Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

Pechmann, Sebastian; Chartron, J.W.; Frydman, Judith

doi:10.1038/nsmb.2919

Cited by 209 publications

(210 citation statements)

References 57 publications

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“…Recent analyses of ribosome profiling data have revealed mRNA-programmed ribosome pauses that enhance SRP binding and faithful membrane integration (39,40). In yeast, these events are mediated by rare codons, whereas in Escherichia coli they are mediated by ORF-internal Shine-Dalgarno elements.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

Zoschke

Barkan

2015

Proc. Natl. Acad. Sci. U.S.A.

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Chloroplast genomes encode ∼37 proteins that integrate into the thylakoid membrane. The mechanisms that target these proteins to the membrane are largely unexplored. We used ribosome profiling to provide a comprehensive, high-resolution map of ribosome positions on chloroplast mRNAs in separated membrane and soluble fractions in maize seedlings. The results show that translation invariably initiates off the thylakoid membrane and that ribosomes synthesizing a subset of membrane proteins subsequently become attached to the membrane in a nucleaseresistant fashion. The transition from soluble to membraneattached ribosomes occurs shortly after the first transmembrane segment in the nascent peptide has emerged from the ribosome. Membrane proteins whose translation terminates before emergence of a transmembrane segment are translated in the stroma and targeted to the membrane posttranslationally. These results indicate that the first transmembrane segment generally comprises the signal that links ribosomes to thylakoid membranes for cotranslational integration. The sole exception is cytochrome f, whose cleavable N-terminal cpSecA-dependent signal sequence engages the thylakoid membrane cotranslationally. The distinct behavior of ribosomes synthesizing the inner envelope protein CemA indicates that sorting signals for the thylakoid and envelope membranes are distinguished cotranslationally. In addition, the fractionation behavior of ribosomes in polycistronic transcription units encoding both membrane and soluble proteins adds to the evidence that the removal of upstream ORFs by RNA processing is not typically required for the translation of internal genes in polycistronic chloroplast mRNAs.ribosome profiling | protein targeting | plastid | chloroplast | SecA

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

Zoschke

Barkan

2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Therefore, this impairment is a striking example in which preceding translational pausing is necessary for the recognition of the ER-targeting signal by SRP. Similarly, Frydman and coworkers (35) recently reported that SRP preferentially recognizes a set of proteins harboring a signal sequence with a downstream cluster of suboptimal codons, which slows translational elongation. Further, Weissman and coworkers (36) showed that artificial translational arrest by cycloheximide treatment enables the ER localization of a subset of cytosolic mRNAs encoding the proteins harboring a first transmembrane segment or a signal sequence in the C-terminal region (from 50 to 150 codons before the termination codons).…”

Section: Discussionmentioning

confidence: 99%

“…The coimmunoprecipitated proteins were eluted by incubation in 2× sample buffer [125 mM Tris·HCl (pH 6.8), 4% SDS, and 15% sucrose] containing 50 mM DTT and analyzed by Western blotting. For immunoprecipitation of in vitrotranslated product, proteins were synthesized by in vitro translation with rabbit reticulocyte lysate (RRL) in the presence of 35 S-labeled methionine and cysteine using EXPRE 35 S 35 S Protein Labeling Mix (PerkinElmer) (Fig. 2E and Fig.…”

Section: Methodsmentioning

confidence: 99%

Autonomous translational pausing is required for XBP1u mRNA recruitment to the ER via the SRP pathway

Kanda

Yanagitani

Yokota

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Unconventional mRNA splicing on the endoplasmic reticulum (ER) membrane is the sole conserved mechanism in eukaryotes to transmit information regarding misfolded protein accumulation to the nucleus to activate the stress response. In metazoans, the unspliced form of X-box-binding protein 1 (XBP1u) mRNA is recruited to membranes as a ribosome nascent chain (RNC) complex for efficient splicing. We previously reported that both hydrophobic (HR2) and translational pausing regions of XBP1u are important for the recruitment of its own mRNA to membranes. However, its precise location and the molecular mechanism of translocation are unclear. We show that XBP1u-RNC is specifically recruited to the ER membrane in an HR2-and translational pausing-dependent manner by immunostaining, fluorescent recovery after photobleaching, and biochemical analyses. Notably, translational pausing during XBP1u synthesis is indispensable for the recognition of HR2 by the signal recognition particle (SRP), resulting in efficient ER-specific targeting of the complex, similar to secretory protein targeting to the ER. On the ER, the XBP1u nascent chain is transferred from the SRP to the translocon; however, it cannot pass through the translocon or insert into the membrane. Therefore, our results support a noncanonical mechanism by which mRNA substrates are recruited to the ER for unconventional splicing. and subsequent protein folding are associated with a number of diseases. Accordingly, a detailed understanding of the mechanisms that mediate these complex processes is necessary. In eukaryotes, secretory proteins are initially translated by cytosolic ribosomes. When the N-terminal signal peptide reaches outside of the peptide exit channel in the ribosome, the ribosome nascent chain (RNC) complex is recognized by the signal recognition particle (SRP) and peptide elongation is slowed (1-5). This SRP-RNC complex is then recruited to the ER via the affinity between SRP and SRP receptor (SR) that exists in the ER membrane (2, 3). The RNC complex is then delivered to the polypeptide channel in the ER (i.e., the Sec61 translocon) (6). SRP is released from the RNC, which cancels the slowed-down elongation. As a result, the ER-targeted ribosome cotranslationally translocates its synthesizing polypeptide into the luminal space of the ER. The translocated protein is folded into its native 3D structure with the help of molecular chaperones and folding enzymes (7). The folded proteins are sorted to their final destinations to exert their functions.The burden of new proteins entering the ER varies widely among conditions, such as cell differentiation, environmental conditions, and the physiological state of the cell (8, 9). In addition, the folding capacity in the ER is easily compromised by many stressful conditions, including glucose starvation, virus infection, and perturbations in the Ca 2+ concentration. Therefore, it is necessary for cells to manage the imbalance between the load of newly entering proteins and the folding capacity in the ER, and this i...

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“…Two recent studies using Neurospora and Synechococcus elongate reported that rare codons present in circadian genes play a critical role in maintaining the circadian rhythm (Xu et al 2013;Zhou et al 2013). In yeast cells, genes encoding membrane and secretory proteins are enriched with rare codons at positions critical for SRP recognition (Pechmann et al 2014). All these phenomena rely on rare codon-mediated translation slowdown that potentially influences co-translational folding (Yu et al 2015).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, non-optimal codons are postulated to slow down translation elongation. By tuning the elongation rate, codon usage bias has been reported to influence the behavior of nascent chains, including cotranslational folding as well as interaction with the signal recognition particle (SRP) (Pechmann et al 2014;Yu et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Codon optimality controls differential mRNA translation during amino acid starvation

Saikia

Wang

Mao

et al. 2016

RNA

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It is common wisdom that codon usage bias has evolved in the selection for efficient translation, in which highly expressed genes are encoded predominantly by optimal codons. However, a growing body of evidence suggests regulatory roles for non-optimal codons in translation dynamics. Here we report that in mammalian cells, non-optimal codons play a critical role in promoting selective mRNA translation during amino acid starvation. During starvation, in contrast to genes encoding ribosomal proteins whose translation is highly sensitive to amino acid deprivation, translation of genes involved in the cellular protein degradation pathways remains unaffected. We found that these two gene groups bear different codon composition, with non-optimal codons being highly enriched in genes encoding the ubiquitin-proteasome system. Supporting the selective tRNA charging model originally proposed in Escherichia coli, we demonstrated that tRNA isoacceptors decoding rare codons are maintained in translating ribosomes under amino acid starvation. Finally, using luciferase reporters fused with endogenous gene-derived sequences, we show that codon optimality contributes to differential mRNA translation in response to amino acid starvation. These results highlight the physiological significance of codon usage bias in cellular adaptation to stress.

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Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

Cited by 209 publications

References 57 publications

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

Autonomous translational pausing is required for XBP1u mRNA recruitment to the ER via the SRP pathway

Codon optimality controls differential mRNA translation during amino acid starvation

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