The bacterial translation stress response

Abstract

Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.

Keywords: antibiotic stress; mRNA truncation; nutrient depletion; stationary phase; toxin-antitoxin modules; translational stalling.

Figure 1. Ribosome-dependent synthesis of ppGpp by RelA

(a) RelA catalyzes conversion of ATP and GTP (or GDP) to AMP and (p)ppGpp. (b) Scheme for RelA recognition of ribosomes stalled by deacylated tRNA and production of (p)ppGpp. (c) Chemical structure for RelA inhibitor Relacin (Wexselblatt et al., 2012, Wexselblatt et al., 2013).

Figure 2. Rescue of ribosomes stalled on polyproline stretches by EF-P

(a) Peptide-bond formation between Pro-tRNA in A- and P-site is slow because Pro acts a poor donor and acceptor. (b) Ribosome stalling on polyproline stretches is alleviated by binding of EF-P, which stimulates peptide-bond formation so that translation can continue. (c) Binding site of EF-P on the 70S ribosome (Blaha et al., 2009), with (d) enlargement indicating the position of the conserved lysine 34 in E. coli EF-P relative to the CCA-end of the P-tRNA (based on (Blaha et al., 2009)).

Figure 3. MazF-mediated translation reprogramming

(a-c) Structure of the E. coli toxin MazF dimer in complex with (a) the antitoxin MazE or (b) mRNA, with (c) enlargement of ACA (cyan) of mRNA in active site (Simanshu et al., 2013). (d) Scheme for MazF cleavage of ACA motif in (I) the 16S rRNA of the 30S subunit, thus removing the anti-SD, and (II) mRNA, adjacent to the AUG start codon, thus generating a leaderless mRNA lacking Shine-Dalgarno (SD) sequence, which is specifically translated by the MazF cleaved ribosomes.

Figure 4. Ribosome-dependent cleavage of the A-site codon by RelE

(a-b) Structure of the E. coli toxin RelE in complex with (a) the antitoxin RelB (Boggild et al., 2012) or (b) mRNA (Neubauer et al., 2009). (c) Binding site of RelE on the 70S ribosome (Neubauer et al., 2009). (d) pre- and (e) post-cleavage states of mRNA by RelE on the 70S ribosome, compared with (f) mRNA conformation in the presence of A-tRNA (Neubauer et al., 2009). (g) Scheme for RelE mediated mRNA cleavage on the ribosome.

Figure 5. Trans-translation of truncated mRNAs by tmRNA and SmpB

(a) Scheme for tmRNA-mediated rescue of ribosomes stalled on truncated mRNAs. (b) Secondary structure for tmRNA, with tRNA-like domain (TLD) and mRNA-like domain (MLD) highlighted. (c) Structure of EF-Tu delivery of tmRNA-TLD-SmpB complex to the A-site of the 70S ribosome (Neubauer et al., 2012). (d) C-terminal domain (CTD) of SmpB overlaps position of A-site codon and 3′ extension of mRNA within the mRNA channel (Neubauer et al., 2012). (e) Structure of complete tmRNA (cyan)-SmpB (teal) complex following translocation into the P-site by EF-G (blue) (Ramrath et al., 2012).

Figure 6. Rescue of truncated mRNAs by ArfA and ArfB

(a) Schematic for ArfA mediated recruitment of RF2 to the 70S ribosome. (b) Structure of ArfB on the 70S ribosome (Gagnon et al., 2012). (c) The C-terminal domain (CTD) of ArfB overlaps position of A-site codon and 3′ extension of mRNA within the mRNA channel (Gagnon et al., 2012). (d) Schematic for ArfB mediated ribosome rescue.

Figure 7. Antagonistic action of pY and RMF/HPF on 100S formation

(a) Structure of pY on the 70S ribosome (Polikanov et al., 2012). (b) Overlap in binding position of pY with mRNA and tRNAs in the A- and P-sites and CTD with RMF (Polikanov et al., 2012). (c) Scheme for antagonistic action of pY to inhibit 100S formation and concerted action of RMF and HPF to promote 100S formation. (d) Structure of RMF and HPF on the 70S ribosome (Polikanov et al., 2012). (e) Overlap in binding position of HPF with mRNA and tRNAs in the A- and P-sites and RMF with SD-antiSD region on the 30S subunit (Polikanov et al., 2012).

Figure 8. Hibernation of translation initiation complex by EttA

(a) Scheme for the influence of the ATP/ADP ratio on EttA-mediated translation inhibition. (b) Structure of EttA on the 70S ribosome (Chen et al., 2014). (c) EttA (blue) contacts the acceptor arm of the P-tRNA (Chen et al., 2014).

Figure 9. Hsp15-mediated rescue of peptidyl-tRNA on 50S subunits

(a) Scheme for the Hsp15-mediated translocation of peptidyl-tRNA from A- to P-site to allow peptidyl-tRNA hydrolysis and release of the polypeptide chain (possibly by recruitment of RF2) and subsequent recycling of the 50S subunits.

Figure 10. Relief of antibiotic stress by TetM- and FusB-like proteins

(a) Scheme for TetM-mediated tetracycline resistance via ribosome binding and removal of tetracycline. (b) Structure of TetM on the 70S ribosome (Donhofer et al., 2012). (c-d) Relative binding position of loop III of domain IV of TetM relative to (c) tetracycline and (d) tigecycline (Donhofer et al., 2012, Jenner et al., 2013). (e) Structure of EF-G stalled by fusidic acid on the 70S ribosome (Gao et al., 2009). (f) Model for the interaction of FusB (teal) with domain IV of EF-G (blue) (based on (Cox et al., 2012)). (g) Scheme for FusB-mediated fusidic acid resistance via ribosome binding and dislodging the EF-G-fusidic acid complex.

Figure 11. Ribosome-associated stress factors Obg, EF4 and BipA

(a) Structure of Obg, with N-terminal OBG and C-terminal OCT domain flanking the G domain bound with ppGpp in the active site (Buglino et al., 2002, Kukimoto-Niino et al., 2004). (b) Scheme for EF4-mediated back-translocation of tRNAs on the ribosome. (c) Structure of EF4 bound to the 70S ribosome (Connell et al., 2008). (d) Interaction of EF4 (blue) with distorted A/L-tRNA (orange), relative to canonical P-tRNA (green) and E-tRNA (red) (Connell et al., 2008). (e) Structure of BipA (teal, PDB3E3X) relative to distorted A/L-tRNA from EF4-70S complex (Connell et al., 2008) (aligned to EF4 based on the conserved G domain).