Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Zhou, Jie; Lancaster, Laura; Donohue, John P.; Noller, Harry F.

doi:10.1073/pnas.1901310116

Cited by 48 publications

(59 citation statements)

References 56 publications

(109 reference statements)

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“…During translocation, A and P site tRNAs move together with their respective mRNA codons. It has been shown that bacterial EFG is crucial to maintain the mRNA‐tRNA interaction during tRNA movement, as the absence or mutation of EFG leads to increased frameshifting and decreased translocation efficiency (Martemyanov et al , ; Savelsbergh et al , 2000a; Holtkamp et al , ; Peng et al , ; Zhou et al , ). An important parameter to maintain the mRNA reading frame is the interaction of mtEFG1 domain IV with the tRNA‐mRNA module via two apical loops that engage with the minor groove of the codon–anticodon base pairs and with the backbone of the peptidyl‐tRNA (Gao et al , ).…”

Section: Resultsmentioning

confidence: 99%

Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1

Kummer

Ban

2020

The EMBO Journal

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Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo‐EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase‐associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid.

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Section: Resultsmentioning

confidence: 99%

Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1

Kummer

Ban

2020

The EMBO Journal

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“…In both cases, the role of the downstream secondary structure element is to slow down the late stages of translocation (97,98,102,104). At this point the ribosome is stalled in a rotated or even hyper-rotated state in which the stabilizing contacts between the ribosome and the codon-anticodon complexes are dis- rupted, which allows the tRNA to sample alternative reading frames (78,102,111). Both the dissociation of the E-site tRNA and the backward rotation of the ribosomal subunits are slow, but the E-site tRNA is released before the ribosome rotates backwards (102).…”

Section: Spontaneous and Programmed Ribosome Frameshiftingmentioning

confidence: 99%

“…Both the dissociation of the E-site tRNA and the backward rotation of the ribosomal subunits are slow, but the E-site tRNA is released before the ribosome rotates backwards (102). EF-G, which usually restricts the A-site tRNA in the 0-frame position (78), can also dissociate prior to the completion of translocation (102). When both EF-G and the deacylated tRNA have been released, a single tRNA in transit from the A to the P site may be particularly prone to frameshifting (78).…”

Section: Spontaneous and Programmed Ribosome Frameshiftingmentioning

confidence: 99%

“…EF-G, which usually restricts the A-site tRNA in the 0-frame position (78), can also dissociate prior to the completion of translocation (102). When both EF-G and the deacylated tRNA have been released, a single tRNA in transit from the A to the P site may be particularly prone to frameshifting (78). There are two ways to resolve the metastable stalled state, either by spontaneous unwinding of the mRNA secondary structure element that hinders the progression of the ribosome, which would allow the ribosome to resume its progression in the 0-frame, or by slippage in the -1 direction (97).…”

Section: Spontaneous and Programmed Ribosome Frameshiftingmentioning

confidence: 99%

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Translational recoding: canonical translation mechanisms reinterpreted

Rodnina

Korniy

Klimova

et al. 2019

Nucleic Acids Research

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During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, -1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.

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“…Chimeric hybrid orientations of tRNA have recently also been identified in T. thermophilus 70S ribosomes in the absence of elongation factor G 24 . One study found that a frameshift-suppressor tRNA binds in an intermediate orientation resembling a translocation intermediate 25 , and another study captured a translocation intermediate complex with two tRNAs in chimeric hybrid states 24 . It is likely that the structure we observe here resulted from the action of EF-G during the translation cycle in vivo.…”

Section: S Conformations In Five Cryo-em Classesmentioning

confidence: 99%

Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis

Murphy

Singh

Avila

et al. 2020

Sci Rep

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Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.

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Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Abstract: The authors declare no conflict of interest.Published under the PNAS license.Data deposition: The atomic coordinates and structure factors have been deposited in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank, www.rcsb. org (RCSB PDB ID code 6N1D).

Cited by 48 publications

References 56 publications

Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1

Structural insights into mammalian mitochondrial translation elongation catalyzed by mt EFG 1

Translational recoding: canonical translation mechanisms reinterpreted

Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis

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