Molecular analysis of the ribosome recycling factor
            <scp>ABCE</scp>
            1 bound to the 30S post‐splitting complex

Nürenberg-Goloub, Elina; Kratzat, Hanna; Heinemann, Holger; Heuer, André; Kötter, Peter; Berninghausen, Otto; Becker, Thomas; Tampé, Robert; Beckmann, Roland

doi:10.15252/embj.2019103788

Cited by 24 publications

(54 citation statements)

References 60 publications

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“…Remodeling the isoAsp motifs in maps from recently-published cryo-EM reconstructions of an archaeal 30S ribosomal subunit complex at 2.8 Å resolution (Nürenberg-Goloub et al, 2020) and a yeast 80S ribosome complex at 2.6 Å resolution (Tesina et al, 2020) shows that isoaspartate also seems to be present in these organisms (Figure 4-figure supplement 2). Taken together, the phylogenetic data and structural data indicate that the isoaspartate in uS11 is nearly universally conserved, highlighting its likely important role in ribosome assembly and function.…”

Section: Post-translational and Post-transcriptional Modifications Inmentioning

confidence: 90%

Structure of the Bacterial Ribosome at 2 Å Resolution

Watson

Ward

Méheust

et al. 2020

Preprint

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Continuing advances in cryo-electron microscopy (cryo-EM) demonstrate the promise it holds for revealing biological structures at chemical resolution, in which noncovalent interactions, RNA and protein modifications, and solvation can be modeled accurately. At present, the best cryo-EM-derived models of the bacterial ribosome are of the large (50S) ribosomal subunit with effective global resolutions of 2.4-2.5 Å, based on map-to-model Fourier shell correlation (FSC). Here we present a model of the E. coli 70S ribosome with an effective global resolution of 2.0 Å, based on maps showcasing unambiguous positioning of residues, their detailed chemical interactions, and chemical modifications. These modifications include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former of which is likely conserved in all domains of life. The model also defines extensive solvation of the small (30S) ribosomal subunit for the first time, as well as interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The high quality of the maps now allows a deeper phylogenetic analysis of ribosomal components, and identification of structural conservation to the level of solvation. The maps and models of the bacterial ribosome presented here should enable future structural analysis of the chemical basis for translation, and the development of robust tools for cryo-EM structure modeling and refinement.

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Section: Post-translational and Post-transcriptional Modifications Inmentioning

confidence: 90%

Structure of the Bacterial Ribosome at 2 Å Resolution

Watson

Ward

Méheust

et al. 2020

Preprint

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“…Subsequently, the released mRNA is degraded by the 5′-3′ exoribonuclease Xrn1 and the exosome complex to prevent the aberrant mRNA from recruiting a new ribosome. The released 40S subunit is recycled (reviewed in ( 98 , 100 )), which likely requires the action of the recycling factor ABCE1 ( 103 , 104 ). The 60S subunit must first be relieved of the trapped tRNA-conjugated polypeptide chain ( 105 ).…”

Section: Other Ribosomal Surveillance Pathwaysmentioning

confidence: 99%

Ribosomal stress-surveillance: three pathways is a magic number

Vind

Genzor

Bekker‐Jensen

2020

Nucleic Acids Research

107

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Cells rely on stress response pathways to uphold cellular homeostasis and limit the negative effects of harmful environmental stimuli. The stress- and mitogen-activated protein (MAP) kinases, p38 and JNK, are at the nexus of numerous stress responses, among these the ribotoxic stress response (RSR). Ribosomal impairment is detrimental to cell function as it disrupts protein synthesis, increase inflammatory signaling and, if unresolved, lead to cell death. In this review, we offer a general overview of the three main translation surveillance pathways; the RSR, Ribosome-associated Quality Control (RQC) and the Integrated Stress Response (ISR). We highlight recent advances made in defining activation mechanisms for these pathways and discuss their commonalities and differences. Finally, we reflect on the physiological role of the RSR and consider the therapeutic potential of targeting the sensing kinase ZAKα for treatment of ribotoxin exposure.

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“…With regard to resolution, in this work we have supplemented the reporting of the "goldstandard" FSC with map-to-model FSC curves for our maps and for comparisons to previous work. Although the map-to-model FSC metric has been described for some time, it is not routinely used in the ribosome field (Halfon et al, 2019;Loveland et al, 2020;Nürenberg-Goloub et al, 2020;Pichkur et al, 2020;Stojković et al, 2020;Tesina et al, 2020 (Halfon et al, 2019;Pichkur et al, 2020;Stojković et al, 2020) (see Methods) ( Figure 7-figure supplement 1). Notably, for the 2.1 Å map of the E. coli 50S subunit based on half-map FSC values (Pichkur et al, 2020), the map-to-model FSC fit of our 50S subunit model to that map has a higher resolution (2.07 Å), compared to the deposited model (2.29 Å, PDB entry 6xz7) (Figure 7-figure supplement 1).…”

mentioning

confidence: 99%

Structure of the bacterial ribosome at 2 Å resolution

Watson

Ward

Méheust

et al. 2020

eLife

177

225

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Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analysis of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.

show abstract

Molecular analysis of the ribosome recycling factor ABCE 1 bound to the 30S post‐splitting complex

Cited by 24 publications

References 60 publications

Structure of the Bacterial Ribosome at 2 Å Resolution

Structure of the Bacterial Ribosome at 2 Å Resolution

Ribosomal stress-surveillance: three pathways is a magic number

Structure of the bacterial ribosome at 2 Å resolution

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