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

Quantitative Plant Science Initiative: Integrating Functional Genomics with Biomolecular-Level Experimentation to Understand Adaptation to Micronutrient Stress in Poplar and Sorghum

Authors:

Meng Xie1* (mxie@bnl.gov), Crysten E. Blaby-Haas2, Tim Paape3, Sam Seaver4, Doreen Ware5,6, Lifang Zhang5, Sunita Kumari5, Janeen Braynen5, Michael Regulski5, Dimiru Tadesse1, Changxu Pang1, Desigan Kumaran1, Nicolas Grosjean1, Nicolas Gladman5, Aditi Bhat1, Sara EI Alaoui4, Qun Liu1

Institutions:

1Brookhaven National Laboratory; 2Lawrence Berkeley National Laboratory; 3U.S. Department of Agriculture, Agricultural Research Service at Children’s Nutrition Research Center; 4Argonne National Laboratory; 5Cold Spring Harbor Laboratory; 6U.S. Department of Agriculture, Agricultural Research Service

URLs:

Goals

The Quantitative Plant Science Initiative (QPSI) is a capability that aims to bridge the knowledge gap between genes and their functions. A central strategy is combining genome-wide experimentation and comparative genomics with molecular-level experimentation. In this way, the project team leverages the scalability of omics data and bioinformatic approaches to capture system-level information, while generating sequence-specific understanding of gene and protein function. Incorporating molecular-level experimentation in the workflow addresses the question of how proteins function and establishes mechanistic insight into how sequence variation impacts phenotype. This knowledge serves as a touchstone for accurate genome-based computational propagation across sequenced genomes and forms a foundation for robust predictive modeling of plant productivity in diverse environments.

Abstract

To understand how the bioenergy crops poplar and sorghum respond to metal bioavailability, with a view toward improving bioenergy crop resilience, the research team performed integrated, large-scale, multi-genotype omics experiments, computational simulation, and gene/protein-focused molecular-level experimentation. The project has two objectives. Objective 1 is to determine the genome-wide responses to zinc (Zn) and iron (Fe) availability in sorghum and poplar and identify the major genes involved in leaf-level acclimation to metal ions. The team performed time-series and genotype-specific multi-omics experiments and obtained datasets useful for the identification of key functional genes.

Objective 2 is to identify the molecular-level functions of key proteins and validate them by overexpression and loss-of-function phenotyping. Following the team’s recent discovery of previously unknown Zn chaperones in eukaryotes (Pasquini et al. 2022), a structure-function study of these novel proteins was completed and a plant-specific Zn-homeostatic mechanism that involves intracellular Zn transferases was identified (Zhang et al. 2023). The team also discovered a new heme sensor involved in cofactor-dependent post-translational regulation at the intersection of photosynthesis and respiration (Grosjean et al. 2024). The structure of a Zn transporter dimer was determined, revealing a flexible loop for sensing cellular Zn content and regulating Zn uptake from the environment (Pang et al. 2023).

In addition to molecular-level discoveries in micronutrient homeostasis, a protoplast-based experimental system was used to discover a key gene regulatory network that controls sorghum flowering time and biomass production (Tadesse et al. 2024). While working with Zn and Fe micronutrient stresses in the current project phase, there will be subsequent opportunities to incorporate other real-world conditions, through the addition of field experiments, which address the impacts of soil geochemistry, microbiome, and rhizosphere and study bioenergy crops and environment interactions.

References

Grosjean, N., et al. 2024. “A Hemoprotein with a Zinc-Mirror Heme Site Ties Heme Availability to Carbon Metabolism in Cyanobacteria,” Nature Communications, under review.

Pang, C., et al. 2023. “Structural Mechanism of Intracellular Autoregulation of Zinc Uptake in ZIP Transporters,” Nature Communications 14(1), 3404. DOI:10.1038/s41467-023-39010-6.

Pasquini, M., et al. 2022. “Zng1 is a GTP-dependent Zinc Transferase Needed for Activation of Methionine Aminopeptidase,” Cell Reports 39(7). DOI:10.1016/j.celrep.2022.110834.

Tadesse, D., et al. 2024. “Sorghum SbGhd7 is a Major Regulator of Floral Transition and Directly Represses Genes Crucial for Flowering Activation,” New Phytologist 242(2), 786–96. DOI:10.1111/nph.19591.

Zhang, L., et al. 2023. “Two Related Families of Metal Transferases, ZNG1 and ZNG2, are Involved in Acclimation to Poor Zn Nutrition in Arabidopsis,” Frontiers in Plant Science 14:1237722. DOI:10.3389/fpls.2023.1237722.

Funding Information

This research was supported by the DOE Office of Science, BER Program.