Ribosome A and P sites revealed by length analysis of ribosome profiling data.
Bottom Line: Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths.Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations.We also show that GC-rich motifs at the 5' ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing.
Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.Show MeSH
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Mentions: Curiously, a similar analysis of E. coli data does not reveal this trend. We find that, overall, proline frequencies in ribosome footprints, at any position and of any length, are similar to those in the mRNA background (Figure 4), suggesting either that proline incorporation in E. coli is not slow or that averaging all footprints together might mask the effect. We posited that individual E. coli genes, containing long proline repeats, do experience ribosome pauses. For example, the E. coli gene amiB has the longest stretch of consecutive proline codons (eight). Contrary to the absence of observed pausing for individual prolines, we do find that repeat prolines coincide with a dramatic ribosome pause (Figure 5), suggesting that, at least in extreme situations, prolines can also induce ribosome stalling in E. coli.
Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.