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

Prabhakaran R, Chithambaram S, Xia X - J. Gen. Virol. (2015)

Bottom Line: Phage genes with strong codon adaptation had significantly stronger SD sequences than those with poor codon adaptation.The former also had significantly weaker secondary structure in sequences flanking the SD sequence and start codon than the latter.Thus, lambdoid phages do not exhibit strong codon adaptation because they have relatively inefficient translation initiation and would benefit little from increased elongation efficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.

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(a) Schematic representation of the SD sequence on mRNA pairing with the aSD sequence on the SSU rRNA. (b–d) The free 3′ end of SSU rRNA (b), the frequency distribution of 4577 putative matches of at least four bases between the rRNA 3′ tail and the upstream 30 nt of coding sequences (c), and the number of times each nucleotide site at the rRNA 3′ tail participated in the SD–aSD matches (d).
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f5: (a) Schematic representation of the SD sequence on mRNA pairing with the aSD sequence on the SSU rRNA. (b–d) The free 3′ end of SSU rRNA (b), the frequency distribution of 4577 putative matches of at least four bases between the rRNA 3′ tail and the upstream 30 nt of coding sequences (c), and the number of times each nucleotide site at the rRNA 3′ tail participated in the SD–aSD matches (d).

Mentions: We also extracted 30 nt upstream of the start codon (Upstream30) from each gene in phage and host genomes, and the last 20 nt of the E. coli small subunit (SSU) rRNA using dambe (Xia, 2013b), to identify SD sequences. As we show below, it is not appropriate to define the SD sequence simply as an AGGAGG motif within a fixed distance range upstream of the start codon. The SD sequence on the mRNA and the aSD sequence on the SSU rRNA pair to position the anticodon of the initiation tRNA at the start codon (Fig. 5a). The optimal location of the SD sequence in the literature is often measured by the distance from the SD sequence to the start codon (e.g. D1 and D2 in Fig. 5a) or from the middle of the SD sequence to the start codon (Osterman et al., 2013). However, this approach is probably incorrect as illustrated in Fig. 5(a). Both SD1 and SD2 position the tRNA anticodon properly at the start codon AUG, but their associated D1 and D2 are different (Fig. 5a). A correct distance measure should take into consideration the relative position of both mRNA and the rRNA 3′ tail. One such distance is the distance from the end of the SSU rRNA to the beginning of the start codon (DtoAUG, Fig. 5a).


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

Prabhakaran R, Chithambaram S, Xia X - J. Gen. Virol. (2015)

(a) Schematic representation of the SD sequence on mRNA pairing with the aSD sequence on the SSU rRNA. (b–d) The free 3′ end of SSU rRNA (b), the frequency distribution of 4577 putative matches of at least four bases between the rRNA 3′ tail and the upstream 30 nt of coding sequences (c), and the number of times each nucleotide site at the rRNA 3′ tail participated in the SD–aSD matches (d).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4631060&req=5

f5: (a) Schematic representation of the SD sequence on mRNA pairing with the aSD sequence on the SSU rRNA. (b–d) The free 3′ end of SSU rRNA (b), the frequency distribution of 4577 putative matches of at least four bases between the rRNA 3′ tail and the upstream 30 nt of coding sequences (c), and the number of times each nucleotide site at the rRNA 3′ tail participated in the SD–aSD matches (d).
Mentions: We also extracted 30 nt upstream of the start codon (Upstream30) from each gene in phage and host genomes, and the last 20 nt of the E. coli small subunit (SSU) rRNA using dambe (Xia, 2013b), to identify SD sequences. As we show below, it is not appropriate to define the SD sequence simply as an AGGAGG motif within a fixed distance range upstream of the start codon. The SD sequence on the mRNA and the aSD sequence on the SSU rRNA pair to position the anticodon of the initiation tRNA at the start codon (Fig. 5a). The optimal location of the SD sequence in the literature is often measured by the distance from the SD sequence to the start codon (e.g. D1 and D2 in Fig. 5a) or from the middle of the SD sequence to the start codon (Osterman et al., 2013). However, this approach is probably incorrect as illustrated in Fig. 5(a). Both SD1 and SD2 position the tRNA anticodon properly at the start codon AUG, but their associated D1 and D2 are different (Fig. 5a). A correct distance measure should take into consideration the relative position of both mRNA and the rRNA 3′ tail. One such distance is the distance from the end of the SSU rRNA to the beginning of the start codon (DtoAUG, Fig. 5a).

Bottom Line: Phage genes with strong codon adaptation had significantly stronger SD sequences than those with poor codon adaptation.The former also had significantly weaker secondary structure in sequences flanking the SD sequence and start codon than the latter.Thus, lambdoid phages do not exhibit strong codon adaptation because they have relatively inefficient translation initiation and would benefit little from increased elongation efficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.

Show MeSH
Related in: MedlinePlus