title: Translation of chloroplast-encoded mRNA: potential initiation and termination signals.
abstract: 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 prokaryotes (-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.
authors.affiliation: Department of Biochemistry, University of Arizona, Tucson 85721.
authors.forename: P C
authors.initials: PC
authors.lastname: Bonham-Smith
authors.forename: D P
authors.initials: DP
authors.lastname: Bourque
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D005075:Biological Evolution; D002736:Chloroplasts / Q000378:metabolism*; D003062:Codon; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational; D010443:Peptide Chain Termination, Translational; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D011387:Prokaryotic Cells / Q000378:metabolism; D021382:Protein Sorting Signals / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D003062:Codon; D010940:Plant Proteins; D021382:Protein Sorting Signals; D012333:RNA, Messenger