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Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
2014 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 289, no 44, 30334-30342 p.Article in journal (Refereed) Published
Abstract [en]

We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million coding sequences of 4684 bacterial sequences. Using a newly developed program called "stop codon counter," the frequencies of the three classical stop codons TAA, TAG, and TGA were analyzed, and a publicly available stop codon database was built. Our analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and that of the TGA codon increases in a reciprocal manner. Interestingly, the release factor 1-specific codon TAG maintains a more or less uniform frequency (similar to 20%) irrespective of the GC content. The low abundance of TAG is also valid with respect to expression level of the genes ending with different stop codons. In contrast, the highly expressed genes predominantly end with TAA, ensuring termination with either of the two release factors. Using three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis, and Bacillus subtilis), we show that the frequency of TAG and TGA codons correlates well with the relative steady state amount of mRNA and protein for release factors RF1 and RF2 during exponential growth. Furthermore, using available microarray data for gene expression, we show that in both fast growing and contrasting biofilm formation conditions, the relative level of RF1 is nicely correlated with the expression level of the genes ending with TAG.

Place, publisher, year, edition, pages
2014. Vol. 289, no 44, 30334-30342 p.
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Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-239577DOI: 10.1074/jbc.M114.606632ISI: 000344549700016PubMedID: 25217634OAI: oai:DiVA.org:uu-239577DiVA: diva2:775120
Available from: 2014-12-30 Created: 2014-12-29 Last updated: 2017-12-05Bibliographically approved

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Korkmaz, GürkanHolm, MikaelSanyal, Suparna

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Korkmaz, G. (2014). Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance. .

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