Searching for ribosome-mRNA hybridization sites

In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis by allowing the two molecules to hybridize and form a double-helix. Many mRNAs, however, lack SD sequences and presumably use another mechanism to recruit ribosomes. We define a hybridization site (HS) as any mRNA sequence that forms as strong a bond to rRNA as a minimal SD sequence. Thus, SD sequences are a class of HSs that occur in a specific region. We scanned the translation initiation regions (TIRs) in 18 prokaryotic genomes and found that only 56% of the TIRs contained SD sequences, and the most stable HSs are not always upstream from start codons. Indeed, we found 2407 genes where the strongest HS in the TIR includes the start codon, deviating from the expected location of 5 to 10 bases upstream. This result suggests an alternative sequence for recruiting ribosomes to mRNAs that has yet to be characterized.