Plastid transcription in higher plants

The plastid genome is transcribed by nucleus-encoded (NEP) and plastid encoded (PEP) RNA polymerases. NEP transcribes housekeeping genes as well as genes coding for PEP core sub-units and its activity is replaced by PEP in chloroplasts resulting in differential expression of genes in a developmental context. PEP is a prokaryotic-type enzyme in which nuclear-encoded sigma factors function as promoter recognition subunit. A phylogenetic analysis for sigma factors identified so far in plants shows that plant sigma factors are members of bacterial sigma(70) family and divided into six groups, Sig1 through Sig6, which are integrated into four clusters consisting of Sig1 and Sig4, Sig2 and Sig3, Sig5 and Sig6. All plastid sigma factors recognize bacterial sigma(70)-type promoters, but they differ in promoter preference and the tissue-, developmental stage- and environmental-dependent expression. Sig5 is distinct from the other sigma factors in its structure, function, and expression in response to light and stress. A promoter of the psbD operon, psbD blue light responsive promoter (psbDBLRP) is a typical example that is under the control of a combination of various signals arising in the nucleus and plastids in response to the tissue specific and developmental stage- and environment-dependent cues. psbDBLRP is recognized only by Sig5, which is expressed by a cryptochrome-mediated blue light signal and signals responding to stress conditions. The activity of psbDBLRP is also under the control of circadian clock. Furthermore, it may be regulated by redox signals generated by photosynthetic electron transport in the chloroplast presumably through the change of the binding affinity of a nuclear encoded transcription factor for the enhancer element located upstream of the core promoter region of the psbD operon.