Within-gene Shine–Dalgarno sequences are not selected for function
Hockenberry AJ, Jewett MC, Amaral LAN, Wilke COMolecular Biology and Evolution 35, 2487 - 2498 (2018)
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.