Robustness by intrinsically disordered C-termini and translational readthrough

Kleppe, April Snøfrid; Bornberg‐Bauer, Erich

doi:10.1093/nar/gkz1106

Cited by 10 publications

(19 citation statements)

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“…However, similar genomic analyses and profiling studies of human genes have so far found only a few candidate genes (44,56,57). Computational analysis of readthrough protein isoforms suggests that these are mostly long, modular proteins with intrinsically disordered C-termini of low sequence complexity (58,59). The lack of a structurally ordered C-terminus might provide conformational flexibility that allows the readthrough extensions to perform functions without distorting the native protein.…”

Section: Translational Readthroughmentioning

confidence: 99%

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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Section: Translational Readthroughmentioning

confidence: 99%

Translational recoding: canonical translation mechanisms reinterpreted

Rodnina

Korniy

Klimova

et al. 2019

Nucleic Acids Research

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“…Previously, we have investigated TR in yeast, to identify protein features 52 that correlate with TR-rate. We identified high gene expression to be the most 53 prevalent feature, next to highly disordered C-termini [9]. However, whether these 54 features are a consistent trait in the presence of TR, remains untested.…”

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confidence: 89%

“…77 For S.pombe, there were 240 identified leaky proteins, and 2830 non-leaky proteins. We 78 compared our sets to the data from our previous inference of TR in S.cerevisiae [9]. We 79 found an overlap of 30 proteins between the leaky sets.…”

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confidence: 96%

“…Proteins that undergo canonical translation, we clustered as 74 the non-leaky set. The clustering of leaky and non-leaky sets were conducted 75 individually for each investigated species, as in [9] and is described in detail in Materials 76 and Methods. We found 80 leaky proteins and 3200 non-leaky proteins for S.cerevisiae.…”

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confidence: 99%

“…These 155 results begs the question if and how the GC-content of the 3'-UTR is associated to TR. 156 The connection between expression and GC-content could be indication of mRNA 157 stability, which was previously explored in the context of TR, but without 158 verification [9].…”

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confidence: 99%

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Translational readthrough goes unseen by natural selection

Kleppe

Bornberg‐Bauer

2019

Preprint

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Occasionally during protein synthesis, the ribosome bypasses the stop codon and continues translation to the next stop codon in frame. This error is called translational readthrough (TR). Earlier research suggest that TR is a relatively common error, in several taxa, yet the evolutionary relevance of this translational error is still unclear. By analysing ribosome profiling data, we have conducted species comparisons between yeasts to infer conservation of TR between orthologs. Moreover, we infer the evolutionary rate of error prone and canonically translated proteins to deduct differential selective pressure. We find that about 40% of error prone proteins in Schizosaccharomyces pombe do not have any orthologs in Saccharomyces cerevisiae, but that 60% of error prone proteins in S. pombe are undergoing canonical translation in S. cerevisiae. Error prone proteins tend to have a higher GC-content in the 3'-UTR, unlike their canonically translated ortholog. We do not find the same trends for GC-content of the CDS. We discuss the role of 3'-UTR and GC-content regarding translational readthrough. Moreover, we find that there is neither selective pressure against or for TR. We suggest that TR is a near-neutral error that goes unseen by natural selection. We speculate that TR yield neutral protein isoforms that are not being purged. We suggest that isoforms, yielded by TR, increase proteomic diversity in the cell, which is readily available upon sudden environmental shifts and which therefore may become adaptive.

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Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

Fonin

Antifeeva

Kuznetsova

et al. 2022

Essays in Biochemistry

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The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid–liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP–LLPS–MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP–LLPS–MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.

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Robustness by intrinsically disordered C-termini and translational readthrough

Cited by 10 publications

References 0 publications

Translational recoding: canonical translation mechanisms reinterpreted

Translational recoding: canonical translation mechanisms reinterpreted

Translational readthrough goes unseen by natural selection

Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

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