pairing may destabilize mRNA by facilitating RNase-mediated degradation resulting in translation inhibition. In contrast, pairing may stabilize mRNA by inhibiting RNase-mediated degradation resulting in translation of the message and increased protein production.

Figure 4

Degradation profiles of S. aureus wild type and pnpA-mutant cells. RNA signal intensity values for each GeneChip transcript are plotted at 0 minute (T0; X-axis) and 5 minutes (T5; Y-axis) posttranscriptional arrest. Red represents transcripts considered “present” in both T0 and T5 samples (Affymetrix algorithms). Yellow represents transcripts that are “absent” in both samples. Blue represents transcripts that are present in one sample but absent in the second. Grey dashed lines indicate calculated lower limit of sensitivity for each sample. Results show that following 5 minutes of transcriptional arrest, 51.1% (1287 transcripts) of mRNA species are completely degraded within wild type S. aureus cells. Conversely, 17.6% (444 transcripts) of mRNA species were undetectable within isogenic pnpA-mutant cells at 5 minutes posttranscriptional arrest, suggesting that PNPase plays a role in global S. aureus mRNA turnover.