The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids

The plastid genome in photosynthetic higher plants encodes subunits of an Escherichia coli-like RNA polymerase (PEP) which initiates transcription from E. coli sigma(70)-type promoters. We have previously established the existence of a second nuclear-encoded plastid RNA polymerase (NEP) in photosynthetic higher plants, We report here that many plastid genes and operons have at least one promoter each for PEP and NEP (Class II transcription unit). However, a subset of plastid genes, including photosystem I and II genes, are transcribed from PEP promoters only (Class I genes), while in some instances (e.g. accD) genes are transcribed exclusively by NEP (Class III genes). Sequence alignment identified a 10 nucleotide NEP promoter consensus around the transcription initiation site, Distinct NEP and PEP promoters reported here provide a general mechanism for group-specific gene expression through recognition by the two RNA polymerases.