Within-gene shine-dalgarno sequences are not selected for function

Adam J. Hockenberry*, Michael C. Jewett, Luıs A.N. Amaral, Claus O. Wilke

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


The Shine-Dalgarno (SD) sequence motif facilitates translation initiation and is frequently found upstream of bacterial start codons. However, thousands of instances of this motif occur throughout the middle of protein coding genes in a typical bacterial genome. Here, we use comparative evolutionary analysis to test whether SD sequences located within genes are functionally constrained. We measure the conservation of SD sequences across Enterobacteriales, and find that they are significantly less conserved than expected. Further, the strongest SD sequences are the least conserved whereas we find evidence of conservation for the weakest possible SD sequences given amino acid constraints. Our findings indicate that most SD sequences within genes are likely to be deleterious and removed via selection. To illustrate the origin of these deleterious costs, we show that ATG start codons are significantly depleted downstream of SD sequences within genes, highlighting the constraint that these sequences impose on the surrounding nucleotides to minimize the potential for erroneous translation initiation.

Original languageEnglish (US)
Pages (from-to)2487-2498
Number of pages12
JournalMolecular biology and evolution
Issue number10
StatePublished - Oct 1 2018


  • Sequence conservation
  • Translation initiation
  • Translational control
  • Translational regulation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


Dive into the research topics of 'Within-gene shine-dalgarno sequences are not selected for function'. Together they form a unique fingerprint.

Cite this