Measurement of average decoding rates of the 61 sense codons in vivo

Abstract

Most amino acids can be encoded by several synonymous codons, which are used at unequal frequencies. The significance of unequal codon usage remains unclear. One hypothesis is that frequent codons are translated relatively rapidly. However, there is little direct, in vivo, evidence regarding codon-specific translation rates. In this study, we generate high-coverage data using ribosome profiling in yeast, analyze using a novel algorithm, and deduce events at the A- and P-sites of the ribosome. Different codons are decoded at different rates in the A-site. In general, frequent codons are decoded more quickly than rare codons, and AT-rich codons are decoded more quickly than GC-rich codons. At the P-site, proline is slow in forming peptide bonds. We also apply our algorithm to short footprints from a different conformation of the ribosome and find strong amino acid-specific (not codon-specific) effects that may reflect interactions with the exit tunnel of the ribosome.DOI: http://dx.doi.org/10.7554/eLife.03735.001

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

“…Experiments without CHX, on the other hand, report positive correlations of varying magnitude (Fig 1D, 0x Gerashchenko NAR points and purple labels). Experiments by Pop [36], Lareau [26], Nedialkova [29], Guydosh [35] and Gardin [33] produce weak to moderate correlations, but experiments by Gerashchenko [34], Jan [41], Williams [42], Weinberg [38], and Young [37] produce fairly strong and highly statistically significant correlations.…”

“…Experiments performed with this protocol have revealed that treatment with CHX affects several high-level characteristics of footprinting data, including the distribution of lengths of nuclease-protected fragments in mammalian cells [39] and the amount of enrichment in ribosome density at the 5' end of coding sequences in yeast [34]. In contrast to data produced using CHX pretreatment, several studies using this alternative protocol have reported that non-optimal codons are in fact translated more slowly [33,38]. The source of this discrepancy between the statistical properties of measured ribosome positions with and without CHX pretreatment has been unclear, leading to uncertainty as to which measurements correspond to actual properties of in vivo translation dynamics.…”

“…An alternative experimental protocol uses an optimized harvesting and flash-freezing process that allows CHX pretreatment to be omitted [15,17,26,29,[33][34][35][36][37][38]. Experiments performed with this protocol have revealed that treatment with CHX affects several high-level characteristics of footprinting data, including the distribution of lengths of nuclease-protected fragments in mammalian cells [39] and the amount of enrichment in ribosome density at the 5' end of coding sequences in yeast [34].…”

Accurate Prediction of Cellular Co-Translational Folding Indicates Proteins can Switch from Post- to Co-Translational Folding

“…For example, ribosome profiling 20 holds out the promise that it may be possible to directly measure the k A,i values for a transcript [21][22][23][24] . In such a situation, assumption A4 is not necessary.…”

“…Individual codon translation rates in CHO cells, however, have not been measured. There have been at least five different estimates of codon translation rates in other organisms extracted from ribosome profiling data [21][22][23] or calculated from theory 24 . These estimated codon translation rates do not correlate with each other, even when calculated for the same organism ( Supplementary Fig.…”