Evolution and the universality of the mechanism of initiation of protein synthesis.

The main mechanisms advanced to account for the specificity of the initiation of protein synthesis are reviewed. A mechanism proposed by Shine and Dalgarno (SD), focused on the base pairing of a unique leader sequence in the initiation site--the SD sequence--with the 3' end of the 30S ribosomal RNA as the only step necessary for selecting the initiation site in prokaryotes. Studies showed, however, that the SD interaction is not obligatory and protein synthesis can occur even in its absence. In fact, comparison of a large number of initiation site sequences revealed that the sites are composed of diverse combinations of preferred bases, and, thus, the apparatus that is able to recognize all these sites is de facto a multisubstrate enzyme system. As such, it has the hallmarks of the cumulative specificity mechanism, and the SD interaction, when present, is only one of a number of contributing factors in the selection of the initiation site. The cumulative specificity mechanism proposed that secondary structure selectively interdicts access to most of the non-initiator methionine codons while leaving open the true initiation site and that the final recognition of the initiation site occurs by cooperativity and cumulative specificity of the several ligand recognition sites of the ribosomes, which confer broad substrate specificity to the system. This mechanism appears to be universal; it can encompass the initiation of all protein syntheses since it is consistent with all the salient observations on the initiation of both eukaryotic and prokaryotic protein syntheses. Studies of eukaryotic/prokaryotic hybrid systems further strengthen this conclusion: They show that the prokaryotic initiation signals are evolutionarily conserved in the eukaryotic mRNAs, since prokaryotic ribosomes are able to translate eukaryotic mRNAs. Conversely, eukaryotic ribosomes also recognize prokaryotic initiation signals and initiate synthesis, indicating that the eukaryotic ribosomes may have also conserved the prokaryotic initiation mechanism. The universality of a single process of protein synthesis in all kingdoms is also manifest in the conservation of a complex apparatus, consisting of ribosomes, mRNA's, tRNA's including an initiator methionyl-tRNA, aminoacyl tRNA synthetases, and other protein factors. Thus, the mechanism of initiation of protein synthesis is conserved, and it is universal. The third initiation mechanism is the scanning mechanism for eukaryotes. It proposes that the 40S ribosome-methionyl-tRNA complex recognizes and binds to the 5'-end of the mRNA and the complex then scans the messenger for the initiator codon. Once it is located, the 80S ribosome initiation complex is formed with the 60S subunit and initiation is completed when a second aminoacyl-tRNA is bound and a peptide bond is formed. Exceptions to this mechanism were observed, where the ribosome bound directly to internal mRNA sites and initiated synthesis. Consideration of the conflicting observations in this review, however, has led to the conclusion that the primary eukaryotic mechanism is a conserved prokaryotic mechanism and that the "scanning process" involves two steps. The first step is an interaction of the initiation factors with the cap, which makes the IS accessible, and the second, initiation of translation by the conserved prokaryotic mechanism.