The stress response of pokeweed and phylogeny of a defense gene family in plants

Pokeweed (Phytolacca americana L.) is a non-model plant known for its resistance to a variety of biotic and abiotic stressors. Part of the reason for this is the presence of ribosome inactivating proteins (RIPs), which can hydrolyze adenine bases from nucleic acids. These proteins are upregulated in pokeweed by jasmonic acid, a plant hormone involved in stress response. The goal of this research was to gain a better understanding of how plants respond to stress and so two different, but complementary, approaches were taken. Firstly, an in-depth look at the diversity and evolution of RIPs in plants was undertaken by curating a dataset of RIPs from publicly available data and using computational approaches to characterize their domain architecture, identify conserved amino acids, and construct a gene tree. This research revealed that despite the damage that RIPs can potentially cause to the plant’s own nucleic acids, RIPs are common among plants and their diversity indicates the potential for a multi-faceted impact on plant defense. Looking more closely at how pokeweed responds to stress, we applied jasmonic acid to leaves and analyzed changes in gene expression, through RNA sequencing (RNA-Seq). Identification of gene clusters involved in defense was aided by the generation of a pokeweed genome assembly. This research revealed that there is a variety of strategies that plants can implement to respond to stress, and that these strategies are applied differently by different species. Overall, this research contributes to a better understanding of the diversity and nuance present in the ways plants defend themselves.