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Nucleic Acids Res. 2014 Feb;42(4):2646-59. doi: 10.1093/nar/gkt1139. Epub 2013 Nov 14.

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites.

Author information

1
Department of Chemical Engineering, Penn State University, University Park, PA 16802, USA and Department of Agricultural and Biological Engineering, Penn State University, University Park, PA 16802, USA.

Abstract

The ribosome's interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5' untranslated regions (5' UTRs) are commonly found in bacterial mRNAs, though the physical mechanisms that determine how the ribosome binds these upstream regions remain poorly defined. Here, we systematically investigate the ribosome's interactions with structured standby sites, upstream of Shine-Dalgarno sequences, and show that these interactions can modulate translation initiation rates by over 100-fold. We find that an mRNA's translation initiation rate is controlled by the amount of single-stranded surface area, the partial unfolding of RNA structures to minimize the ribosome's binding free energy penalty, the absence of cooperative binding and the potential for ribosomal sliding. We develop a biophysical model employing thermodynamic first principles and a four-parameter free energy model to accurately predict the ribosome's translation initiation rates for 136 synthetic 5' UTRs with large structures, diverse shapes and multiple standby site modules. The model predicts and experiments confirm that the ribosome can readily bind distant standby site modules that support high translation rates, providing a physical mechanism for observed context effects and long-range post-transcriptional regulation.

PMID:
24234441
PMCID:
PMC3936740
DOI:
10.1093/nar/gkt1139
[Indexed for MEDLINE]
Free PMC Article
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