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Identification of an rRNA operon promoter from Zea mays chloroplasts which excludes the proximal tRNAValGAC from the primary transcript

The transcriptional start site of the rRNA operon from Zea mays chloroplasts has been identified by a combination of S1 mapping and Southern hybridization with in vitro capped chloroplast RNA as radioactive probe. This is the first example in which the transcriptional start site of a choloroplast gene has been established by identification of the triphosphate‐bearing RNA terminus. The start site is located at position −117 proximal to the 16S rRNA gene and is preceded by −10 and −35 sequences homologous to prokaryotic promoters. The primary transcript directed by this promoter does not include tRNAValGAC sequences which are coded further upstream between positions −302 and −231. A major processing site of the primary rRNA transcript was identified at position −30 which is embedded in a secondary structure typical for prokaryotic RNase III processing sites. Several putative processing and start sites of the tRNAValGAC transcipts have been mapped by primer extension with reverse transcriptase.