Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli

Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli

Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (the correlation in relative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (be...

Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles

Rapid biosynthesis is key to the success of bacteria and viruses. Highly expressed genes in bacteria exhibit a strong codon bias corresponding to the differential availability of tRNAs. However, a large clade of lambdoid coliphages exhibits relatively poor codon adaptation to the host translation machinery, in contrast to other coliphages that exhibit strong codon adaptation to the host. Three ...

The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage

Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes ...

Enzymatic-Like Properties of dsDNA and Its Comparison with ssDNA

Simulations of single grafted polyelectrolyte chains: ssDNA and dsDNA

The structure of a single, grafted polyelectrolyte, DNA, is investigated by molecular dynamics simulations. The polyelectrolyte is treated as a bead–spring model with explicit charges using parametrizations of both flexible ~ssDNA! and stiff ~dsDNA! polyelectrolytes. In this single chain limit with no added salt, the flexible ssDNA is always highly extended. Counterion condensation on both mole...