Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development

Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos

Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic embryogenesis. Here, we investigate the spatial and single-cell expression profiles of key genes and the metabolic patterns of key metabolites by integrated single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (ST), and spatial metabolomics (SM). To evaluate the results of these analyses, we functionally characterized the potential roles of two representative marker genes, AATP1 and DOX2, in the regulation of cotton somatic embryo development. A publicly available web-based resource database ( https://cotton.cricaas.com.cn/somaticembryo/ ) in this study provides convenience for future studies of the expression patterns of marker genes at specific developmental stages during the process of SE in cotton.

Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development

Cotton fibers are single cells that develop from the epidermal cells in the outer integument of developing seeds. The processes regulating fiber cell development have been extensively studied; however, the spatiotemporal transcriptome and metabolome profiles during the early stages of fiber development remain largely unknown. In this study, we profile the dynamics of transcriptome and metabolome during the early stages of cotton fiber cell development using a combination of spatial transcriptomic, single-cell transcriptomic, and spatial metabolomic analyses. We identify the key genes (e.g., DOX2, KCS19.4, BEE3, and HOS3.7) and metabolites (e.g., linoleic acid, spermine, spermidine, and α-linolenic acid) that may regulate the early development of fiber cells. Finally, knockdown and gain-of-function analyses identify the crucial role of GhBEE3/Gh_A09G062900 in cotton fiber initiation. We also construct a publicly accessible website ( https://cotton.cricaas.com.cn/ovule/ ) for visualization of the spatiotemporal gene expression in cotton, providing a reference dataset for further studies on cotton fiber development.

Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration

The plasticity of plant cells underlies their wide capacity to regenerate, with increasing evidence in plants and animals implicating cell-cycle dynamics in cellular reprogramming. To investigate the cell cycle during cellular reprogramming, we developed a comprehensive set of cell-cycle-phase markers in the Arabidopsis root. Using single-cell RNA sequencing profiles and live imaging during regeneration, we found that a subset of cells near an ablation injury dramatically increases division rate by truncating G1 phase. Cells in G1 undergo a transient nuclear peak of glutathione (GSH) prior to coordinated entry into S phase, followed by rapid divisions and cellular reprogramming. A symplastic block of the ground tissue impairs regeneration, which is rescued by exogenous GSH. We propose a model in which GSH from the outer tissues is released upon injury, licensing an exit from G1 near the wound to induce rapid cell division and reprogramming.

Differentiation of genome-wide DNA methylation between japonica and indica rice

Rice (Oryza sativa L.) subspecies japonica and indica show distinct morphological and genetic differentiation. However, the differences in the genome-wide DNA methylation and its effects on gene expression and metabolic levels between japonica and indica rice remain unclear. In this study, we investigated the genome-wide DNA methylation, transcriptomes and metabolomes of 12 representative japonica and indica rice accessions, to reveal the differentiation between rice subspecies. We detected 83 327 differentially methylated regions (DMRs) and 14 903 DMR-associated genes between two subspecies. Indica rice showed significantly lower levels of the CG, CHG, and CHH methylation compared with japonica rice. Subsequently, we identified 5596 differentially expressed genes between the two subspecies, predominantly enriched in pathways related to carbohydrate and amino acid metabolism. By integrating DNA methylation with transcriptomic data, a significant correlation was established between methylation patterns and the expression level of key agronomic genes in rice. Furthermore, multi-omics analyses reveal that carbohydrate metabolism pathways, especially the tricarboxylic acid (TCA) cycle metabolites, are remarkable differentiation between rice subspecies. These results provide a foundation for future studies in rice domestication and genetic improvement.

TCA cycle impairment leads to PIN2 internalization and degradation via reduced MAB4 level and ARA6 components in Arabidopsis roots

The mitochondrial pyruvate dehydrogenase complex (PDC) plays a crucial role in linking the glycolysis pathway and the tricarboxylic acid (TCA) cycle. Previously, we reported that a mutation of MAB1, encoding an E1β subunit of PDC, affects the abundance of auxin efflux carriers PIN-FORMED proteins (PINs) via reduced recycling and enhanced degradation in vacuoles. Here, we further analyzed the effects of TCA cycle inhibition on vesicle trafficking using both the mab1-1 mutant and 3-BP, a TCA cycle inhibitor. Pharmacological and genetic impairment of the TCA cycle induced the aggregated components of ARA6, which is a plant-unique RAB5 GTPase that mediates endosomal trafficking to the plasma membrane. In addition, MAB4, which is an NPH3-like protein that inhibits PIN internalization from the plasma membrane, was severely reduced in 3-BP-treated roots and mab1-1. Furthermore, TCA cycle impairment led to the accumulation of reactive oxygen species in root tips, and treatment with H2O2 reduced MAB4 levels while increasing the internalization of PIN2 from the plasma membrane, and aggregated ARA6-positive compartments. These results suggest that TCA cycle impairment targets PIN proteins for degradation in the vacuole by disrupting both the MAB4-mediated block of internalization and the ARA6-mediated endocytic pathway.

Response of Ceratophyllum demersum L. and its epiphytic biofilms to 6PPD and 6PPD-Q exposure: Based on metabolomics and microbial community analysis

The emerging contaminant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and its ozone conversion product N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) pose a threat to aquatic ecosystems. Aquatic animals and plants exhibit vigorous responses at very low ambient concentrations. However, studies of submerged macrophytes, key producers in aquatic ecosystems, are limited and the full extent of their toxic effects and feedback mechanisms is unknown. To investigate the phytotoxicity of 6PPD and 6PPD-Q, we modeled plant responses to abiotic stress using Ceratophyllum demersum L. (C. demersum) as a representative submerged plant. Our findings indicate that 6PPD and 6PPD-Q disrupt physiological and biochemical processes in C. demersum, encompassing growth inhibition, reduction in photosynthetic pigments, induction of oxidative damage, and metabolic alterations. Moreover, unfavorable modifications to biofilms induced were also discernible supported by confocal laser scanning microscopy (CLSM) images and microbial community profiling. More importantly, we found a robust correlation between differentially expressed metabolites (DEMs) and dominant genera, and 6PPD and 6PPD-Q significantly altered their correlation. Overall, our results imply that even though C. demersum is a resilient submerged macrophyte, the toxic effects of 6PPD and 6PPD-Q cannot be disregarded.

Visualization of metabolite distribution based on matrix-assisted laser desorption/ionization-mass spectrometry imaging of tea seedlings (Camellia sinensis)

Tea seedlings (Camellia sinensis) have a well-developed root system with a strong taproot and lateral roots. Compared with ordinary cuttings, tea has stronger vitality and environmental adaptability, thus facilitating the promotion of good varieties. However, there is less of detailed research on the rooting and germination process of tea seeds. In this study, matrix-assisted laser desorption ionization time-of-flight-mass spectrometry was used to conduct non-targeted spatial mass spectrometry imaging of the main organs during growth of tea seedlings. A total of 1234 compounds were identified, which could be divided into 24 classes. Among them, theanine, as the most prominent nitrogen compound, was synthesized rapidly at the early stage of embryo germination, accounting for >90% of the total free amino acids in the radicle, and it was then transferred to each meristem region through the mesocolumnar sheath, indicating that theanine-based nitrogen flow plays a decisive role in organ formation during the development of tea seedlings. Nutrients stored in the cotyledon were rapidly hydrolyzed to dextrin and 3-phosphoglyceraldehyde at the early stages of germination, and subsequently converted to other forms that provided carbon and energy for development, such as raffinose and d-galactose (glucose), which were mainly distributed in the growing zones of the root apex and the apical meristems of the stem. This study provides a new perspective on the synthesis and metabolism of substances during the development of tea seedlings and contributes to a better understanding of the biological characteristics of tea varieties.

Source-sink synergy is the key unlocking sweet potato starch yield potential

Sweet potato starch is in high demand globally for food and industry. However, starch content is negatively correlated with fresh yield. It is urgent to uncover the genetic basis and molecular mechanisms underlying the starch yield of sweet potato. Here we systematically explore source-sink synergy-mediated sweet potato starch yield formation: the production, loading, and transport of photosynthates in leaves, as well as their unloading and allocation in storage roots, lead to starch content divergence between sweet potato varieties. Moreover, we find that six haplotypes of IbPMA1 encoding a plasma membrane H+-ATPase are significantly linked with starch accumulation. Overexpression of IbPMA1 in sweet potato results in significantly increased starch and sucrose contents, while its knockdown exhibits an opposing effect. Furthermore, a basic helix-loop-helix (bHLH) transcription factor IbbHLH49 directly targets IbPMA1 and activates its transcription. Overexpression of IbbHLH49 notably improves source-sink synergy-mediated fresh yield and starch accumulation in sweet potato. Both IbbHLH49 and IbPMA1 substantially influence sugar transport and starch biosynthesis in source and sink tissues. These findings expand our understanding of starch yield formation and provide strategies and candidate genes for high starch breeding in root and tuber crops.

In situ mass spectrometry imaging reveals pesticide residues and key metabolic pathways throughout the entire cowpea growth process

Cowpea plants, renowned for their high edibility, pose a significant risk of pesticide residue contamination. Elucidating the behavior of pesticide residues and their key metabolic pathways is critical for ensuring cowpea safety and human health. This study investigated the migration of pesticide residues and their key metabolic pathways in pods throughout the growth process of cowpea plants via in situ mass spectrometry. To this end, four pesticides--including systemic (thiram), and nonsystemic (fluopyram, pyriproxyfen, and cyromazine) pesticides--were selected. The results indicate the direct upward and downward transmission of pesticides in cowpea stems and pods. Systemic pesticides gradually migrate to the core of cowpea plants, whereas nonsystemic pesticides remain on the surface of cowpea peels. The migration rate is influenced by the cowpea maturity, logarithmic octanol-water partition coefficient (log Kow) value, and molecular weight of the pesticide. Further, 20 types of key metabolites related to glycolysis, tricarboxylic acid cycle, and flavonoid synthesis were found in cowpea pods after pesticide treatment. These findings afford insights into improving cowpea quality and ensuring the safe use of pesticides.

Phase separation of S-RNase promotes self-incompatibility in Petunia hybrida

Self-incompatibility (SI) is an intraspecific reproductive barrier widely present in angiosperms. The SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box (SLF) genes found in the Solanaceae, Plantaginaceae, Rosaceae, and Rutaceae. Recent studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box (SCF)SLF-mediated ubiquitin-proteasome system in a collaborative manner in Petunia, but how self-RNase functions largely remains mysterious. Here, we show that S-RNases form S-RNase condensates (SRCs) in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia hybrida. We further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs, which then sequester several actin-binding proteins, including the actin polymerization factor PhABRACL, the actin polymerization activity of which is reduced by S-RNase in vitro. Meanwhile, we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth inhibition. Taken together, our results demonstrate that phase separation of S-RNase promotes SI response in P. hybrida, revealing a new mode of S-RNase action.

A century of studying plant secondary metabolism-From "what?" to "where, how, and why?"

Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

Imaging plant metabolism in situ

Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

How metabolism and development are intertwined in space and time

Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.

Non-canonical and developmental roles of the TCA cycle in plants

Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.