AUTHOR=Ding Geng , Mugume Yosia , Dueñas Maria Emilia , Lee Young Jin , Liu Meiling , Nettleton Daniel S. , Zhao Xuefeng , Li Ling , Bassham Diane C. , Nikolau Basil J. 

TITLE=Biological insights from multi-omics analysis strategies: Complex pleotropic effects associated with autophagy

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1093358

DOI=10.3389/fpls.2023.1093358

ISSN=1664-462X

ABSTRACT=<p>Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two <italic>AuTophaGy-related</italic> (<italic>ATG</italic>) genes of <italic>Arabidopsis</italic>. Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the <italic>atg7</italic> and <italic>atg9</italic> mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, <italic>atg7</italic> and <italic>atg9</italic> mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the <italic>a priori</italic> knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.</p>