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

Abstract

BackgroundThere 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.ResultsTo 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 as a measure of translation efficiency at gene level. On the other hand, the RP data showed that codon-specific ribosome density at the decoding site negatively correlated with codon usage, consistent with the hypothesis that preferred codons display lower ribosome densities due to their faster decoding rate. However, highly codon-adapted genes showed higher ribosome densities at the gene level, indicating that the efficiency of translation initiation, rather than higher elongation efficiency of preferred codons, exerted a greater effect on ribosome density and thus translation efficiency.ConclusionsThese findings indicate that evolutionary pressure on highly expressed genes influenced both codon bias and translation initiation efficiency and therefore explains contradictory findings that codon usage bias correlates with translation efficiency of native genes, but not with the artificially created gene pool, which was not subjected to evolution pressure.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1115) contains supplementary material, which is available to authorized users.

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

“…These pauses are strikingly similar to those observed when chloramphenicol is added to a culture to arrest translation prior to harvesting the cells (Figure 4E). As shown previously by Mori and co-workers, chloramphenicol arrests ribosomes in a sequence-specific manner, pausing ribosomes when the same five amino acids are encoded in the E site (Nakahigashi et al, 2014). This sequence specificity was also observed by Mankin and co-workers, who detected pauses with Gly, Ser, Ala, and Thr codons in the E site using toeprinting assays, but only in the presence of chloramphenicol (Orelle et al, 2013).…”

“…Earlier studies distributed information about the position of the ribosome over multiple nucleotides at the center of reads, blurring the signal (Li et al, 2012; Oh et al, 2011). We and others found that by assigning ribosome occupancy to the 3’-end of the reads, we obtain a more precise measurement of ribosome position (Balakrishnan et al, 2014; Nakahigashi et al, 2014; Woolstenhulme et al, 2015). With this higher resolution, we see that the previously observed enrichment of ribosome occupancy at SD motifs can explained by pauses at Gly codons and by failure to isolate the entire population of ribosome-protected mRNA fragments.…”

Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center

“…Because CHL has been traditionally viewed as a universal inhibitor of peptide bond formation, it has been used to "freeze" the ribosomes on mRNA in some profiling experiments (30,35), an approach challenged by several studies where trends similar to the ones we presented here were noted (29,31,36,37). We show that exposure of the cells to high concentrations of CHL (or LZD) does not in fact freeze the ribosomes on mRNA, but allows them to redistribute from the sites less favorable for the drug-dependent arrest to the downstream strong-arrest codons.…”

Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing

“…complexes, biased conversion of the mRNA fragments into complementary DNAs, and procedures for aligning the ribosomeprotected base sequences (9,(22)(23)(24)(25)(26)(27)(28)(29)(30)(31). These considerations underscore the importance of profiling the translation progression directly.…”