Associate Research Scientist University of Delaware
XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5’ end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among the decapped XRN4 substrates, gene products associated with photosynthesis, nitrogen (N) responses, and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during recovery from N starvation, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3’ fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Our work shows that XRN4 is a major player in multiple decay pathways and analysis of its substrates has revealed functional contributions of the enzyme at the whole-plant level. The results of additional experiments and progress towards examining the contributions of XRN4 in NMD will also be discussed.
Coauthors: Pamela Green – Department of Plant and Soil Sciences – University of Delaware