Abstract
Background In prokaryotes, the Shine-Dalgarno (SD) sequence in the 5’ untranslated region (UTR) of mRNA forms a duplex with the anti-Shine-Dalgarno (anti-SD) sequence to initiate translation [1]. The mechanism has been regarded as universal, as the core of the anti-SD sequence (5’-CCTCC3’, anti-SD motif) is completely conserved in every prokaryote genome according to previous reports [2]. Recent accelerated accumulation of complete genomic sequences motivated us to conduct an updated screening for anti-SD sequence variants.
Highlights
In prokaryotes, the Shine-Dalgarno (SD) sequence in the 5’ untranslated region (UTR) of mRNA forms a duplex with the anti-Shine-Dalgarno sequence to initiate translation [1]
Loss of the anti-SD motif in these ‘non-anti-SD’ genomes is always accompanied by loss of SD-like sequences in 5’ UTR
* Correspondence: ikobaya@ims.u-tokyo.ac.jp 1Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan Full list of author information is available at the end of the article
Summary
The Shine-Dalgarno (SD) sequence in the 5’ untranslated region (UTR) of mRNA forms a duplex with the anti-Shine-Dalgarno (anti-SD) sequence to initiate translation [1]. Results By comparison analysis of 1,182 completely sequenced eubacterial genomes, we found fifteen genomes in which no 16S rRNA genes carry the anti-SD motif. Loss of the anti-SD motif in these ‘non-anti-SD’ genomes is always accompanied by loss of SD-like sequences in 5’ UTR.
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