title: 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.
authors.affiliation: Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States.
authors.forename: Justin
authors.initials: J
authors.lastname: Gardin
authors.affiliation: Department of Computer Science, Stony Brook University, Stony Brook, United States.
authors.forename: Rukhsana
authors.initials: R
authors.lastname: Yeasmin
authors.affiliation: Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States.
authors.forename: Alisa
authors.initials: A
authors.lastname: Yurovsky
authors.affiliation: Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States.
authors.forename: Ying
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Department of Computer Science, Stony Brook University, Stony Brook, United States.
authors.forename: Steve
authors.initials: S
authors.lastname: Skiena
authors.affiliation: Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, United States.
authors.forename: Bruce
authors.initials: B
authors.lastname: Futcher
mesh_terms: D000465:Algorithms; D000841:Anisomycin / Q000494:pharmacology; D003062:Codon / Q000235:genetics*; D004151:Dipeptides / Q000378:metabolism; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics; D015203:Reproducibility of Results; D012270:Ribosomes / Q000187:drug effects / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics; D012694:Serine / Q000172:deficiency; D013997:Time Factors
chemical_list: D003062:Codon; D004151:Dipeptides; D012694:Serine; D000841:Anisomycin
keywords: S. cerevisiae; biochemistry; codon bias; codon usage; decoding; evolutionary biology; genomics; ribosome; synonymous codons; translation