10.2 Synthetic Control of Transcript Stability 195sRNAs can enhance translation when binding to the mRNA eliminates cis-
acting secondary structure involving the SD sequence. In turn, ribosomes can
bind to the SD and initiate translation, protecting the mRNA from degradation
[54–57]. sRNAs can repress translation when binding to the mRNA occludes
ribosome binding [58, 59], rendering the transcript susceptible to endonuclease
cleavage due to a lack of protective ribosomes. In the latter case, sRNA binding
seems to recruit RNase E through interaction with Hfq and the 5′-P of the
sRNA[48], hastening degradation of both the sRNA and targeted mRNA. It is
interesting to note that sRNA-mediated RBS occlusion is sufficient for down-
regulation; thus in some cases, degradation serves only to make the downregula-
tion irreversible [53, 60].
10.1.5 Polyadenylation and Transcript Stability
Unlike in eukaryotes, polyadenylation of bacterial mRNA is not associated with
transcript maturation and increased stability [5], but instead has been associated
with mRNA destabilization (Figure 10.2c). Interestingly, although generally
implicated in the degradation of nonfunctional or mutated RNAs as part of qual-
ity control mechanisms [61], there are several examples where polyadenylation
is employed to modulate gene expression [5, 62, 63]. The half-life of rpoS mRNA
in E. coli decreased when polyadenylated in the absence of RNase E, where
polyadenylation depended on pcnB [64], the gene coding for poly(A) polymer-
ase [65]. Poly(A) tails are used as footholds for exoribonucleases, such as PNPase,
that bind the poly(A) tails and perform 3′ → 5 ′ degradation [30, 62]. The half-life
of three mRNA different transcripts increased when pcnB was knocked out,
coinciding with poly(A) tails shortened up to 90% [66].
10.2 Synthetic Control of Transcript Stability
10.2.1 Transcript Stability Control as a “Tuning Knob”
As outlined in Section 10.1, transcript stability is determined through the collec-
tive impact of a multitude of sequence and structural features. The 5′ terminus
identity (i.e., 5′-PPP vs 5′-P vs 5′-OH) and the presence of stable secondary
structures within the 5′ UTR affect 5′ end accessibility by RppH and RNase E.
Active translation creates steric hindrance and ribosome occlusion that reduces
internal accessibility by RNase E. Finally, 3′ end accessibility by PNPase varies
according to 3′ UTR secondary structure, polyadenylation state, and the pres-
ence or absence of sRNAs that mediate degradation. Because RNAs can be tran-
scribed and degraded within the space of only a few minutes, variations in
transcript stability can have dramatic effects on RNA levels. This implies that
gene expression can be controlled quickly and dynamically by modulating the
sequence and structural features that directly affect transcript stability. In natu-
rally occurring systems, swings in transcript abundance allow cells to respond to
changing conditions and, for instance, reestablish perturbed homeostasis or
respond to the buildup of intra- or extracellular toxins [2]. TSC thus presents a