Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits.
Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.|Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China.
Yaqiong
Y
Wang
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.|Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China.|Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China.
Hong
H
Ma
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D021122:Protein Subunits; D012321:DNA-Directed RNA Polymerases
Pol IV; Pol V; RNA polymerase; gene duplication; parallel evolution; protein complex