The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation

Abstract

Gene evolution is one of the most significant contributors to the extensive number and diversity of organisms that have arisen on planet Earth. Gene duplication is a major driving force in gene evolution by allowing the development of novel functions and the creation of new pathways. Every gene within an organism’s genome has been retained through numerous duplication events and has a unique evolutionary history that dictates structure and function. As organisms retain increasing numbers of related genes, more complex pathways evolve. Whole genome duplications have occurred numerous times within the land plant lineage and are a contributing factor in the complexity of plant genomes. The plant-specific epigenetic pathway of RNA-directed DNA Methylation (RdDM) arose through evolution of specialized genes following gene duplications in the ancestor of plants. RdDM is responsible for de novo methylation associated with transcriptional gene silencing of transposons and other repetitive sequences. Evolution of RdDM components is dynamic and ongoing with many lineage specific paralogs, leading to further complexity of the pathway. Understanding the evolutionary history and relationship among gene families can drive the formation of hypotheses regarding the molecular necessity of related genes. RdDM requires the cooperative activity of plant-specific DNA-dependent RNA polymerases (Pol) IV and V, which evolved from RNA Pol II subunits. Although many subunits are shared among the polymerases, the largest subunit of Pol IV and V are unique and harbor distinct carboxyl terminal domains. In addition to separate largest subunits, Pol IV and V possess other specialized subunits and interacting partners that influence their functions. The evolutionary origin of these subunit and interacting proteins is unclear and requires further investigation. Determining the origin and evolutionary history of these proteins will be valuable for translating research from model organisms to other species, such as crops which are economically and agronomically important. Additionally, investigating ongoing evolution of these proteins will not only improve our current models and understanding of RdDM, but the mechanisms by which multi-subunit complex can evolve. This dissertation is the culmination of three studies investigating the evolution of genes involved in the RdDM pathway, in particular the plant-specific DNA-dependent RNA polymerases IV and V. In Chapter 1, I elucidate the evolutionary origin of Pol IV and V subunits in Charophytic Green Algae and describe early Pol evolution. In Appendix A, my coauthors and I describe a recent duplication and retention of distinct Pol subunits and associated proteins in the grass (Poaceae) lineage of monocots. The results of this study led us to generate a hypothesis for the existence of a distinct, Pol VI complex within grasses. Lastly in Appendix B, I analyzed a highly variable region within the carboxyl terminal domain of the Pol V largest subunit to better understand the molecular function and evolutionary history of this specialized region.