Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylat...

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Bibliographic Details
Published in:Molecular biology and evolution 2018-10, Vol.35 (10), p.2454-2462
Main Authors: Trujillo, Joshua T, Seetharam, Arun S, Hufford, Matthew B, Beilstein, Mark A, Mosher, Rebecca A
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Discoveries
DNA-Directed RNA Polymerases - genetics
Edible Grain - enzymology
Edible Grain - genetics
Gene Duplication
Grain Proteins
Phylogeny
Poaceae - enzymology
Poaceae - genetics
Selection, Genetic
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Summary:Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msy146