The Transcription of Plant Organelle Genomes

Mitochondria and plastids possess their own genomes and transcription machineries. Although both organelles preserve features of eubacterial genomes, they have acquired during their evolution specialized components for gene expression, which are encoded in the nucleus. Plant mitochondria contain at least one nuclear-encoded, phage-type RNA polymerase that occurs widely throughout the eukaryotic lineage. Mitochondrial promoters transcribed by this RNA polymerase are rather variable, and only a certain subset of them can be distinguished by conserved tetra- and nonanucleotide sequence motifs in monocot and dicot plants, respectively. Plastids harbour at least two types of different RNA polymerases. One is a plastid-encoded eubacterial-type polymerase resembling the E. coli enzyme, composed of four core subunits (α, β, β′ and β″) and one of several nuclear-encoded sigma factors. This holoenzyme is the plastid-encoded RNA polymerase (PEP). The other plastid polymerase is a nuclearencoded single-subunit enzyme of the same type as the mitochondrial RNA polymerase, i.e. a phage-type enzyme, and has been named NEP (nuclear-encoded polymerase). The development of photosynthetically active chloroplasts requires both PEP and NEP. While PEP recognizes σ70-like promoters with conserved –10 (TATAAT) and – 35 (TTGACA) elements, NEP recognizes promoter sequences unique to this enzyme. Two structurally different classes of plastid promoters engaged in transcription by nuclearencoded RNA polymerases have been dissected in the plastid genome. Whereas most NEP promoters are characterized by a conserved YRTA motif and share homolgy with certain mitochondrial transcription initiation sites, a second class of NEP promoters, lacking the YRTA motif, contains a conserved sequence element downstream from the initiation site which is sufficient to support specific transcription. The organelle phage-type RNA polymerases are encoded by a small family of nuclear RpoT genes that consists of three members in dicot plants and only two RpoT genes in monocots. Aside from RpoTm encoding the mitochondrial RNA polymerase, a second RpoT enzyme (RpoTp) is imported into plastids both in monocot and dicot plants. Immunoblot analyses as well as studies on transgenic plants indicate that RpoTp indeed specifies a chloroplast-localized NEP. A third RpoT gene found exclusively in dicots (RpoTmp) has been shown to encode a protein that is dually targeted into both mitochondria and plastids. The principal specificity factors that interact with the plant RpoT polymerases to confer promoter-specific binding and transcription specificity have not been identified yet. It is tempting to assume that mitochondrial RpoT polymerase and plastid NEP promoter recognition is dependent on mitochondrial and plastid homologs of yeast and mammalian mitochondrial specificity factors.