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Background  In mono- and eudicotyledonous plants, a small nuclear gene family ( RpoT, R NA  po lymerase of the  T 3/ T 7 type) encodes mitochondrial as well as chloroplast RNA polymerases homologous to the T-odd bacteriophage enzymes.  RpoT  genes from angiosperms are well characterized, whereas data from deeper branching plant species are limited to the moss  Physcomitrella  and the spikemoss  Selaginella . To further elucidate the molecular evolution of the RpoT polymerases in the plant kingdom and to get more insight into the potential importance of having more than one phage-type RNA polymerase (RNAP) available, we searched for the respective genes in the basal angiosperm  Nuphar advena .    Results  By screening a set of BAC library filters, three  RpoT  genes were identified. Both genomic gene sequences and full-length cDNAs were determined. The  NaRpoT  mRNAs specify putative polypeptides of 996, 990 and 985 amino acids, respectively. All three genes comprise 19 exons and 18 introns, conserved in their positions with those known from  RpoT  genes of other land plants. The encoded proteins show a high degree of conservation at the amino acid sequence level, including all functional crucial regions and residues known from the phage T7 RNAP. The N-terminal transit peptides of two of the encoded polymerases, NaRpoTm1 and NaRpoTm2, conferred targeting of green fluorescent protein (GFP) exclusively to mitochondria, whereas the third polymerase, NaRpoTp, was targeted to chloroplasts. Remarkably, translation of NaRpoTp mRNA has to be initiated at a CUG codon to generate a functional plastid transit peptide. Thus, besides  AGAMOUS  in  Arabidopsis  and the  Nicotiana RpoTp  gene,  N. advena RpoTp  provides another example for a plant mRNA that is exclusively translated from a non-AUG codon. In contrast to the RpoT of the lycophyte  Selaginella  and those of the moss  Physcomitrella , which are according to phylogenetic analyses in sister positions to all other phage-type polymerases of angiosperms, the  Nuphar  RpoTs clustered with the well separated clades of mitochondrial (NaRpoTm1 and NaRpoTm2) and plastid (NaRpoTp) polymerases.    Conclusions   Nuphar advena  encodes two mitochondrial and one plastid phage-type RNAP. Identification of a plastid-localized phage-type RNAP in this basal angiosperm, orthologous to all other RpoTp enzymes of flowering plants, suggests that the duplication event giving rise to a nuclear gene-encoded plastid RNA polymerase, not present in lycopods, took place after the split of lycopods from all other tracheophytes. A dual-targeted mitochondrial and plastididal RNA polymerase (RpoTmp), as present in eudicots but not monocots, was not detected in  Nuphar  suggesting that its occurrence is an evolutionary novelty of eudicotyledonous plants like  Arabidopsis .

bmc evolutionary biology

Evolution of plant phage-type RNA polymerases: the genome of the basal angiosperm Nuphar advena encodes two mitochondrial and one plastid phage-type RNA polymerases