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Mechanisms of the initiation of protein synthesis: in reading frame binding of ribosomes to mRNA

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Abstract

The various mechanisms proposed to describe the initiation of protein synthesis are reviewed with a focus on their initiation signals. A characteristic feature of the various mechanisms is that each one of them postulates a distinct initiation signal. The signals of the Shine–Dalgarno (SD), the scanning and the internal ribosome entry site (IRES) mechanisms are all located exclusively in the 5′ leader sequence, whereas, the signal of the cumulative specificity (CS) mechanism includes the entire initiation site (IS). Computer analysis of known E. coli IS sequences showed signal characteristics in the entire model IS consisting of 47 bases, in segments of the 5′ leader and of the protein-coding regions. The proposal that eukaryotic translation actually occurs in two steps is scrutinized. In a first step, initiation factors (eIF4F) interact with the cap of the mRNA, thereby enhancing the accessibility of the IS. In the second step, initiation is by the conserved prokaryotic mechanism in which the ribosomes bind directly to the mRNA without ribosomal scanning. This binding occurs by the proposed process of in reading frame binding of ribosomes to mRNA, which is consistent with the CS mechanism. The basic CS mechanism is able to account for the initiation of translation of leaderless mRNAs, as well as for that of canonical mRNAs. The SD, the scanning and the IRES mechanisms, on the other hand, are inconsistent with the initiation of translation of leaderless mRNAs. Based on these and other observations, it is deemed that the CS mechanism is the universal initiation mechanism.

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Abbreviations

CS:

Cumulative specificity

eIF2, eIF4F:

Eukaryotic initiation factors

IF2:

Prokaryotic initiation factor

IRES:

Internal ribosome entry site

IS:

Initiation site

SD:

Shine–Dalgarno

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Acknowledgments

The author thanks Dr. Ferenc J. Kézdy for his invaluable contributions in reviewing this manuscript, and his grandson, Dr. Jonathan Nakamoto, for his help in the literature search.

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  1. Department of Biochemistry and Molecular Biology, The University of Chicago, 5801 S. Ellis Av, Chicago, IL, 60637, USA

    Tokumasa Nakamoto

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  1. Tokumasa Nakamoto
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Correspondence to Tokumasa Nakamoto.

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Nakamoto, T. Mechanisms of the initiation of protein synthesis: in reading frame binding of ribosomes to mRNA. Mol Biol Rep 38, 847–855 (2011). https://doi.org/10.1007/s11033-010-0176-1

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  • DOI: https://doi.org/10.1007/s11033-010-0176-1

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