Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo.

ABSTRACT:

Background

There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there are conflicting reports on the existence of a correlation between codon adaptation and translation efficiency, even in the same organism.

Results

To resolve this issue, we cultured Escherichia coli under conditions designed to maintain constant levels of mRNA and protein and subjected the cells to ribosome profiling (RP) and mRNA-seq analyses. We showed that the RP results correlated more closely with protein levels generated under similar culture conditions than with the mRNA abundance from the mRNA-seq. Our result indicated that RP/mRNA ratio could be used

SUBMITTER: Nakahigashi K 

PROVIDER: S-EPMC4378010 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature