Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

Abstract

In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.

Expanded Molecular Imaging of Phytocompounds by Mass Spectrometry Using Novel On-Tissue Chemical Derivatization

“…An ideal OTCD workflow should have a number of key attributes: (1) it should be performed under mild conditions, (2) provide a high reaction yield on-tissue, (3) prevent the delocalization of analytes, (4) preserve tissue integrity, and (5) provide robust and reproducible results [12] . Through these experiments, we observed that 4-APEBA provided the greatest potential, with a significant sensitivity boost for derivatized abscisic acid, whereas BTA, GT, and DNPH provided enhancement, but were 1.6 to 2.9 log2-fold less responsive (Fig.…”

“…[1] However, only about 14,000 metabolites in the plant kingdom have been detected, suggesting that advanced analytical methods are needed to more thoroughly investigate such highly complex metabolomes. [2] This is even more evident at the level of single cells or single cell-types, where volumes and quantities of analytes are low and generally limit detection to only a small set of compounds. [3] Significant advancements in spatially-resolved and cell-specific metabolomics have emerged in the last decade, [3][4] and the use of these technologies have suggested a central role of cellular heterogeneity in biological systems (including plants) under different conditions where bulk measurements would mask relevant mechanistic insights.…”

Comparative metabolomic profiling of Arabidopsis thaliana roots and leaves reveals complex response mechanisms induced by a seaweed extract

“…In particular, using an untargeted metabolomic approach allows comprehensive assessment of numerous compounds in a single biological sample ( Patel et al., 2021 ). The untargeted approach is especially useful for providing an overview of changes in the plant metabolome under different conditions ( Katam et al., 2022 ). For example, this technique has recently been successfully applied to investigate the metabolic changes induced by seaweed extracts from the kelp, Ecklonia maxima in corn ( Zea mays ) under drought stress ( Tinte et al., 2022 ).…”

Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA

“…There are an estimated 200 000 to 1 000 000 distinct metabolites in the plant kingdom, where any single plant species can produce tens of thousands of unique metabolites, far more than most other organisms . However, only about 14 000 metabolites in the plant kingdom have been characterized, suggesting that advanced analytical methods are needed to more thoroughly investigate such highly complex metabolomes . This issue is further compounded when considering metabolite levels within single cells, where volumes and quantities of analytes are low and generally detection is limited to only a small set of compounds .…”