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Chloroplast Promoter Sequences
Searches for conserved promoter like sequences upstream from chloroplast genes have revealed elements with considerable homology to bacterial promoter sequences. The E. coli "consensus" promoter sequence contains two conserved regions, one normally found about 35 nucleotides and the other about 10 nucleotides upstream from the start of transcription and referred to as the "35" and "-10" elements respectively;

5'... TTGACA/T... (16-18 nucleotides).. .TATG/AAT... 3'. The chloroplast consensus sequence described by L. Bogorad and his colleagues at Harvard University is as follows: 5' . . . A/g TTG/cA/cNa/t. . . (15-20 nucleotides) . . . T A/tA/tG/aA T. . . 3'. I (In the preceding line, lower case letters represent less frequent alternative bases.)

In several cases wherein the start of the RNA transcript has been identified by SI nuclease protection experiments, it occurs within eight nucleotides of the proximal promoter elements. The conservation of these sequence elements and their homology with bacterial promoters support, but does not prove, the notion that they function as chloroplast gene promoters.

Proof requires the direct demonstration that removing or changing these sequences actually affects promoter activity. One way of obtaining such proof is to test altered genes in an in, vitro transcription system.

The studies undertaken made progressive deletions of sequences 5' to the gene, moving gradually closer to the start of transcription. Each deletion mutant was characterized by DNA sequencing and then tested for its ability to support accurate transcription. Deletions of sequences further upstream than position -85 had little effect on the production of transcripts, but there was a rapid drop in transcription caused by deletions between -80 and -75.

This region contains the sequence TTGCTTA, the first three nucleotides of which are homologous to the E. coli -35 consensus sequence. There is also a TATAAT sequence between -54 and -59 which is fully homologous to the E. coli -10 consensus sequence. Since transcription was already inhibited by the removal of the sequences further upstream, little effect was seen when the TATAAT sequence was deleted.