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. 2002 Nov 23;299(1):1–34. doi: 10.1016/S0378-1119(02)01056-9

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Copyright © 2002 Published by Elsevier B.V.

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Fig. 2 — Examples of minimally leaky scanning in which a strong, but not quite perfect, context at AUG#1 causes most ribosomes to initiate there while allowing a low level of initiation downstream. With the depicted viral mRNAs (A,B), the predominant product of translation is the capsid protein initiated from AUG#1. Low-level leaky scanning generates a small but adequate amount of the indicated second protein. With bovine coronavirus, a mutation in position +4 (U→G, indicated in red) flanking AUG#1 strongly reduced translation from the downstream site (Senanayake and Brian, 1997), supporting the interpretation that the natural mRNA is slightly leaky because the context flanking AUG#1 is not a perfect match to the consensus sequence. With hepatitis B virus, ribosomes en route to the P start site (AUG#5) apparently bypass the weak AUG#2 by leaky scanning, while translation of the small ORF initiated at AUG#3 enables some ribosomes to miss the inhibitory AUG#4 (inhibitory because it resides in a strong context and overlaps the P ORF) and thus to reach AUG#5. Whereas the core protein start codon (AUG#1) here depicted resides in a context which allows a low level of leaky scanning, a slightly longer mRNA which encodes the pre-core protein has a stronger start codon (A in position −3) and polymerase cannot be translated from that form of mRNA (Fouillot and Rossignol, 1996). The publications on which the scheme shown here is based (Fouillot et al., 1993, Hwang and Su, 1998) also discuss some alternative possibilities vis-à-vis translation of polymerase. (C) The first AUG codon in rat histone H4 mRNA initiates translation of the full-length protein. The second AUG, 85 codons downstream and in the same reading frame, initiates production of a peptide which has growth-regulatory properties (Bab et al., 1999). (D) With rat A_2AR adenosine receptor mRNA, an overlapping upORF that initiates at an AUG codon in a strong context is used to minimize production of A_2AR protein. The overlapping arrangement precludes reinitiation but the not-quite-perfect context at the upstream start site allows low-level leaky scanning. This interpretation is supported by the observed ten-fold increase in translation of A_2AR in vivo when the start codon of the upORF was eliminated (Lee et al., 1999). Via a second promoter, the rat A_2A-R gene produces some transcripts with additional upORFs, but no transcript has yet been found that lacks the inhibitory upORF discussed here. Here and in Fig. 3, the major coding domain is shaded gray. Small regulatory ORFs (blue rectangles) are not drawn to scale.