title: Ancient Origin and Recent Innovations of RNA Polymerase IV and V.
abstract: Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.
authors.affiliation: The School of Plant Sciences, The University of Arizona.
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.affiliation: The School of Plant Sciences, The University of Arizona.
authors.forename: Timmy
authors.initials: T
authors.lastname: Kendall
authors.affiliation: The School of Plant Sciences, The University of Arizona.
authors.forename: Evan S
authors.initials: ES
authors.lastname: Forsythe
authors.affiliation: Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México.
authors.forename: Ana
authors.initials: A
authors.lastname: Dorantes-Acosta
authors.affiliation: Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside.
authors.forename: Shaofang
authors.initials: S
authors.lastname: Li
authors.affiliation: Facultad de Ingeniería, Universidad Autónoma de Querétaro, Querétaro, México.
authors.forename: Juan
authors.initials: J
authors.lastname: Caballero-Pérez
authors.affiliation: Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Chen
authors.affiliation: Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México.
authors.forename: Mario
authors.initials: M
authors.lastname: Arteaga-Vázquez
authors.affiliation: The School of Plant Sciences, The University of Arizona.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Beilstein
authors.affiliation: The School of Plant Sciences, The University of Arizona The Bio5 Institute, The University of Arizona rmosher@email.arizona.edu.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Mosher
mesh_terms: D000595:Amino Acid Sequence; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics; D020440:Gene Duplication; D020868:Gene Silencing; D017343:Genes, Plant; D019684:Magnoliopsida / Q000201:enzymology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D010944:Plants / Q000201:enzymology* / Q000235:genetics*; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000235:genetics; D013045:Species Specificity
chemical_list: D010940:Plant Proteins; D021122:Protein Subunits; D012321:DNA-Directed RNA Polymerases
keywords: Escape from Adaptive Conflict; Gene duplication; RNA Polymerase IV; RNA Polymerase V; RNA Silencing; small RNA-directed DNA methylation