Abstract
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.
Highlights
Protein synthesis initiates at a “start” codon, typically AUG
If internal SD sequences are depleted because they cause translation problems when they bind to the anti-SD sequence on the 16S ribosomal RNA (rRNA), species lacking the anti-SD sequence should not suffer such depletion
We found little if any specific depletion of SD-like motifs from inside open reading frames
Summary
Protein synthesis initiates at a “start” codon, typically AUG. In random RNA sequence, 1 in 64 triplets is an AUG (considering all three frames). An open reading frame of 1281 nucleotides would contain about 20 AUG triplets, only one of which is the start codon. In prokaryotes, mRNAs are often polycistronic, so that ribosomes have the problem of finding internal start codons as well as the start codon nearest the 5’ end [1].
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