Elongation factor P is required to maintain proteome homeostasis at high growth rate

Tollerson, Rodney; Witzky, Anne; Ibba, Michael

doi:10.1073/pnas.1812025115

Cited by 33 publications

(22 citation statements)

References 42 publications

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“…Because suppressors were directly associated with translation initiation, we first grew cells at 25°C ( Fig. S4G ), which is known to decrease the translation initiation rate ( 45 ), and we found that growth at 25°C decreased both translation initiation and elongation rates. The initiation rate (0.02 sites s −1 ) and elongation rate (6 aa s −1 ) of SRP − cells grown at 25°C were reduced by 1.5 times relative to those of cells grown at 37°C ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate

Zhao

Cui

et al. 2021

mBio

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The signal recognition particle (SRP) is conserved in all living organisms, and it cotranslationally delivers proteins to the inner membrane or endoplasmic reticulum. Recently, SRP loss was found not to be lethal in either the eukaryote Saccharomyces cerevisiae or the prokaryote Streptococcus mutans. In Escherichia coli, the role of SRP in mediating inner membrane protein (IMP) targeting has long been studied. However, the essentiality of SRP remains a controversial topic, partly hindered by the lack of strains in which SRP is completely absent. Here we show that the SRP was nonessential in E. coli by suppressor screening. We identified two classes of extragenic suppressors—two translation initiation factors and a ribosomal protein—all of which are involved in translation initiation. The translation rate and inner membrane proteomic analyses were combined to define the mechanism that compensates for the lack of SRP. The primary factor that contributes to the efficiency of IMP targeting is the extension of the time window for targeting by pausing the initiation of translation, which further reduces translation initiation and elongation rates. Furthermore, we found that easily predictable features in the nascent chain determine the specificity of protein targeting. Our results show why the loss of the SRP pathway does not lead to lethality. We report a new paradigm in which the time delay in translation initiation is beneficial during protein targeting in the absence of SRP. IMPORTANCE Inner membrane proteins (IMPs) are cotranslationally inserted into the inner membrane or endoplasmic reticulum by the signal recognition particle (SRP). Generally, the deletion of SRP can result in protein targeting defects in Escherichia coli. Suppressor screening for loss of SRP reveals that pausing at the translation start site is likely to be critical in allowing IMP targeting and avoiding aggregation. In this work, we found for the first time that SRP is nonessential in E. coli. The time delay in initiation is different from the previous mechanism that only slows down the elongation rate. It not only maximizes the opportunity for untranslated ribosomes to be near the inner membrane but also extends the time window for targeting translating ribosomes by decreasing the speed of translation. We anticipate that our work will be a starting point for a more delicate regulatory mechanism of protein targeting.

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Section: Resultsmentioning

confidence: 99%

Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate

Zhao

Cui

et al. 2021

mBio

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“…To be sure, introducing proline residues in the polypeptide chain slows down translation so much that it becomes difficult or even impossible for runs of proline residues. In the early times of the origin of translation, evolution has selected a specific factor to alleviate this limitation, translation elongation factor EIF5A/EF‐P (Woolstenhulme et al , 2015; Tollerson et al , 2018). Strikingly, this factor is also important for synthesis of a variety of initiator peptides in Bacteria (Aoki et al , 1997; Katoh et al , 2016), implying that the formylation step is a latecomer that has emerged once this essential compensatory process had evolved so as to accommodate proline in polypeptides.…”

Section: The Formylation Of Methionine‐loaded Initiator Trna Its Rolmentioning

confidence: 99%

One‐carbon metabolism, folate, zinc and translation

Danchin

Sekowska

You

2020

Microbial Biotechnology

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The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells.Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.

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“…Given this apparent slowdown at proline codons, we examined if genes involved in proline biosynthesis had altered expression levels. However, the three enzymes directly involved in proline biosynthesis -proA, proB, and proC, the proline tRNA ligase -proS, and elongation factor P involved in alleviating ribosome pausing at polyproline motif 40 , were not significantly altered in any of the lines (Fig. S8B).…”

Section: Transcriptional Changes Drive Translational Changesmentioning

confidence: 98%

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

Favate

Liang

Yadavalli

et al. 2021

Preprint

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Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here we use the E. coli long-term evolution experiment (LTEE) as a model to address this challenge. To bridge the gap between disparate genomic changes and parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 11 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar to each other in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the bulk of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes, thereby linking genomic changes to parallel fitness gains in the LTEE. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.

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Elongation factor P is required to maintain proteome homeostasis at high growth rate

Cited by 33 publications

References 42 publications

Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate

Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate

One‐carbon metabolism, folate, zinc and translation

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

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