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

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.

Establishment, maintenance, and biological roles of non-CG methylation in plants

“…Some key components have only been found in angiosperms [58,59]. For instance, Pol IV and V evolved from duplication of various subunits of Pol II [57,58], and there is evidence of further lineage-specific duplication and evolution of a putative Pol VI in grasses [60]. From an evolutionary perspective, RdDM is a powerful example of how novelty and complexity can arise through gene duplication.…”

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

“…Several of the Pol IV and Pol V subunits, as well as other proteins of the RdDM pathway, are encoded by a variable number of gene paralogs across species. Most notable are duplications of the largest and second largest Pol IV/V-like subunits in cereal monocots compared to eudicot plants [ 62 , 191 ]. Although the molecular and biological functions of these extra RNA polymerase subunits remain unknown, they might reinforce or even extend the RdDM machinery in species like rice, barley and maize.…”

Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

“…Such a targeting mediated by suppressed sRNAs might act as strong deterrent for the loss of pol IV activity, and might contribute towards evolution of additional copies of this polymerase. In fact, monocots that have large genomes, also code for pol VI that is expressed and appears to have neo-functionalized carrying signatures of pol IV activity at least in part (Trujillo et al, 2018).…”

“…Indeed, unlike Arabidopsis, loss of silencing players display exacerbated phenotypes in the monocot model rice in the cases of drm2, met1b, pol iv, pol v, dcl3 (Moritoh et al, 2012;Yamauchi et al, 2014;Zheng et al, 2021;Wei et al, 2014). In agreement with this, grass family (Poaceae) members have evolved specific neo-functionalized RNA polymerase paralog called RNA polymerase VI, functions of which are still unclear (Trujillo et al, 2018). These phenomena substantiate that complex gene arrangement interleaved by repeats mandates very robust and agile mechanism of epigenetic silencing in a very localised manner.…”