The ribosome moves: RNA mechanics and translocation

Noller, Harry F.; Lancaster, Laura; Zhou, Jie; Mohan, Srividya

doi:10.1038/nsmb.3505

Cited by 81 publications

(87 citation statements)

References 57 publications

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“…Importantly, to dissociate mRNA from S3 in the stick‐slip route at a significant rate, the ribosome must have evolved to perform work that exceeds (or is within a few k B T of) this binding energy, ~ 9 kcal·mol −1 per codon. The main energy sources for translocation are peptidyl transfer and GTP hydrolysis by EF‐G , the latter alone being ~ 12 kcal·mol −1 , suggesting that stick‐slip is indeed affordable by the ribosome under this model.…”

Section: Discussionmentioning

confidence: 89%

A tandem active site model for the ribosomal helicase

Amiri

Noller

2019

FEBS Letters

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During protein synthesis, the messenger RNA (mRNA) helicase activity of the ribosome ensures that codons are made single stranded before decoding. Here, based on recent structural and functional findings, a quantitative model is presented for a tandem arrangement of two helicase active sites on the ribosome. A distal site encounters mRNA structures first, one elongation cycle earlier than a proximal site. Although unwinding of encountered mRNA structures past the proximal site is required for translocation, two routes exist for translocation past the distal site: sliding, which requires unwinding, and stick‐slip, which does not. The model accounts in detail for a number of findings related to the ribosomal helicase and provides a testable framework to further study mRNA unwinding.

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Section: Discussionmentioning

confidence: 89%

A tandem active site model for the ribosomal helicase

Amiri

Noller

2019

FEBS Letters

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“…The movement of the peptidyl‐tRNA in the A site to the P site has to be coordinated with the movement of the P site tRNA to the E site, and the tRNA occupying the E site has to be ejected from the ribosome with the assistance of the L1 stalk. During this process, it is of capital importance that the correct reading frame on the mRNA be maintained (Voorhees & Ramakrishnan, ; Noller et al , ,). This is accomplished by the participation of specific components of the ribosome (mainly RNA bases) which interact with tRNAs and mRNA defining specific checkpoints so as to prevent in‐transit tRNAs from slipping or loosing contact with the mRNA on the correct frame (Zhou et al , ).…”

Section: Resultsmentioning

confidence: 99%

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

et al. 2019

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Colony collapse disorder (CCD) is a multi‐faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non‐coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single‐particle cryo‐electron microscopy (cryo‐EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre‐translocation and a post‐translocation state of the IAPV‐IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV‐IRES from the early small subunit recruitment to the final post‐translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre‐translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV‐IRES using RNA‐interference technology are underway, and the structural framework presented here may assist in further refining these approaches.

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“…No longer stabilized by the tRNA and A2602, the GGQ loop reorganizes into an extended -hairpin that blocks the peptide tunnel (Structure II), thus biasing the diffusion of nascent peptide toward the exit of the peptide tunnel at the surface of the 50S subunit ( Figure 4D). Furthermore, the exit of the CCA end from the P site supports formation of the P/E-tRNA hybrid conformation via spontaneous intersubunit rotation (Structures III and IV), which is also essential for translocation of tRNA-mRNA (reviewed in (Ling and Ermolenko, 2016;Noller et al, 2017)). The large counterclockwise rotation of the small subunit destabilizes the catalytic domain of RF2 (Structure IV), so that it begins to collapse toward domain 2 bound to the 30S subunit ( Figure 4E).…”

Section: Mechanism Of Translation Termination By Rf2mentioning

confidence: 99%

Extensive Ribosome and RF2 Rearrangements during Translation Termination

Svidritskiy

Demo

Loveland

et al. 2019

Preprint

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Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long -hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.

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The ribosome moves: RNA mechanics and translocation

Cited by 81 publications

References 57 publications

A tandem active site model for the ribosomal helicase

A tandem active site model for the ribosomal helicase

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

Extensive Ribosome and RF2 Rearrangements during Translation Termination

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