generic algorithm to predict the speed of translational elongation implications for protein biogenesis泛型算法预测的速度转化对蛋白质生物起源伸长的影响.pdfVIP

Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis Gong Zhang, Zoya Ignatova* Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany Abstract Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions. Citation: Zhang G, Ignatova Z (2009) Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis. PLoS ONE 4(4): e5036. doi:10.1371/journal.pone.0005036 Editor: Alexander Idnurm, University of Missouri-Kansas City, United States of America Received January 11, 2009; Accepted March 3, 2009; Published April 3, 2009 Copyright: 2009 Zhang et al. This is an open-access article distributed u