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A plausible role for the presence of internal shine-dalgarno sites.

Ponnala L - Bioinform Biol Insights (2010)

Bottom Line: In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons.We study this phenomenon in genes of high and low expression separately.Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Service Unit, Cornell University, Ithaca NY USA.

ABSTRACT
The presence of nucleotide hybridization between the 3' end of 16S rRNA and mRNA sequence upstream of the start codon is well known in bacteria. In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons. We study this phenomenon in genes of high and low expression separately. Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.

No MeSH data available.


Examples of SD-like hybridization sites inside coding region of genes in E.coli, illustrating the relationship between nature of complementarity and absolute free-energy values (shown on the right side).
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f2-bbi-2010-055: Examples of SD-like hybridization sites inside coding region of genes in E.coli, illustrating the relationship between nature of complementarity and absolute free-energy values (shown on the right side).

Mentions: We calculated the hybridization free-energy signal for each of these genes based on position-wise incremental alignments between mRNA and the 3′ end of 16S rRNA. We began by aligning the two RNA strands at the position of the start codon, and estimated their hybridization free-energy using a dynamic programming approach as discussed in our earlier work.18 If no hybridization is possible, a value of zero is assigned to the free-energy estimate. Greater complementarity between the two RNA strands in consecutive positions yields higher values of free-energy, as illustrated in Figure 2.


A plausible role for the presence of internal shine-dalgarno sites.

Ponnala L - Bioinform Biol Insights (2010)

Examples of SD-like hybridization sites inside coding region of genes in E.coli, illustrating the relationship between nature of complementarity and absolute free-energy values (shown on the right side).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2901628&req=5

f2-bbi-2010-055: Examples of SD-like hybridization sites inside coding region of genes in E.coli, illustrating the relationship between nature of complementarity and absolute free-energy values (shown on the right side).
Mentions: We calculated the hybridization free-energy signal for each of these genes based on position-wise incremental alignments between mRNA and the 3′ end of 16S rRNA. We began by aligning the two RNA strands at the position of the start codon, and estimated their hybridization free-energy using a dynamic programming approach as discussed in our earlier work.18 If no hybridization is possible, a value of zero is assigned to the free-energy estimate. Greater complementarity between the two RNA strands in consecutive positions yields higher values of free-energy, as illustrated in Figure 2.

Bottom Line: In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons.We study this phenomenon in genes of high and low expression separately.Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Service Unit, Cornell University, Ithaca NY USA.

ABSTRACT
The presence of nucleotide hybridization between the 3' end of 16S rRNA and mRNA sequence upstream of the start codon is well known in bacteria. In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons. We study this phenomenon in genes of high and low expression separately. Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.

No MeSH data available.