title: Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives.
abstract: Protein translation has been elucidated to be dictated by evolutionary constraints, namely, variations in tRNA availabilities and/or variations in codon-anticodon binding that is manifested in biased codon usage. Taking advantage of publicly available mRNA expression and protein abundance data for Saccharomyces cerevisiae, we have performed a comprehensive analysis of the diverse factors guiding translation leading to desired protein levels irrespective of the corresponding high or low mRNA levels. It has been elucidated in this study that different combinations of most abundant/non abundant tRNA isoacceptors are selected for in S. cerevisiae that helps in achieving the optimum speed and accuracy in the protein translation process. This is also accompanied by the strategic location of codon pairs in coherence to mRNA secondary structure folding stability for the above mentioned combinations of tRNA isoacceptors. We thus find that codon pair contextual effects; in addition to tRNA abundance and mRNA folding stability during translation elongation process play plausible roles in maintaining translation accuracy and speed that can achieve desired protein levels.
authors.affiliation: Bioinformatics Centre, Bose Institute, C.I.T. Scheme VII M, Kolkata, India. bratati@bic.boseinst.ernet.in
authors.forename: Bratati
authors.initials: B
authors.lastname: Kahali
authors.forename: Shandar
authors.initials: S
authors.lastname: Ahmad
authors.forename: Tapash Chandra
authors.initials: TC
authors.lastname: Ghosh
mesh_terms: D003062:Codon; D015870:Gene Expression; D005800:Genes, Fungal; D008968:Molecular Conformation; D015394:Molecular Structure; D014176:Protein Biosynthesis; D020871:RNA Stability; D012343:RNA, Transfer / Q000032:analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D003062:Codon; D012343:RNA, Transfer