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EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation

Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the de...

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Autores principales: Elgamal, Sara, Katz, Assaf, Hersch, Steven J., Newsom, David, White, Peter, Navarre, William Wiley, Ibba, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140641/
https://www.ncbi.nlm.nih.gov/pubmed/25144653
http://dx.doi.org/10.1371/journal.pgen.1004553
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author Elgamal, Sara
Katz, Assaf
Hersch, Steven J.
Newsom, David
White, Peter
Navarre, William Wiley
Ibba, Michael
author_facet Elgamal, Sara
Katz, Assaf
Hersch, Steven J.
Newsom, David
White, Peter
Navarre, William Wiley
Ibba, Michael
author_sort Elgamal, Sara
collection PubMed
description Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell.
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spelling pubmed-41406412014-08-25 EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation Elgamal, Sara Katz, Assaf Hersch, Steven J. Newsom, David White, Peter Navarre, William Wiley Ibba, Michael PLoS Genet Research Article Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell. Public Library of Science 2014-08-21 /pmc/articles/PMC4140641/ /pubmed/25144653 http://dx.doi.org/10.1371/journal.pgen.1004553 Text en © 2014 Elgamal et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Elgamal, Sara
Katz, Assaf
Hersch, Steven J.
Newsom, David
White, Peter
Navarre, William Wiley
Ibba, Michael
EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title_full EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title_fullStr EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title_full_unstemmed EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title_short EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
title_sort ef-p dependent pauses integrate proximal and distal signals during translation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140641/
https://www.ncbi.nlm.nih.gov/pubmed/25144653
http://dx.doi.org/10.1371/journal.pgen.1004553
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