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Influence of the stacking potential of the base 3′ of tandem shift codons on −1 ribosomal frameshifting used for gene expression

Published online by Cambridge University Press:  11 January 2002

CLAIRE BERTRAND ,
MARIE FRANÇOISE PRÈRE ,
RAYMOND F. GESTELAND ,
JOHN F. ATKINS  and
OLIVIER FAYET
CLAIRE BERTRAND
Affiliation:
Laboratoire de Microbiologie et de Génétique Moléculaire, Centre National de la Recherche Scientifique et Université Paul Sabatier-UMR5100, 31062 Toulouse Cedex, France
MARIE FRANÇOISE PRÈRE
Affiliation:
Laboratoire de Microbiologie et de Génétique Moléculaire, Centre National de la Recherche Scientifique et Université Paul Sabatier-UMR5100, 31062 Toulouse Cedex, France
RAYMOND F. GESTELAND
Affiliation:
Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330, USA
JOHN F. ATKINS
Affiliation:
Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330, USA
OLIVIER FAYET
Affiliation:
Laboratoire de Microbiologie et de Génétique Moléculaire, Centre National de la Recherche Scientifique et Université Paul Sabatier-UMR5100, 31062 Toulouse Cedex, France
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Abstract

Translating ribosomes can shift reading frame at specific sites with high efficiency for gene expression purposes. The most common type of shift to the −1 frame involves a tandem realignment of two anticodons from pairing with mRNA sequence of the form X XXY YYZ to XXX YYY Z where the spaces indicate the reading frame. The predominant −1 shift site of this type in eubacteria is A AAA AAG. The present work shows that in Escherichia coli the identity of the 6 nt 3′ of this sequence can be responsible for a 14-fold variation in frameshift frequency. The first 3′ nucleotide has the primary effect, with, in order of decreasing efficiency, U > C > A > G. This effect is independent of other stimulators of frameshifting. It is detected with other X XXA AAG sequences, but not with several other heptameric −1 shift sites. Pairing of E. coli tRNALys with AAG is especially weak at the third codon position. We propose that strong stacking of purines 3′ of AAG stabilizes pairing of tRNALys, diminishing the chance of codon:anticodon dissociation that is a prerequisite for the realignment involved in frameshifting.

Keywords

−1 frameshifting3′ context effectcodon–anticodon interactionEscherichia colirecodingtRNALysX XXY YYZ frameshift motifs
Type
Research Article
Information
RNA , Volume 8 , Issue 1 , January 2002 , pp. 16 - 28
Copyright
2002 RNA Society

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