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bioRxiv · 10.1101/272708

Evidence for a unique DNA-dependent RNA polymerase in cereal crops

Trujillo, J. T.·Seetharam, A. S.·Hufford, M. B.·Beilstein, M. A.·Mosher, R. A.
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Abstract

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.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC=\"FIGDIR/small/272708_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@13d3515org.highwire.dtl.DTLVardef@16831d5org.highwire.dtl.DTLVardef@19f99b8org.highwire.dtl.DTLVardef@1253e70_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Significance statementThe grass family is critically important for humans, as this group contains cereal grains such as rice, wheat, and corn that form the bulk of the human diet. Here we provide evidence that grasses have evolved a unique polymerase complex of unknown function, suggesting a novel mechanism of gene regulation in the grass lineage. In addition to implications for the biology of grasses, this system offers an opportunity to understand how evolution shapes multi-subunit complexes through duplication of individual components.

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Trujillo, J. T., Seetharam, A. S., Hufford, M. B., Beilstein, M. A., Mosher, R. A.. 2018-02-28. Evidence for a unique DNA-dependent RNA polymerase in cereal crops. https://doi.org/10.1101/272708

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