Format

Send to

Choose Destination
Elife. 2016 Sep 20;5. pii: e13479. doi: 10.7554/eLife.13479.

Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.

Umu SU1,2, Poole AM1,2, Dobson RC1,2,3, Gardner PP1,2,4.

Author information

1
School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
2
Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
3
Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia.
4
BioProtection Research Centre, University of Canterbury, Christchurch, New Zealand.

Abstract

A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.

KEYWORDS:

Archaea; E. coli; bacteria; bioinformatics; computational biology; evolutionary biology; gene expression; genomics; ncRNA; systems biology

PMID:
27642845
PMCID:
PMC5028192
DOI:
10.7554/eLife.13479
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for eLife Sciences Publications, Ltd Icon for PubMed Central
Loading ...
Support Center