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Nucleic Acids Research, 1989, Vol. 17, No. 5 2057-2080
© 1989

MOLECULAR BIOLOGY

Translation of chloroplast-encoded mRNA: potential initiation and termination signals

Peta C. Bonham-Smith1 and Don P. Bourque1,2

1Department of Biochemistry, University of Arizona Tucson, AZ 85721, USA 2Department of Molecular and Cellular Biology, University of Arizona Tucson, AZ 85721, USA

Received September 20, 1988. Revised February 2, 1989. Accepted February 2, 1989.

A survey of 196 protein-coding chloroplast DNA sequences demonstrated the preference for AUG and UAA codons for initiation and termination of translation, respectively. As in prokaryotes at every nucleotide position from –25 to +25 (AUG is +1 to +3) and for 25 nucleotides 5' and 3' to the termination codon an A or U is predominant, except for C at +5 and G at +22. A Shine-Dalgarno (SD) sequence (GGAGG or tri- or tetranucleotide variant) was found within 100 bp 5' to the AUG codon in 92% of the genes. In 40% of these cases, the location of the SD sequence was similar to that of the consensus for prokaryotea (–12 to –7 5' to AUG) presumed to be optimal for translation initiation. A SD sequence could not be located in 6% of the chloroplast sequences. We propose that mRNA secondary structures may be required for the relocation of a distal SD sequences to within the optimal region (–12 to –7) for initiation of translation. We further suggest that termination at UGA codons in chloroplast genes may occur by a mechanism, involving 16S rRNA secondary structure, which has been proposed for UGA termination in E.coli.


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