@article{Hockenberry2018,
title={Within-gene Shine–Dalgarno sequences are not selected for function},
author={Hockenberry AJ,  
Jewett MC,
Amaral LAN,
Wilke CO},
abstract={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.},
journal={Molecular Biology and Evolution},
volume={35},
doi={10.1093/molbev/msy150},
year={2018},
month={AUG},
day={1},
pages={2487--2498},
}