On the accessibility and selection of the initiator site of mRNA in protein synthesis

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.

The initiation of eukaryotic and prokaryotic protein synthesis: A selective accessibility and multisubstrate enzyme reaction

An extension of our unique accessibility hypothesis for the initiation of protein synthesis is proposed following a review of the initiation of protein synthesis. The E. coli model initiation sequence generated by computer from 68 initiation sequences and the eukaryotic consensus initiation sequence derived by non-computer analysis of 211 initiation sequences do not contain a specific base in any position; they are only assigned preferred bases. The initiation site, in other words, is a varied sequence of preferred bases and its sequence is non-unique. This indicates that the ribosomal recognition of the initiation site may be the result of multiple interactions that are cooperative and cumulative and typical of multisubstrate enzymes. Because of this characteristic, the model of multisubstrate enzymes with broad substrate specificity is proposed as a paradigm for the initiation of protein synthesis. As predicted by this model, changes in the leader and downstream sequences that improve the agreement with the preferred base sequence do indeed enhance the rate of protein synthesis. The eukaryotic/prokaryotic hybrid studies show a considerable overlap in the specificities of the two groups of ribosomes. The scanning of the mRNA from the 5'-end postulated by the scanning hypothesis is not a necessary step since eukaryotic ribosomes are able to bind to internal mRNA sites and initiate synthesis. Our unique accessibility hypothesis, which is extended by coupling cooperative and cumulative specificity in ribosomal function, is referred to for brevity as the cumulative specificity hypothesis. The hypothesis actually postulates a selective accessibility and cooperative-cumulative specificity mechanism; it is able to account for the behavior of both eukaryotic and prokaryotic initiation of protein synthesis. From another perspective, the hypothesis can be regarded as providing a mechanism that enables ribosomes to recognize the IS in the absence of a unique initiation sequence.

A unified view of the initiation of protein synthesis

The mechanism of the initiation of protein synthesis is discussed in terms of two different hypotheses in which each emphasized a different possible element of the process: the Shine-Dalgarno (SD) hypothesis ascribed an essential role to recognition of the SD segment by the ribosomal RNA; it is supported by a variety of experiments but conflicting evidence negates its obligatory nature. In contrast, our hypothesis highlighted the role of the structure of the mRNA and proposes that the initiation codon is selected by virtue of its unique accessibility. The rationale for the importance of accessibility in the selection of the initiation site is discussed. An analysis and a recapitulation of the initiation process and ribosomal specificity are presented. The apparent conflicts with the SD hypothesis are resolved in a unified mechanism where accessibility is the dominant factor.

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.