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.

I. Introduction

In 1974 Shine and Dalgarno [1] sequenced the end of E. coli's 16S ribosomal RNA (rRNA) and observed that part of the sequence, -ACCUCC-, was complementary to a motif, -GGAGGU - , located of the initiation codons in several messenger RNAs (mRNAs). They combined this observation with previously published experimental evidence and suggested that complementarity between the tail of the 16S rRNA and the region of the start codon on the mRNA was sufficient to create a stable, double-stranded structure that could position the ribosome correctly over the start codon during translation initiation. The motif on the mRNAs, -GGAGGU - , and variations on it that are also complementary to parts of the 16S rRNA tail, have since been referred to as Shine-Dalgarno (SD) sequences and their ability to increase the efficiency in translation initiation has been experimentally verified [2]. Thus, an SD sequence is defined by both its ability to hybridize with the rRNA tail and its location relative to the start codon.