Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses

The Influence of Bisphenol A on Parsley: A Biochemical and Metabolomics Integrative Perspective

Bisphenol A (BPA), a widely used industrial chemical, poses environmental concerns due to its persistence and potential effects on plant systems. This study examines the impact of three BPA exposure levels on parsley plants, focusing on physiological, biochemical, and metabolomic responses. BPA exposure significantly shaped the plant's defense mechanisms, mainly through increased phenolic (up to 16.81%) and flavonoid (up to 37.94%) accumulation compared to the control group, which, in turn, enhanced antioxidant activity [up to 34% in 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 51% in cupric reducing antioxidant capacity (CUPRAC)]. A moderate correlation between phenolic content and radical scavenging ability [R: 0.61 for DPPH and R: 0.44 for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] highlights phenolics' role in mitigating BPA-induced oxidative stress. Low BPA concentrations stimulated gas exchange and photosynthesis, while higher levels (≥3 mg/L) disrupted these processes, causing physiological damage, especially in stomatal conductance (gs) and photochemical efficiency (Fv/Fo). Metabolomic profiling revealed concentration-dependent shifts in secondary metabolism, lipid biosynthesis, and stress-response pathways. At higher BPA levels, plants elicited defense mechanisms, such as flavonoids (rhamnetin, luteolin-7-O-β-D-glucronide, and quercetin-7-O-glucoside) and anthocyanin pathways, to tackle oxidative stress, though these systems became overwhelmed. Our findings show that while parsley can initially adapt to low BPA exposure, higher concentrations compromise its physiological and metabolic balance, threatening plant health and productivity.

Metabolomic Profiling of Pogostemon cablin Reveals Disruption of Secondary Metabolite Biosynthesis Induced by Corynespora cassiicola Infection

Pogostemon cablin (patchouli) is an economically important aromatic plant widely used in the fragrance and pharmaceutical industries. This study investigates the effects of Corynespora leaf spot disease (CLSD) on the metabolic profiles and patchouli alcohol content of patchouli leaves. Utilizing gas chromatography-mass spectrometry (GC-MS), real-time PCR (qPCR), and comprehensive non-targeted metabolomic analyses (HS-SPME-GC-MS and LC-MS/MS), we compared diseased (LD-TJ) and healthy (CK) leaves. Results revealed a significant 51% reduction in patchouli alcohol content in CLSD-infected leaves, which was correlated with a 94% decrease in expression of the patchoulol synthase (PTS)-encoding gene (p < 0.01) and a 79% reduction in farnesyl pyrophosphate synthase (FPPS)-encoding gene expression (p < 0.05), both critical for terpenoid biosynthesis. Metabolomic analyses identified extensive disruptions in both volatile and non-volatile compounds, with the majority of differential abundance metabolites (DAMs) being downregulated. Key metabolic pathways, including beta-alanine metabolism and nicotinate/nicotinamide metabolism, were notably affected, indicating broader metabolic instability. Additionally, crucial transcription factors involved in terpenoid biosynthesis were significantly downregulated, indicating a potential mechanism by which C. cassiicola may compromise patchouli quality through modulation of host metabolic processes. These findings underscore the urgent need to develop disease-resistant P. cablin cultivars through genetic and metabolic engineering to enhance the sustainability and productivity of this valuable industrial crop.

Utilizing Microbial Inoculants to Alleviate Continuous Cropping Obstacles: Insights into the Metabolites and Transcriptomic Responses of Pinellia ternata

Pinellia ternata (Thunb.) Breit is a widely used medicinal herb in Traditional Chinese Medicine (TCM). Still, its sustainable cultivation is threatened by continuous cropping obstacles, which disrupt soil ecosystems, reduce yield, and degrade quality. Objectives: This study explores the potential of microbial inoculants to mitigate these challenges through integrated metabolomic and transcriptomic analyses. Methods: Soil samples from fields with and without continuous cropping issues were used to compare the effects of microbial inoculants on the secondary metabolism and gene expression of P. ternata. Results and Discussion: Metabolomic profiling identified 20,969 metabolites, with significant changes in lipid-like molecules (22.2%), organic acids (9.1%), and phenylpropanoids (7.0%) under microbial treatment. Notable increases in phenylalanine and caffeic acid levels were observed in microbial-inoculated plants. Correspondingly, transcriptomic analysis revealed the upregulation of phenylalanine ammonia-lyase (PAL) and other stress-related genes, confirming the metabolic shifts. Clustering and machine learning analyses highlighted the critical roles of metabolites and genes in enhancing plant resilience. Microbial inoculants improved secondary metabolite production. Implications: These findings provide valuable insights into the mechanisms of microbial-plant interactions and establish a sustainable approach for cultivating P. ternata, addressing the challenges of continuous cropping while improving crop productivity and quality.

Plant secondary metabolites against biotic stresses for sustainable crop protection

Sustainable agriculture practices are indispensable for achieving a hunger-free world, especially as the global population continues to expand. Biotic stresses, such as pathogens, insects, and pests, severely threaten global food security and crop productivity. Traditional chemical pesticides, while effective, can lead to environmental degradation and increase pest resistance over time. Plant-derived natural products such as secondary metabolites like alkaloids, terpenoids, phenolics, and phytoalexins offer promising alternatives due to their ability to enhance plant immunity and inhibit pest activity. Recent advances in molecular biology and biotechnology have improved our understanding of how these natural compounds function at the cellular level, activating specific plant defense through complex biochemical pathways regulated by various transcription factors (TFs) such as MYB, WRKY, bHLH, bZIP, NAC, and AP2/ERF. Advancements in multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, have significantly improved the understanding of the regulatory networks that govern PSM synthesis. These integrative approaches have led to the discovery of novel insights into plant responses to biotic stresses, identifying key regulatory genes and pathways involved in plant defense. Advanced technologies like CRISPR/Cas9-mediated gene editing allow precise manipulation of PSM pathways, further enhancing plant resistance. Understanding the complex interaction between PSMs, TFs, and biotic stress responses not only advances our knowledge of plant biology but also provides feasible strategies for developing crops with improved resistance to pests and diseases, contributing to sustainable agriculture and food security. This review emphasizes the crucial role of PSMs, their biosynthetic pathways, the regulatory influence of TFs, and their potential applications in enhancing plant defense and sustainability. It also highlights the astounding potential of multi-omics approaches to discover gene functions and the metabolic engineering of genes associated with secondary metabolite biosynthesis. Taken together, this review provides new insights into research opportunities for enhancing biotic stress tolerance in crops through utilizing plant secondary metabolites.

Specialized metabolome and transcriptome atlas of developing Arabidopsis thaliana seed under warm temperatures

Seed development, which depends on parent plants genetic background and mother plant environmental conditions, is a major component determining seed composition. Seed quality is a main agricultural concern, impacting both food and non-food applications, while also playing a central role in biodiversity conservation and environment protection. Climate change, in particular the emergence of extremely high temperatures, constitute a critical global threat to agriculture. Specialized metabolites (SMs) play crucial roles in the interactions of plants and seeds with their environments. Several SMs are known to be protective compounds involved in seed stress responses, thus impacting their quality. In this study, we performed untargeted metabolomic (LC-MS/MS) and transcriptomic (RNA-Seq) analyses of Arabidopsis thaliana seeds harvested at six developmental stages (Globular, Transition, Torpedo, Bent cotyledon, Mature green and Dry seed), and developed under control and warm temperature conditions. Those data provide an original and valuable resource that could be used to identify SMs and genes involved in seed heat stress responses and for the study of their regulation and functions during seed development.

Adaptable Alchemy: Exploring the Flexibility of Specialized Metabolites to Environmental Perturbations Through Post-Translational Modifications (PTMs)

Plants are subjected to various stresses during the growth process, including biotic stresses, as well as abiotic stresses such as temperature, drought, salt, and heavy metals. To cope with these biotic and abiotic adversities, plants have evolved complex regulatory mechanisms during their long-term environmental adaptations. In a suddenly changing environment, protein modifiers target other proteins to induce post-translational modification (PTM) in order to maintain cell homeostasis and protein biological activity in plants. PTMs modulate the activity of enzymes and transcription factors in their respective metabolic pathways, enabling plants to produce essential compounds for their survival under stress conditions. Examples of post-translational mechanisms include phosphorylation, ubiquitination, glycosylation, acetylation, protein-protein interactions, and targeted protein degradation. Furthermore, the role of histone modifications in regulating secondary metabolism deserves attention due to its potential impact on heritability and its contribution to stress tolerance. Understanding the epigenetic aspect of these modifications can provide valuable insights into the mechanisms underlying stress response. In this context, also examining PTMs that impact the biosynthesis of secondary metabolites is meaningful. Secondary metabolites encompass a wide range of compounds such as flavonoids, alkaloids, and terpenoids. These secondary metabolites play a crucial role in plant defense against herbivores, pathogens, and oxidative stress. In this context, it is imperative to understand the contribution of secondary metabolism to plant tolerance to abiotic stresses and how this understanding can be leveraged to improve long-term survival. While many studies have focused on the transcriptional regulation of these metabolites, there is a growing interest in understanding various changes in PTMs, such as acetylation, glycosylation, and phosphorylation, that are able to modulate plants' response to environmental conditions. In conclusion, a comprehensive exploration of post-translational mechanisms in secondary metabolism can enhance our understanding of plant responses to abiotic stress. This knowledge holds promise for future applications in genetic improvement and breeding strategies aimed at increasing plant resilience to environmental challenges.

Microscopy and spatial-metabolomics identify tissue-specific metabolic pathways uncovering salinity and drought tolerance mechanisms in Avicennia marina and Phoenix dactylifera roots

In arid and semi-arid climates, native plants have developed unique strategies to survive challenging conditions. These adaptations often rely on molecular pathways that shape plant architecture to enhance their resilience. Date palms (Phoenix dactylifera) and mangroves (Avicennia marina) endure extreme heat and high salinity, yet the metabolic pathways underlying this resilience remain underexplored. Here, we integrate tissue imaging with spatial metabolomics to uncover shared and distinct adaptive features in these species. We found that mangrove roots accumulate suberin and lignin in meristematic tissues, this is unlike other plant species, where only the differentiation zones contain these compounds. Our metabolomic analysis shows that date palm roots are enriched in metabolites involved in amino acid biosynthesis, whereas compounds involved in lignin and suberin production were more abundant in mangrove roots. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed tissue- and species-specific metabolite distributions in root tissues. We identified common osmoprotectants accumulating in the exodermis/epidermis of date palm and mangrove root meristems, along with a unique metabolite highly abundant in the inner cortex of date palm roots. These findings provide valuable insights into stress adaptation pathways and highlight key tissue types involved in root stress response.

Thriving in a salty future: morpho-anatomical, physiological and molecular adaptations to salt stress in alfalfa (Medicago sativa L.) and other crops

BACKGROUND

With soil salinity levels rising at an alarming rate, accelerated by climate change and human interventions, there is a growing need for crop varieties that can grow on saline soils. Alfalfa (Medicago sativa) is a cool-season perennial leguminous crop, commonly grown as forage, biofuel feedstock and soil conditioner. It demonstrates significant potential for agricultural circularity and sustainability, for example by fixing nitrogen, sequestering carbon and improving soil structures. Although alfalfa is traditionally regarded as a moderately salt-tolerant species, modern alfalfa varieties display specific salt-tolerance mechanisms, which could be used to pave its role as a leading crop able to grow on saline soils.

SCOPE

Alfalfa's salt tolerance underlies a large variety of cascading biochemical and physiological mechanisms. These are partly enabled by its complex genome structure and out-crossing nature, but which entail impediments for molecular and genetic studies. This review first summarizes the general effects of salinity on plants and the broad-ranging mechanisms for dealing with salt-induced osmotic stress, ion toxicity and secondary stress. Second, we address the defensive and adaptive strategies that have been described for alfalfa, such as the plasticity of alfalfa's root system, hormonal crosstalk for maintaining ion homeostasis, spatiotemporal specialized metabolite profiles and the protection of alfalfa-rhizobia associations. Finally, bottlenecks for research of the physiological and molecular salt-stress responses as well as biotechnology-driven improvements of salt tolerance are identified and discussed.

CONCLUSION

Understanding morpho-anatomical, physiological and molecular responses to salinity is essential for the improvement of alfalfa and other crops in saline land reclamation. This review identifies potential breeding targets for enhancing the stability of alfalfa performance and general crop robustness for rising salt levels as well as to promote alfalfa applications in saline land management.

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.

Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review

A number of consequences of climate change, notably salinity, put global food security at risk by impacting the development and production of lentils. Salinity-induced stress alters lentil genetics, resulting in severe developmental issues and eventual phenotypic damage. Lentils have evolved sophisticated signaling networks to combat salinity stress. Lentil genomics and transcriptomics have discovered key genes and pathways that play an important role in mitigating salinity stress. The development of saline-smart cultivars can be further revolutionized by implementing proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, machine learning, and speed breeding approaches. All these cutting-edge approaches represent a viable path toward creating saline-tolerant lentil cultivars that can withstand climate change and meet the growing demand for high-quality food worldwide. The review emphasizes the gaps that must be filled for future food security in a changing climate while also highlighting the significant discoveries and insights made possible by omics and other state-of-the-art biotechnological techniques.

Integrative physiological, transcriptomic, and metabolomic analysis of Abelmoschus manihot in response to Cd toxicity

Rapid industrialization and urbanization have caused severe soil contamination with cadmium (Cd) necessitating effective remediation strategies. Phytoremediation is a widely adopted technology for remediating Cd-contaminated soil. Previous studies have shown that Abelmoschus manihot has a high Cd accumulation capacity and tolerance indicating its potential for Cd soil remediation. However, the mechanisms underlying its response to Cd stress remain unclear. In this study, physiological, transcriptomic, and metabolomic analyses were conducted to explore the response of A. manihot roots to Cd stress at different time points. The results revealed that Cd stress significantly increased malondialdehyde (MDA) levels in A. manihot, which simultaneously activated its antioxidant defense system, enhancing the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) by 19.73%-50%, 22.87%-38.89%, and 32.31%-45.40% at 12 h, 36 h, 72 h, and 7 days, respectively, compared with those in the control (CK). Moreover, transcriptomic and metabolomic analyses revealed 245, 5,708, 9,834, and 2,323 differentially expressed genes (DEGs), along with 66, 62, 156, and 90 differentially expressed metabolites (DEMs) at 12 h, 36 h, 72 h, and 7 days, respectively. Through weighted gene coexpression network analysis (WGCNA) of physiological indicators and transcript expression, eight hub genes involved in phenylpropanoid biosynthesis, signal transduction, and metal transport were identified. In addition, integrative analyses of metabolomic and transcriptomic data highlighted the activation of lipid metabolism and phenylpropanoid biosynthesis pathways under Cd stress suggesting that these pathways play crucial roles in the detoxification process and in enhancing Cd tolerance in A. manihot. This comprehensive study provides detailed insights into the response mechanisms of A. manihot to Cd toxicity.

Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox

Floral color and scent profiles vary across species, geographical locations, and developmental stages. The exclusive floral color and fragrance of Chimonanthus praecox is contributed by a range of endogenous chemicals that distinguish it from other flowers and present amazing ornamental value. This comprehensive review explores the intricate interplay of environmental factors, chemicals and genes shaping the flower color and fragrance of Chimonanthus praecox. Genetic and physiological factors control morpho-anatomical attributes as well as pigment synthesis, while environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Specific genes control pigment synthesis, and environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Physiological processes including plant hormone contribute to flower color and fragrance. Hormones, notably ethylene, exert a profound influence on varioustraits. Pigment investigations have spotlighted specific flavonoids, including kaempferol 3-O-rutinoside, quercetin, and rutin. Red tepals exhibit unique composition with cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside being distinctive components. Elucidating the molecular basis of tepal color variation, particularly in red and yellow varieties, involves the identification of crucial regulatory genes. In conclusion, this review unravels the mysteries of Chimonanthus praecox, providing a holistic understanding of its flower color and fragrance for landscape applications. This comprehensive review uniquely explores the genetic intricacies, chemical and environmental influences that govern the mesmerizing flower color and fragrance of Chimonanthus praecox, providing valuable insights for its landscape applications. This review article is designed for a diverse audience, including plant geneticists, horticulturists, environmental scientists, urban planners, and students, offering understandings into the genetic intricacies, ecological significance, and practical applications of Chimonanthus praecox across various disciplines. Its appeal extends to professionals and enthusiasts interested in plant biology, conservation, and industries dependent on unique floral characteristics.