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High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.

ABSTRACT: Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define translational pauses. Here, we report improvements that yield much higher resolution in E. coli profiling data, enabling us to more accurately assess ribosome pausing and refine earlier studies of the impact of polyproline motifs on elongation. We comprehensively characterize pausing at proline-rich motifs in the absence of elongation factor EFP. We find that only a small fraction of genes with strong pausing motifs have reduced ribosome density downstream, and we identify features that explain this phenomenon. These features allow us to predict which proteins likely have reduced output in the efp-knockout strain.

SUBMITTER: Woolstenhulme CJ

PROVIDER: S-EPMC4835038 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.

Woolstenhulme Christopher J CJ Guydosh Nicholas R NR Green Rachel R Buskirk Allen R AR

Cell reports 20150402 1

Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define translational pauses. Here, we report improvements that yield much higher resolution in E. coli profiling data, enabling us to more accurately assess ribosome pausing and refine earlier studies of the impact of polyproline motifs on elongation. We ...[more]

PMID: 25843707

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High Precision Analysis of Translational Pausing in Bacteria Lacking EFP by Ribosome Profiling

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