Drug sensing by the ribosome induces translational arrest via active site perturbation

Abstract

During protein synthesis, nascent polypeptide chains within the ribosomal tunnel can act in cis to induce ribosome stalling and regulate expression of downstream genes. The Staphylococcus aureus ErmCL leader peptide induces stalling in the presence of clinically important macrolide antibiotics, such as erythromycin, leading to the induction of the downstream macrolide resistance methyltransferase ErmC. Here, we present a cryo-electron microscopy (EM) structure of the erythromycin-dependent ErmCL-stalled ribosome at 3.9 Å resolution. The structure reveals how the ErmCL nascent chain directly senses the presence of the tunnel-bound drug and thereby induces allosteric conformational rearrangements at the peptidyltransferase center (PTC) of the ribosome. ErmCL-induced perturbations of the PTC prevent stable binding and accommodation of the aminoacyl-tRNA at the A-site, leading to inhibition of peptide bond formation and translation arrest.

Figure 1. Cryo-EM structure of the ErmCL-SRC

(A) Schematic for ermCL-dependent regulation of ermC translation in the presence of erythromycin (ERY). (B) Transverse section of the ErmCL-SRC, with 30S (yellow), 50S (grey), P-tRNA (green), ErmCL (teal) and ERY (red). (C) Zoom showing electron density (grey) and model for the ErmCL nascent chain (teal) attached to CCA-end of the P-tRNA (green). (D) as (B) but coloured according to local resolution. (E–H) Examples of electron density in the ErmCL-SRC map including (E) β-strands and (F) α-helix in ribosomal proteins, (G) rRNA helix and (H) coordinated Mg²⁺ ions. See also Figure S1.

Figure 2. Interaction of the ErmCL nascent chain within the ribosomal tunnel

(A,B) ErmCL (teal) contacts (arrowed) with 23S rRNA nucleotides (A) U2506, U2586 and (B) A2062. (C) Toe-printing of wild-type (wt) and mutant (I6A) ErmCL translation on E. coli ribosomes with wt (U2586) or U2586A/C/G mutants, in the presence (+) or absence (−) of ERY. All reactions contained the Thr-tRNA synthetase inhibitor borrelidin which halts translation at the Thr (T11) codon in the absence of ERY-induced arrest at the Ile (I9) codon. Error bars represent one standard deviation of the mean. (D) Spacefill representation of ErmCL (teal) illustrating the steric clash with A2062 positions from PDB3OFR (Dunkle et al., 2010) (yellow) and ErmBL-SRC (PDB ID 3J5L, grey) (Arenz et al., 2014). For comparison, the A2062 position in ErmCL-SRC is shown (blue). (E) Sensing of the C3 cladinose sugar of ERY (Dunkle et al., 2010) (red) by the ErmCL nascent chain (teal). See also Figure S2–S4.

Figure 3. Conformational changes at the PTC of the ErmCL-SRC

(A,B) Flipped conformation of 23S rRNA nucleotide U2585 in ErmCL-SRC (teal) compared to canonical position of U2585 in the uninduced (PDB1VQ6, orange) and induced (PDB1VQN, yellow) states of the PTC (Schmeing et al., 2005a; Schmeing et al., 2005b). (C) Comparison of ErmCL (teal) and ErmBL (PDB3J5L, tan) (Arenz et al., 2014) nascent chains and respective U2585 positions. (D,E) Relative positions of (D) U2585 and U2506, and (E) A2602 in ErmCL-SRC (teal), uninduced (PDB1VQ6, orange) and induced (PDB1VQN, yellow) states of the PTC (Schmeing et al., 2005a; Schmeing et al., 2005b). In (E), A2602 position of ErmBL-SRC (PDB3J5L, tan) (Arenz et al., 2014) is included for reference. (F) The flipped U2585 position in ErmCL-SRC (teal) prevents stabilization of the A-tRNA as observed in the uninduced (PDB1VQ6, orange) and induced (PDB1VQN, yellow) state of the PTC (Schmeing et al., 2005a; Schmeing et al., 2005b). See also Figure S3.

Figure 4. Schematic model of ErmCL-mediated translation arrest

(A) In the absence of erythromycin (−ERY), Ser-tRNA accommodates at the A-site enabling peptide bond formation with the ErmCL-tRNA in the P-site. (B) In contrast, the presence of erythromycin, the ErmCL nascent chain adopts a distinct conformation that promotes conformational rearrangements of 23S rRNA nucleotides A2062, A2602 and most dramatically, flipping of U2585. Collectively, this global rearrangement of the peptidyltransferase center prevents stable binding and accommodation of Ser-tRNA at the ribosomal A-site and thus results in translational arrest.