The levels of RPODmRNA increased 2– 3-fold in the mid-to-late dark period of light-dark cycling cells, just prior to, or coincident with, the peak in chloroplast transcription. Southern blot hybridization and BLAST searches of the genome and EST databases suggest that RPODmay be the only sigma factor gene in C. PEST sequences were also found in ∼40% of sigma factors examined, indicating they may be of general significance.
We also identified two motifs not previously recognized for sigma factors, adjacent PEST sequences and a leucine zipper, both suggested to be involved in protein–protein interactions. We describe a nuclear gene ( RPOD) that is predicted to encode an 80 kDa protein that, in addition to a predicted chloroplast transit peptide at the N-terminus, has the conserved motifs (2.1– 4.2) diagnostic of bacterial sigma-70 factors. Since transcription of much, if not most, of the chloroplast genome in Chlamydomonas reinhardtii is regulated by the circadian clock and the nucleus, we sought to identify sigma factor genes that might be responsible for this regulation.
Green algae, however, appear to possess only the bacterial enzyme. In higher plants, the transcription of plastid genes is mediated by at least two types of RNA polymerase (RNAP) a plastid-encoded bacterial RNAP in which promoter specificity is conferred by nuclear-encoded sigma factors, and a nuclear-encoded phage-like RNAP.
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