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Nucleic Acids Research, 1987, Vol. 15, No. 1 345-360
© 1987

Articles

Potential secondary structure at translation-initiation sites

M.C. Ganoza, E.C. Kofoid*, P. Marlière+ and B.G. Louis

Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto Ontario M5G 1L6, Canada

Received May 21, 1986. Revised October 2, 1986. Accepted November 17, 1986.

Since translational start codons also occur internally, more-complex features within mRNA must determine initiation. We compare the potential secondary structure of 123 prokaryotic mRNA start regions to that of regions coding for internal methionines. The latter display an unexpectedly-uniform, almost-periodic pattern of pairing potential. In contrast, sequences 5' to start codons have little self-pairing, and do not pair extensively with the proximal coding region. Pairing potential surrounding start codons was found to be less than half of that found near internal AUGs. In groups of random sequences where the distribution of nucleotides at each position, or of trinucleotides at each in-frame codon position, matched the observed natural distribution, there was no periodicity in the pairing potential of the internal sequences. Randomized internal sequences had less pairing: the ratio of pairing intensity between internals and starts was reduced from 2.0 to 1.6 by randomization.

We propose that the transition from the relatively-unstructured start domains to the highly-structured internal sequences may be an important determinant of translational start-site recognition.

*Present address: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA

+Institut Pasteur, 25 et 28 rue du docteur Roux, F-75724 Paris, Cedex 15, France


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Home page
 Microbiol. Mol. Biol. Rev.Home page
M. C. Ganoza, M. C. Kiel, and H. Aoki
Evolutionary Conservation of Reactions in Translation
Microbiol. Mol. Biol. Rev., September 1, 2002; 66(3): 460 - 485.
[Abstract] [Full Text] [PDF]


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