Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility.

ABSTRACT: RNA secondary structure around translation initiation sites strongly affects the abundance of expressed proteins in Escherichia coli. However, detailed secondary structural features governing protein abundance remain elusive. Recent advances in high-throughput DNA synthesis and experimental systems enable us to obtain large amounts of data. Here, we evaluated six types of structural features using two large-scale datasets. We found that accessibility, which is the probability that a given region around the start codon has no base-paired nucleotides, showed the highest correlation with protein abundance in both datasets. Accessibility showed a significantly higher correlation (Spearman's ρ = 0.709) than the widely used minimum free energy (0.554) in one of the datasets. Interestingly, acces

SUBMITTER: Terai G 

PROVIDER: S-EPMC7641306 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature