Structure of the bacterial ribosome at 2 Å resolution

Watson, Zoe L; Ward, Fred R.; Méheust, Raphaël; Ad, Omer; Schepartz, Alanna; Banfield, Jillian F.; Cate, Jamie H. D.

doi:10.7554/elife.60482

Cited by 208 publications

(253 citation statements)

References 129 publications

(259 reference statements)

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“… Regulation of the A-site accessibility by unconventional mRNA secondary structures formed upon ribosome pausing. (A) Positions of the P- (dark blue) and A-site (light blue) tRNAs on the mRNA (dark red) in Escherichia coli ribosome (PDB: 7K00; Watson et al, 2020 ). The density of the ribosome is omitted for clarity.…”

Section: Non-uniform Rate Of Translation and Translational Efficiencymentioning

confidence: 99%

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

et al. 2021

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Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.

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Section: Non-uniform Rate Of Translation and Translational Efficiencymentioning

confidence: 99%

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

et al. 2021

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“…It is instructive to compare the pattern of RP loss during prokaryote evolution with the location of the respective RPs in the ribosome structure (51–56) and a related characteristic, the order of RP joining during the ribosome assembly (3, 57–61). Figure 2 and Table S5 show that neither of these features provides a clear-cut prediction of the RP loss propensity and/or (non)essentiality.…”

Section: Resultsmentioning

confidence: 99%

“…A, B. Crystal structure of the E. coli ribosome (PDB: 7K00), solved at 2 Å resolution by Watson et al , 2020 (56). C, D. Cryo-EM structure of the P. furiosus ribosome (PDB: 4V6U), solved at 6.6 Å resolution by Armache et al , 2012 (55).…”

Section: Resultsmentioning

confidence: 99%

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Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Galperin

Wolf

Garushyants

et al. 2021

Preprint

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Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from the one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 21 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis. These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.

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“…The mitochondrial translation uses 55S ribosomes comprising a 28S small subunit (consisting of 12S rRNA and about 31 proteins) and a 39S large subunit (consisting of 16S rRNA and about 51 proteins) ( 31 , 32 , 33 , 34 ). Even though the mitochondrial ribosomes are distinct in having an RNA to protein ratio of ∼1:2 (as opposed ∼2:1 in bacteria), the overall mechanism of protein synthesis by the two is similar ( 35 , 36 , 37 , 38 ). However, mitochondria possess leaderless mRNAs (lacking SD sequence).…”

Section: Overview Of Protein Synthesis In Bacteria and Eukaryotic Orgmentioning

confidence: 99%

Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles

Shetty

Varshney

2021

Journal of Biological Chemistry

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Protein synthesis is an energetically costly cellular activity. It is therefore important that the process of mRNA translation remains in excellent synchrony with cellular metabolism and its energy reserves. Unregulated translation could lead to the production of incomplete, mistranslated, or misfolded proteins, squandering the energy needed for cellular sustenance, and causing cytotoxicity. One-carbon metabolism (OCM), an integral part of cellular intermediary metabolism, produces a number of one-carbon unit intermediates (formyl, methylene, methenyl, methyl). These OCM intermediates are required for the production of amino acids like methionine, and biomolecules such as purines, thymidylate, and redox regulators. In this review, we discuss how OCM impacts the translation apparatus (composed of ribosome, tRNA, mRNA, and translation factors) and regulates crucial steps in protein synthesis. More specifically, we address how the OCM metabolites regulate the fidelity and rate of translation initiation in bacteria and eukaryotic organelles such as mitochondria. Modulation of the fidelity of translation initiation by OCM opens new avenues to understand alternative translation mechanisms involved in stress tolerance and drug resistance.

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Structure of the bacterial ribosome at 2 Å resolution

Cited by 208 publications

References 129 publications

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles

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