Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective

Abstract

In all living cells, the ribosome translates the genetic information carried by messenger RNAs (mRNAs) into proteins. The process of ribosome recycling, a key step during protein synthesis that ensures ribosomal subunits remain available for new rounds of translation, has been largely overlooked. Despite being essential to the survival of the cell, several mechanistic aspects of ribosome recycling remain unclear. In eubacteria and mitochondria, recycling of the ribosome into subunits requires the concerted action of the ribosome recycling factor (RRF) and elongation factor G (EF-G). Recently, the conserved protein HflX was identified in bacteria as an alternative factor that recycles the ribosome under stress growth conditions. The homologue of HflX, the GTP-binding protein 6 (GTPBP6), has a dual role in mitochondrial translation by facilitating ribosome recycling and biogenesis. In this review, mechanisms of ribosome recycling in eubacteria and mitochondria are described based on structural studies of ribosome complexes.

Mechanistic insights into the alternative ribosome recycling by HflXr

“…The interaction between the NTD-I of HflXr and H69 results in a displacement of H69 and h44 by ∼4 Å toward the platform domain of the 30S subunit, maintaining the conserved A-minor interactions with h44 (Figures 1D and 2A ). The observation that the integrity of bridge B2a is maintained in our structures suggests that HflXr catalyzes ribosome recycling by a mechanism that is distinct from that mediated by RRF and EF-G, which together ablate bridge B2a ( Supplementary Figure S12A ) ( 6 , 28–36 ).…”

“…In contrast to the mode of action of RRF and EF-G ( 6 , 28–36 ), binding of HflXr to the 70S ribosome does not initially disrupt the central inter-subunit bridge B2a mediated by the contact between helices H69 in the 50S subunit and h44 in the 30S subunit (Figure 2A – C ; Supplementary Tables S2 and S3 ; Supplementary Movie S1 ). Despite the close interaction between the N-terminal subdomain I (NTD-I) of HflXr and H69 in complex II-C, the buried surface area by bridge B2a is unchanged relative to the equivalent ribosome lacking HflXr (I-B) (Figure 3A and D ; Supplementary Table S2 ).…”

Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation

“…During transcription, ribosomes initiate the translation process at the same time. Generally, the translation process is divided into four steps: initiation, elongation, termination, and recycling, while each step is accomplished accurately based on the interaction between the relevant translation factors and the ribosome . In addition, ribosomal proteins, such as 30s ribosomal protein S4, S5, and S12, and tRNA (e.g., aa-tRNA) are necessary for translation.…”

“…Generally, the translation process is divided into four steps: initiation, elongation, termination, and recycling, while each step is accomplished accurately based on the interaction between the relevant translation factors and the ribosome. 32 In addition, ribosomal proteins, such as 30s ribosomal protein S4, S5, and S12, and tRNA (e.g., aa-tRNA) are necessary for translation. The metaproteomic and metagenomic analyses were further applied to reveal the changes in the expression of these components and elucidate the effects on translation.…”

Special focus on the ribosome life cycle

“…The authors explore how mitochondrial ribosomes are recycled and rescued in the context of limited translation factors or on aberrant mRNAs and draw comparisons to the ancestral bacterial system. Seely and Gagnon, also focus on the mitochondrial ribosome in their review and consider recently gained knowledge about mechanisms and factors involved in ribosome recycling in mitochondria and eubacteria based on X-ray crystallography and cryo-electron microscopy studies of ribosome complexes [ 29 ]. In particular, the authors examine how these steps require the concerted and synergistic action of both ribosome recycling and elongation factors.…”