There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.
Abstract
Comparative analyses of natural and mutated sequences have been used to probe mechanisms
of gene expression, but small sample sizes may produce biased outcomes. We applied
an unbiased design-of-experiments approach to disentangle factors suspected to affect
translation efficiency in E. coli. We precisely designed 244,000 DNA sequences implementing
56 replicates of a full factorial design to evaluate nucleotide, secondary structure,
codon and amino acid properties in combination. For each sequence, we measured reporter
transcript abundance and decay, polysome profiles, protein production and growth rates.
Associations between designed sequences properties and these consequent phenotypes
were dominated by secondary structures and their interactions within transcripts.
We confirmed that transcript structure generally limits translation initiation and
demonstrated its physiological cost using an epigenetic assay. Codon composition has
a sizable impact on translatability, but only in comparatively rare elongation-limited
transcripts. We propose a set of design principles to improve translation efficiency
that would benefit from more accurate prediction of secondary structures in vivo.