Quality control of bacterial mRNA decoding and decay

Abstract

Studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. Indeed, the expression level of a protein is strongly affected by the steady state level of its mRNA. RNA decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding during translation. Alterations in mRNA stability can in turn have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have evolved unique post transcriptional control mechanisms to enact such adaptive responses through: 1) general mRNA decay, 2) differential mRNA degradation using small non-coding RNAs (sRNAs), and 3) selective mRNA degradation using the tmRNA quality control system. Here, we review our current understanding of these molecular mechanisms, gleaned primarily from studies of the model gram negative organism Escherichia coli, that regulate the stability and degradation of normal and defective transcripts.

Figure 1. Schematic representation of a major pathway for mRNA decay in E. coli

A typical primary transcript possesses a single stranded, triphosphorylated 5’-terminus and a 3’-end with a stem-loop structure. Decay is initiated by the RppH-dependent pyrophosphate removal step at the 5’-terminus. Internal, endonucleolytic cleavages are performed by RNase E, which requires the monophosphorylated 5’-end for catalytic activity. The monophosphorylated 5’-fragment is then subject to further endonucleolytic cleavages or 3’-5’ exonucleolytic decay by exoribonucleases such as RNase II, RNase R, and PNPase. Fragments that contain a 3’ stem-loop structure are polyadenylated by poly (A) polymerase (PAP I), allowing 3’-5’ exonucleolytic decay to be initiated by PNPase or RNase R. The final oligoribonucleotide product of this process is degraded to individual nucleotides by oligoribonuclease.

Figure 2. sRNA-mediated translation repression and mRNA decay

A. In the absence of sRNA, translating ribosomes protect mRNA from endonucleolytic degradation by blocking endonuclease sensitive sites. B. sRNA regulator is expressed and bound by Hfq, or another chaperone protein, that stabilizes it and facilitates its binding to the vicinity of the Shine-Delgarno (SD) element and initiation codon of the target mRNA. sRNA binding leads to cleavage of both the mRNA and sRNA by RNase III and/or RNase E. The blocking of translation might also exposes cryptic RNase E- sensitive sites within the mRNA. Initial endonucleolytic cleavage generates 5’-monophospate ends that stimulate further cleavage by RNase E, followed by 3’ to 5’ exonucleolytic digestion of both mRNA and sRNA remnants.

Figure 3. The consequences of translation of a non-stop mRNA, and how they are alleviated by trans-translation

A. Translation of non-stop mRNAs leads to ribosome stalling, and as mRNAs are translated by poly-ribosomes, a single stalling event can sequester many ribosomes. Furthermore, stalling could lead to the release of aberrant protein products that may be harmful to the bacterium. B. The SmpB•tmRNA-mediated trans-translation process rescues stalled ribosomes and directs the degradation of the associated incomplete protein products. The SmpB•tmRNA system also facilitates selective decay of the causative non-stop mRNA, preventing future cycles of futile translation and ribosome stalling events.