ArticleBMC genomics2009
Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 10 citations in OpenAlex.
- Rapid monitoring of the target protein expression with a fluorescent signal based on a dicistronic construct in Escherichia coli.AMB Express · 2018Article
- A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.PloS one · 2015Article
- Haloferax volcanii, a prokaryotic species that does not use the Shine Dalgarno mechanism for translation initiation at 5'-UTRs.PloS one · 2014Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may influence the stop codon usage or the spacing lengths between co-directional genes.
resultsThe SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large number of genes with the SD sequence concentrate this regulatory motif from 4 to 11 bps before the start codon. However, not all genes seem to have the SD sequence. Genes separated from 1 to 4 bps from a co-directional upstream gene show a high SD presence, though this regulatory signal is located towards the 3' end of the coding sequence of the upstream gene. Genes separated from 9 to 15 bps show the highest SD presence as they accommodate the SD sequence within an intergenic region. However, genes separated from around 5 to 8 bps have a lower percentage of SD presence and when the SD is present, the stop codon usage of the upstream gene changes to accommodate the overlap between the SD sequence and the stop codon.
conclusionThe SD presence makes the intergenic lengths from 5 to 8 bps less frequent and causes an adaptation of the stop codon usage. Our results introduce new elements to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes.
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