Organ-specific transcription of the rrn operon in spinach plastids

The spinach rrn operon is used as a model system to study transcriptional regulation in higher plant photosynthetic and non-photosynthetic plastids. We performed capping experiments to determine whether P1, PC, or P2 promoters are employed for rrn transcription start sites in cotyledon and root tissues. By using a new method of analysis of capped RNA we demonstrate for the first time that 1) in both organs the rrn operon is expressed in a constitutive manner by cotranscription with the preceding tRNA(GAC)(Val) gene, and 2) the PC transcription start site is used only in cotyledons and leaves, i.e. we demonstrate the organ specific usage of a plastid promoter. Both start sites, PC and that of the tRNA(GAC)(Val) cotranscript, lack Escherichia coli-like consensus sequences. The cotranscript is initiated 457 base pairs upstream of the tRNA(GAC)(Val) gene. The PC specific DNA-binding factor, CDF2, is not detectable in root tissues confirming its regulatory role in PC-initiated rnn expression and the organ specificity of PC expression. Furthermore, our results show that rrn operon expression patterns differ in spinach and tobacco indicating species-specific transcriptional regulation of plant plastid gene expression.