Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus

Abstract

The complete chloroplast DNA sequence (122 890 bp) of the moss Physcomitrella patens has been determined. The genome contains 83 protein, 31 tRNA and four rRNA genes, and a pseudogene. Four protein genes (rpoA, cysA, cysT and ccsA) found in the liverwort Marchantia polymorpha and the hornwort Anthoceros formosae are absent from P.patens. The overall structure of P.patens chloroplast DNA (cpDNA) differs substantially from that of liverwort and hornwort. Compared with its close relatives, a 71 kb region from petD to rpoB of P.patens is inverted. To investigate whether this large inversion and the loss of rpoA usually occur in moss plants, we analyzed amplified cpDNA fragments from four moss species. Our data indicate that the large inversion occurs only in P.patens, whereas the loss of the rpoA gene occurs in all mosses. Moreover, we have isolated and characterized the nuclear rpoA gene encoding the alpha subunit of RNA polymerase (RNAP) from P.patens and examined its subcellular localization. When fused to green fluorescent protein, RpoA was observed in the chloroplasts of live moss protonemata cells. This indicates that chloroplast RNAP is encoded separately by chloroplast and nuclear genomes in the moss. These data provide new insights into the regulation and evolution of chloroplast transcription.

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

“…Substitutions in a nuclear-encoded rpoA in Geraniaceae would then incur compensatory substitutions in rpoB, rpoC1, and rpoC2 to maintain the function of the polymerase. Indeed in the nuclearencoded rpoA of the moss Physcomitrella patens, substitutions are numerous and show a strong bias toward nuclear codon use (44). Alternatively, we cannot exclude the possibility that in the plastid genome of Pelargonium the rpoA-like ORFs identified by Chumley et al (16) are actually highly divergent functional genes, and compensatory substitutions in other subunits of the polymerase result.…”

“…It is notable that one genus of Geraniaceae, Pelargonium, has lost a functional copy of the PEP gene rpoA; however, rpoA-like ORFs were found dispersed throughout the plastid genome (16). rpoA was transferred from the plastid genome to the nuclear genome in a moss (44) and in the nonphotosynthetic angiosperm Cuscuta (42), but little is known about rpoA in Pelargonium and other Geraniaceae (45)(46)(47). In the case of Cuscuta, loss of rpoA and rpoB results in a change from PEP-to NEP-based promoter sequences in the rrn16 gene (42).…”

Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The Signal Recognition Particle RNA Is Conserved in Plastids of a Wide Range of Photosynthetic Organisms

“…In most cases, this region is part of the conserved petNtrnC-rpoB-rpoC1-rpoC2 cluster, although the cluster has been split in the bryophyte P. patens and several monilophytes. In P. patens, the petN-trnC region is clustered with pet genes due to an inversion of a large part of the plastome (Sugiura et al, 2003). Such inversions leading to structural rearrangements of the gene order have also been described for plastid genomes of monilophytes (Gao et al, 2011).…”

Distinct, Ecotype-Specic Genome and Proteome Signatures in the Marine Cyanobacteria Prochlorococcus

“…However, T. ruralis lacks the large~71 kb inversion in the LSC region of the genome that is found in P. patens. This large inversion is found only in the moss order Funariales, whereas other moss lineages have a more plesiomorphic gene order similar to the liverwort Marchantia polymorpha [16,17]. It is interesting that the Tortula ruralis chloroplast genome lacks the petN gene because the protein encoded by this gene plays an important role in photosynthesis electron transport.…”