Transcripts of the ndhH-D operon of barley plastids: possible role of unedited site III in splicing of the ndhA intron

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Abstract
The plastid ndhH–D operon produces several transcripts containing ndhA sequence with and without its group II intron. After sequencing an 8125 bp fragment of barley plastid DNA including the ndhH–D operon, we investigated the editing–splicing status of transcripts in the range 1.0–7.8 kb. Reverse transcription and sequencing of RNA bands separated by electrophoresis were used to determine C→U editing sites. Sites I, II and IV of ndhA and site V of ndhD were edited in all transcripts analysed and, probably, were edited before any splicing had taken place. In contrast, site III of ndhA (13 bp from the 5′-end base of the second exon) was not edited in transcripts containing the intron (including the 1.7 kb inter­mediary transcript consisting of the intron and the second exon) but was edited in all transcripts lacking the ndhA intron. Comparison of the secondary structures of the ndhA intron and intron–second exon intermediate suggests that G pairing prevents editing of site III in transcripts containing the intron and maintains the secondary structure required for splicing. Splicing of the ndhA intron releases the site III C from pairing and, probably, brings it close to cis- acting elements for editing upstream in the first exon.