Analysis of SD sequences in completed microbial genomes: Non-SD-led genes are as common as SD-led genes

Shine–Dalgarno (SD) sequence has been considered as one of the common features of 5′ end untranslated region (5′UTR) of prokaryotic transcripts. However, more leaderless bacteria and archaea mRNAs are being increasingly reported in recent years. To understand the distribution of SD-led genes and non-SD-led genes, we have analyzed 162 completed prokaryotic genomes leading to various new conclusions and validations of previous smaller scale studies. The fact that the number of the SD-led genes among those genomes varies from 11.6% to 90.8% implies that the populations of non-SD-led genes as well as leaderless genes are significant. We found that there is a strong SD conserved region in genomes with high proportion of SD-led genes. Following a t-test we showed that SD sequence content (SDSC) has no correlation with GC content. We observed that the closely related phylogenetic microbes mostly possess a similar SDSC value, and archaeal nonleading genes possess higher SDSC. This study shows that the 5′UTR of prokaryotic genes are highly diverse, particularly when genomes of distantly related organisms are compared, suggesting that more flexible mechanisms are used for translation initiation process in various prokaryotes.