Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood Traits

Authors:

Jacob Moe-Lange1* (jmoelange@ucdavis.edu), F. Daniela Rodriguez-Zaccaro1,2, Andrew Groover1,2, Justin Walley3, Nitzan Shabek1

Institutions:

1Department of Plant Biology, University of California–Davis; 2Pacific Southwest Research Station, U.S. Forest Service; 3Department of Plant Pathology, Entomology and Microbiology, Iowa State University–Ames

Goals

Wood vessel trait candidate genes coding for E3 ligase proteins will be functionally characterized through the creation of CRISPR-cas9 mutants, TurboID proximity labeling, and through drought and ABA treatments to study gene expression, protein ubiquitination, degradation, and abundance in poplar wood forming tissues.

Abstract

Angiosperm wood contains highly lignified tube-like cells called vessel elements, which provide a pathway for the upward movement of water under tension. The dimensions and distribution of vessels in wood (i.e. wood anatomy) affect water transport and growth rates, as well as susceptibility to hydraulic failure during drought. Despite their crucial role in determining the hydraulic physiology of trees, the genetic regulation of vessel element anatomical traits is poorly understood. In a dosage-dependent genome-wide screen, researchers detected a significant correlation between the height-adjusted mean vessel diameter and frequency. A subsequent gene coexpression network analysis on poplar wood forming tissues found that height-corrected vessel frequency was significantly correlated to genes that code for E3 ubiquitin ligase, key components of the ubiquitin proteasome system (UPS). The team selected vessel trait-related E3 ligase candidates for further functional characterization of ubiquitin-proteasome regulation in poplar wood forming tissue. To achieve this goal, CRISPR-Cas9 mutants targeting poplar E3 ligase candidate genes have been generated to assess alterations in wood phenotype, gene expression, protein abundance, and ubiquitinomes. Additionally, TurboID transgenic lines are being generated to elucidate protein interacting partners for the candidate proteins through proximity labeling. In anticipation of poplar E3 ligase datasets, researchers examined the interactome of similar components in Arabidopsis transgenic lines subjected to drought and ABA treatments, revealing substantial treatment-induced alterations in the UPS compared to controls. These approaches aim to enhance the understanding of the role of the ubiquitin-proteasome system in wood formation, vessel trait variation, and tree responses to environmental stressors.