Base Pairing between Ribosomal RNA and Messenger
Ribosomes must recognize the start codons AUG or GUG on the mes-senger RNA to initiate protein synthesis. Characterization of the pro-teins that are synthesized when the lac operon or other operons are induced show that normally only one AUG or GUG of a gene is utilized to initiate protein synthesis. Many of the internal AUG or GUG codons are not used to initiate protein synthesis. This means that something in addition to the initiating codon itself must signal the point at which translation begins.
Studies of bacterial translation show that the first step in initiation is the binding of messenger to the smaller of the two ribosomal subunits, the 30S subunit. The absence of a strictly conserved sequence preceding start codons suggested that whatever first bound the messenger to the 30S subunit might be an RNA-RNA interaction between mRNA and ribosomal RNA. The originators of this idea, Shine and Dalgarno, were so confident of their proposal that they proceeded to sequence the 3’ end of the 16S rRNA which is found in the smaller ribosomal subunit. They found that the rRNA sequence provided strong support for their idea. The sequence on mRNA which binds to the 16S ribosomal RNA is called the Shine-Dalgarno sequence or the ribosome binding site.
Bacterial messengers contain a ribosome-binding sequence slightly ahead of an initiating AUG. This sequence base pairs well with a region
near the 3’ end of the 16S ribosomal RNA. This upstream region has been examined in more than hundreds of messenger start sequences. Typically it is three or four bases and is centered about ten nucleotides ahead of the start codon. Despite the data to be described below, the ribosome-binding sequence lying ahead of the AUG initiation codon is not the whole story. Undoubtedly, secondary structure in the mRNA also can alter translation efficiency. Occasionally, a sequence upstream or downstream from the Shine-Dalgarno sequence pairs with it and blocks translation initiation. Examination of the sequence in the vicinity of the AUG and ribosome-binding sequence has shown the existence of preferences for some nucleotides. Were no other factors involved, the identity of all these other nucleotides would be random.