Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs.

PLoS One 2018 23;13(8):e0202768. Epub 2018 Aug 23.

Dept. of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York City, New York, United States of America.

The Shine-Dalgarno motif occurs in front of prokaryotic start codons, and is complementary to the 3' end of the 16S ribosomal RNA. Hybridization between the Shine-Dalgarno sequence and the anti-Shine-Dalgarno region of the16S rRNA (CCUCCU) directs the ribosome to the start AUG of the mRNA for translation. Shine-Dalgarno-like motifs (AGGAGG in E. coli) are depleted from open reading frames of most prokaryotes. This may be because hybridization of the 16S rRNA at Shine-Dalgarnos inside genes would slow translation or induce internal initiation. However, we analyzed 128 species from diverse phyla where the 16S rRNA gene(s) lack the anti-Shine-Dalgarno sequence, and so the 16S rRNA is incapable of interacting with Shine-Dalgarno-like sequences. Despite this lack of an anti-Shine-Dalgarno, half of these species still displayed depletion of Shine-Dalgarno-like sequences when analyzed by previous methods. Depletion of the same G-rich sequences was seen by these methods even in eukaryotes, which do not use the Shine-Dalgarno mechanism. We suggest previous methods are partly detecting a non-specific depletion of G-rich sequences. Alternative informatics approaches show that most prokaryotes have only slight, if any, specific depletion of Shine-Dalgarno-like sequences from open reading frames. Together with recent evidence that ribosomes do not pause at ORF-internal Shine-Dalgarno motifs, these results suggest the presence of ORF-internal Shine-Dalgarno-like motifs may be inconsequential, perhaps because internal regions of prokaryotic mRNAs may be structurally "shielded" from translation initiation.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202768PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107199PMC
February 2019
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References

(Supplied by CrossRef)
Anatomy of Escherichia coli ribosome binding sites
RK Shultzaberger et al.
J Mol Biol 2001
Depletion of Shine-Dalgarno Sequences within Bacterial Coding Regions Is Expression Dependent
C Yang et al.
G3 (Bethesda) 2016

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