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

Overview of attention for article published in PLoS ONE, August 2018
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  • Above-average Attention Score compared to outputs of the same age (61st percentile)
  • Above-average Attention Score compared to outputs of the same age and source (56th percentile)

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25 Mendeley
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Title
Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs
Published in
PLoS ONE, August 2018
DOI 10.1371/journal.pone.0202768
Pubmed ID
Authors

Alisa Yurovsky, Mohammad Ruhul Amin, Justin Gardin, Yuping Chen, Steve Skiena, Bruce Futcher

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.

Twitter Demographics

The data shown below were collected from the profiles of 5 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 25 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 25 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 12 48%
Student > Ph. D. Student 4 16%
Researcher 3 12%
Professor 1 4%
Student > Doctoral Student 1 4%
Other 1 4%
Unknown 3 12%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 13 52%
Agricultural and Biological Sciences 2 8%
Immunology and Microbiology 2 8%
Business, Management and Accounting 1 4%
Chemical Engineering 1 4%
Other 3 12%
Unknown 3 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 August 2018.
All research outputs
#4,115,078
of 13,804,624 outputs
Outputs from PLoS ONE
#52,550
of 145,696 outputs
Outputs of similar age
#102,401
of 270,716 outputs
Outputs of similar age from PLoS ONE
#771
of 1,787 outputs
Altmetric has tracked 13,804,624 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 145,696 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 12.3. This one has gotten more attention than average, scoring higher than 63% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 270,716 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 61% of its contemporaries.
We're also able to compare this research output to 1,787 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.