In silico analysis of 5′-UTRs highlights the prevalence of Shine–Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively

• Prokaryotic genes are closely packed and generally have an intergenic length of <40 bp.
• Bacteria mostly contain SD-dependent genes while archaea contains leaderless genes.
• SD-led and leaderless genes show opposite correlation with the genome size.
• Like SD-led genes, leaderless genes also utilize ATG as the most dominant start codon.

In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine–Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5′-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led & leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.