Structural analysis of ribosomal rescue complexes in bacteria

Abstract

Protein biosynthesis or translation is a basal process in the cells of all organisms, which is performed by ribosomes in cooperation with numerous protein factors. However, translating ribosomes can be stalled by various mechanisms, such as the presence of damaged, truncated, or stop codon lacking messenger-RNAs (mRNAs). To prevent accumulation of stalled ribosomes and thus minimize the pool of active ribosomes, all organisms have evolved ribosomal rescue mechanisms. These include trans-translation and ribosome-associated quality control (RQC). Both pathways cause the degradation of the incomplete and potentially toxic nascent polypeptide chain attached to the transfer RNA (tRNA) and rescue stalled ribosomes. A crucial point in RQC is the recognition of the peptidyl-tRNA-containing large ribosomal subunit, which is performed by Rqc2/NEMF in eukaryotes and RqcH (the Rqc2 homolog) in prokaryotes. Unlike for eukaryotes, structural data for prokaryotic RQC complexes were lacking at this time. One project of this doctoral thesis aimed for the visualization of RqcH on ribosomal 50S subunits using cryo-EM. The structural analysis of B. subtilis 50S subunits co-purified with wild-type RqcH did not show a density for this factor, possibly due to its flexibility. However, the structure provided important and complementary evidence for the study in Lytvynenko et al. 2019, as it suggests that peptidyl-tRNA 50S subunits are substrates for RqcH, and thus RqcH appears to be involved in prokaryotic RQC. In a second attempt to visualize RqcH, the RqcH protein mutated in its NFACT-N domain was co-purified with 50S subunits and additionally crosslinked before EM analysis, both to decrease flexibility. The subsequent cryo-EM analysis revealed a mutant RqcH-50S structure with a resolution of 3.1 Å. The structure likely represents the initial recognition step in prokaryotic RQC and shows how the individual domains of RqcH (NFACT-N-HhH, CC1-M-CC2 and NFACT-R) interact with the P-tRNA-50S complex. The combined structure-function analysis provided evidence for specific RqcH region that are functionally relevant for P-tRNA-50S binding and RqcH function within the RQC pathway. Comparison with existing RQC structures indicate that the M-CC2 region anchors RqcH to the 50S subunit and serves as a potential pivot point for the NFACT-N-HhH and NFACT-R domains which seem to be more flexible. While RQC targets stalled ribosomal subunits, trans-translation aims to rescue stalled 70S ribosomes. Trans-translation requires the small protein SmpB and a transfer-messenger RNA (tmRNA) and allows by using the amino acid coding sequence in the mRNA-like domain (MLD) in the tmRNA to elongate and tag the nascent polypeptide chain for degradation. The second part of this doctoral thesis focused on the cryo-EM analysis of the E. coli 70S-tmRNA-EF-G-FA specimen previously used in the cryo-EM study in Ramrath et al., 2012. Using advanced technologies for the cryo-EM analysis of the same specimen resulted into high-resolution structures and moreover revealed additional trans-translation states. The five cryo-EM structures were resolved to 3.5 Å to 3.8 Å and shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its accommodation into the ribosomal A-site to the translocation towards the ribosomal P-site and passed the E-site. The observation of a state before translocation (tmRNA-PRE) and states (PAST-E-TI-POST and PAST-POST) of subsequent translocation complement and are consistent with the similar structural data. However, the tmRNA-SmpB translocation and also the process of MLD (mRNA-like domain) loading were poorly understood. The structures in this work show how the tmRNA-SmpB module specifically acts on the ribosome revealing new insights of how the translation is switched from the old defective mRNA to the reading frame of the MLD. The intermediate states (tmRNA-TI-POST I and II) that formed during the first translocation round show density for the complete SmpB protein and the MLD allowing to gain new insights of the process of MLD loading into the mRNA channel. In addition, the structures provide molecular insights into the process by which the large tmRNA-SmpB complex overcomes the physical barriers within the ribosome during the trans-translation.