![]() did informatic studies on a range of prokaryotes, and, consistent with Li et al, found a slight but statistically significant depletion of SD-like sequences from inside open reading frames. To follow up on this idea, Diwan and Agashe and Yang et al. Thus, one might expect SD-like sequences to be depleted from open reading frames, and, in E. Such internal pauses could be detrimental. This originally suggested that the ribosome pauses at SD-like motifs even inside open reading frames. coli, and saw an enrichment of ribosome footprints that contained SD-like sequences. used ribosome profiling to monitor translation in E. Hybridization between this anti-Shine-Dalgarno (antiSD) in the tail of the 16S rRNA and the Shine-Dalgarno (SD) motif(s) of the mRNA assists in positioning the ribosome at the correct start codon for initiation of translation. submitted), and the 3’ end of many 16S rRNAs contains the sequence CAC CUCCUUA-3’OH, which can hybridize with the SD sequence (bold). The single most common Shine-Dalgarno (SD) sequence is AGGAG (Amin et al. Four to ten bases (optimally, 7 bases, ) 5’ of a start codon, there is often a four to six nucleotide “Shine-Dalgarno” sequence, recognized by a complementary sequence near the 3’ end of the 16S rRNA. One mechanism that aids prokaryotic ribosomes in finding the correct start codon is nucleotide complementarity between the tail of the 16S ribosomal RNA (rRNA) and a region immediately upstream of the start codon. Furthermore, 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. ![]() Thus an open reading frame of 1281 nucleotides would contain about 20 AUG triplets, only one of which is the start codon. However, in random RNA sequence, 1 in 64 triplets is an AUG (considering all three frames). Protein synthesis initiates at a “start” codon, typically AUG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the paper.įunding: This work was supported by NIH grant RO1 GM119175-01 (to BF) and NSF grants DBI-1060572 and DBI-1355990 (to SS). Received: MaAccepted: AugPublished: August 23, 2018Ĭopyright: © 2018 Yurovsky et al. PLoS ONE 13(8):Įditor: Thomas Preiss, John Curtin School of Medical Research, AUSTRALIA 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.Ĭitation: Yurovsky A, Amin MR, Gardin J, Chen Y, Skiena S, Futcher B (2018) Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs. Alternative informatics approaches show that most prokaryotes have only slight, if any, specific depletion of Shine-Dalgarno-like sequences from open reading frames. We suggest previous methods are partly detecting a non-specific depletion of G-rich sequences. Depletion of the same G-rich sequences was seen by these methods even in eukaryotes, which do not use the Shine-Dalgarno mechanism. 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. 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. This may be because hybridization of the 16S rRNA at Shine-Dalgarnos inside genes would slow translation or induce internal initiation. coli) are depleted from open reading frames of most prokaryotes. Shine-Dalgarno-like motifs ( AGGAGG in E. 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. The Shine-Dalgarno motif occurs in front of prokaryotic start codons, and is complementary to the 3’ end of the 16S ribosomal RNA.
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