Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter

Fujiwara, K.; Katagi, Yutaro; Ito, Koreaki; Chiba, Shinobu

doi:10.1016/j.celrep.2020.108250

Cited by 15 publications

(13 citation statements)

References 95 publications

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“…For an arrest peptide to function as a Sec- or YidC-monitoring substrate, the translation arrest must be released in a secretion- or membrane-insertion-dependent manner 27 . An optimal distance between the N-terminal TM segment and the arrest site is crucial for the membrane-insertion-dependent arrest cancellation if the TM segment adopts the type I (N-out/C-in) orientation 36,37 , which is a topology that is often observed for YidC substrates 38 . Conversely, this distance can vary without impairing the localization-dependent arrest release if the N-terminal localization signal is either the Sec-dependent secretion signal or type II (N-in/C-out) TM segment 37 .…”

Section: Resultsmentioning

confidence: 99%

“…An optimal distance between the N-terminal TM segment and the arrest site is crucial for the membrane-insertion-dependent arrest cancellation if the TM segment adopts the type I (N-out/C-in) orientation 36,37 , which is a topology that is often observed for YidC substrates 38 . Conversely, this distance can vary without impairing the localization-dependent arrest release if the N-terminal localization signal is either the Sec-dependent secretion signal or type II (N-in/C-out) TM segment 37 . We envisioned that this trend might be shared by known monitoring substrates, i.e., SecM, MifM, and VemP, as well as by other arrest peptides if they actually function as monitoring substrates.…”

Section: Resultsmentioning

confidence: 99%

Section: Bioinformatics Analysis Of the Length Of The Spacer Between ...mentioning

confidence: 99%

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Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

Fujiwara,

Tsuji,

Yoshida

et al. 2023

Preprint

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Regulatory arrest peptides exert cellular functions via mechanisms involving regulated translational arrest. Monitoring substrates, a class of arrest peptides, feedback-regulate the expression of the Sec or YidC protein localization machinery. Previously, only a limited number of monitoring substrates were identified. In this study, we performed a bacterial domain-wide search, followed byin vivoandin vitroanalyses, leading to a comprehensive identification of many novel Sec/YidC-related arrest peptides that showed patchy, but widespread, phylogenetic distribution throughout the bacterial domain. Identification of five novel arrest-inducing sequences suggests that bacteria have evolved various arrest-inducing mechanisms. We also identified many arrest peptides that share an R-A-P-P like sequence, suggesting that this sequence could serve as a common evolutionary seed that could overcome the species-specific structures of ribosomes, to evolve arrest peptides. Our comprehensive phylogenetic study revealed that arrest peptide is a prevalent mechanism for the gene regulation of the protein localization machinery.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Bioinformatics Analysis Of the Length Of The Spacer Between ...mentioning

confidence: 99%

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Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

Fujiwara,

Tsuji,

Yoshida

et al. 2023

Preprint

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“…Using such a simulation approach, we postulate that explaining the translation-enhancing mechanism may be through mechanical forces generated between MSKIK and RAPs during translation. In addition, because many RAPs other than SecM or CmlA leader have been found (Su et al, 2021),and a recent study showed a force-sensitive arrest by MifM in Bacillus subtilis was cancelled by N-terminally adjacent dynamic nascent chain (Fujiwara et al, 2020), we expect that there are still many translation-promoting peptides remain to be undiscovered.…”

Section: Discussionmentioning

confidence: 99%

Nascent MSKIK peptide prevents or releases translation arrest in Escherichia coli

Ojima-Kato

Nishikawa

Yuki

et al. 2022

Preprint

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The insertion of the sequence encoding SKIK peptide adjacent to the M start codon of a difficult-to-express protein enhances protein production in Escherichia coli. In this report, we show that the increased production of the SKIK-tagged protein is not due to codon usage of the SKIK sequence. In addition, insertion of SKX, KKX, and AKX (X = G, L, H, Y, E, and F) at the N-terminus increased protein production. Furthermore, insertion of MSKIK just before the SecM arrest peptide (FSTPVWISQAQGIRAGP), which causes translational stalling on mRNA, greatly increased the production of the protein containing the SecM arrest peptide in the E. coli reconstituted cell-free protein synthesis system (PURE system). A similar phenomenon was observed for CmlA leader whose arrest is induced by chloramphenicol. These results suggest that the nascent MSKIK peptide prevents or releases translational stalling immediately following its generation during the translation process.

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“…Rare codons have also been shown to be positioned to facilitate interactions between nascent proteins and the signal recognition particle ( Pechmann et al., 2014 ) as well as with other proteins in the cell ( Chartier et al , 2012 ). However, rare codons are not the only factor that influences translation times: mRNA structure ( Hershey et al , 2012 ), the chemistry of the amino acid being added to the nascent protein ( Artieri and Fraser, 2014 ; Pavlov et al., 2009 ), mechanical forces generated by nascent proteins ( Fritch et al , 2018 ; Fujiwara et al , 2020 ; Leininger et al., 2019 ) and interactions between the nascent protein and the ribosome ( Gumbart et al , 2012 ) are all part of the picture.…”

Section: Introductionmentioning

confidence: 99%

Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains

et al. 2021

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Motivation Protein synthesis is a non-equilibrium process, meaning that the speed of translation can influence the ability of proteins to fold and function. Assuming that structurally similar proteins fold by similar pathways, the profile of translation speed along an mRNA should be evolutionarily conserved between related proteins to direct correct folding and downstream function. The only evidence to date for such conservation of translation speed between homologous proteins has used codon rarity as a proxy for translation speed. There are, however, many other factors including mRNA structure and the chemistry of the amino acids in the A- and P-sites of the ribosome that influence the speed of amino acid addition. Results Ribosome profiling experiments provide a signal directly proportional to the underlying translation times at the level of individual codons. We compared ribosome occupancy profiles (extracted from five different large-scale yeast ribosome profiling studies) between related protein domains to more directly test if their translation schedule was conserved. Our analysis reveals that the ribosome occupancy profiles of paralogous domains tend to be significantly more similar to one another than to profiles of non-paralogous domains. This trend does not depend on domain length, structural classes, amino acid composition or sequence similarity. Our results indicate that entire ribosome occupancy profiles and not just rare codon locations are conserved between even distantly related domains in yeast, providing support for the hypothesis that translation schedule is conserved between structurally related domains to retain folding pathways and facilitate efficient folding. Availability and implementation Python3 code is available on GitHub at https://github.com/DanNissley/Compare-ribosome-occupancy. Supplementary information Supplementary data are available at Bioinformatics online.

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Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter

Abstract: Highlights d TnDR is an arrest-sequence-based and transposable protein-dynamics reporter d TnDR captures co-translational protein localization and assembly d Proteome-wide screening has been conducted d Co-translational protein maturation is a frequently occurring event in the cell

Cited by 15 publications

References 95 publications

Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery

Nascent MSKIK peptide prevents or releases translation arrest in Escherichia coli

Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains

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