Systems biology of plant metabolic interactions.

Metabolism is the key cellular process of plant physiology. Understanding metabolism and its dynamical behavior under different conditions may help plant biotechnologists to design new cultivars with desired goals. Computational systems biochemistry and incorporation of different omics data unravelled active metabolism and its variations in plants. In this review, we mainly focus on the basics of flux balance analysis (FBA), elementary flux mode analysis (EFMA), and some advanced computational tools. We describe some important results that were obtained using these tools. Limitations and challenges are also discussed.

Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites.

Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.

Molecular Insight of Plants Response to Drought Stress: Perspectives and New Insights towards Food Security.

In the face of climate-induced challenges, understanding the intricate molecular mechanisms underlying drought tolerance in plants has become imperative [...].

Molecular Mechanisms of CBL-CIPK Signaling Pathway in Plant Abiotic Stress Tolerance and Hormone Crosstalk.

Abiotic stressors, including drought, salt, cold, and heat, profoundly impact plant growth and development, forcing elaborate cellular responses for adaptation and resilience. Among the crucial orchestrators of these responses is the CBL-CIPK pathway, comprising calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs). While CIPKs act as serine/threonine protein kinases, transmitting calcium signals, CBLs function as calcium sensors, influencing the plant's response to abiotic stress. This review explores the intricate interactions between the CBL-CIPK pathway and plant hormones such as ABA, auxin, ethylene, and jasmonic acid (JA). It highlights their role in fine-tuning stress responses for optimal survival and acclimatization. Building on previous studies that demonstrated the enhanced stress tolerance achieved by upregulating CBL and CIPK genes, we explore the regulatory mechanisms involving post-translational modifications and protein-protein interactions. Despite significant contributions from prior research, gaps persist in understanding the nuanced interplay between the CBL-CIPK system and plant hormone signaling under diverse abiotic stress conditions. In contrast to broader perspectives, our review focuses on the interaction of the pathway with crucial plant hormones and its implications for genetic engineering interventions to enhance crop stress resilience. This specialized perspective aims to contribute novel insights to advance our understanding of the potential of the CBL-CIPK pathway to mitigate crops' abiotic stress.

Investigation of heavy metals uptake in root-shoot of native plant species adjoining wastewater channels.

Metal pollution in water, soil, and vegetation is an emerging environmental issue. Therefore, this study investigated the abundance of heavy metals (HMs) within roots and shoots of native plant species i.e., Bromus pectinatus, Cynodon dactylon, Poa annua, Euphorbia heliscopa, Anagallis arvensis, and Stellaria media grown in the adjoining area of municipal wastewater channels of a Pakistani city of Abbottabad. HMs concentrations (mg L-1) in municipal wastewater were: chromium (Cr) (0.55) > nickel (Ni) (0.09) > lead (Pb) (0.07) > cadmium (Cd) (0.03). Accumulation of HMs in both roots and shoots of plant species varied as B. pectinatus > C. dactylon > P. annua > E. heliscopa > A. arvensis > S. media. Irrespective of the plant species, roots exhibited higher concentrations of HMs than shoots. Higher amount of Cr (131.70 mg kg-1) was detected in the roots of B. pectinatus and the lowest amount (81 mg kg-1) in A. arvensis, Highest Cd concentration was found in the shoot of B. pectinatus and the lowest in the E. heliscopa. The highest concentration of Ni was found in the roots of S. media (37.40 mg kg-1) and the shoot of C. dactylon (15.70 mg kg-1) whereas the lowest Ni concentration was achieved in the roots of A. arvensis (12.10 mg kg-1) and the shoot of E. heliscopa (5.90 mg kg-1). The concentration of HMs in individual plant species was less than 1000 mg kg-1. Considering the higher values (> 1) of biological concentration factor (BCF), biological accumulation co-efficient (BAC), and translocation factor (TF), B. pectinatus and S. media species showed greater potential for HMs accumulation than other species. Therefore, these plants might be helpful for the remediation of HM-contaminated soil.

The CRZ1 transcription factor in plant fungi: regulation mechanism and impact on pathogenesis.

Calcium (Ca2+) is a universal signaling molecule that is tightly regulated, and a fleeting elevation in cytosolic concentration triggers a signal cascade within the cell, which is crucial for several processes such as growth, tolerance to stress conditions, and virulence in fungi. The link between calcium and calcium-dependent gene regulation in cells relies on the transcription factor Calcineurin-Responsive Zinc finger 1 (CRZ1). The direct regulation of approximately 300 genes in different stress pathways makes it a hot topic in host-pathogen interactions. Notably, CRZ1 can modulate several pathways and orchestrate cellular responses to different types of environmental insults such as osmotic stress, oxidative stress, and membrane disruptors. It is our belief that CRZ1 provides the means for tightly modulating and synchronizing several pathways allowing pathogenic fungi to install into the apoplast and eventually penetrate plant cells (i.e., ROS, antimicrobials, and quick pH variation). This review discusses the structure, function, regulation of CRZ1 in fungal physiology and its role in plant pathogen virulence.

Effect of plant-soil system on the restoration of community stability after wildfire in the northeast margin of Qinghai-Tibet plateau.

Wildfires, as an environmental filter, are pivotal ecological disturbances that reshape plant communities and soil dynamics, playing a crucial role in regulating biogeographic patterns and ecosystem services. In this study, we aim to explore the effects of wildfires on forest ecosystems, specifically focusing on the plant-soil feedback mechanisms within the northeastern margin of the Qinghai-Tibet Plateau (QTP). Utilizing Partial Least Squares Path Modeling (PLS-PM), we investigated the interrelationships among soil physicochemical properties, enzyme activities, species diversity, and community stability at varying post-fire recovery stages (5, 15, and 23 years). Results indicated that in the early recovery stages, rapid changes in soil properties such as decreased pH (p < 0.001) and increased nutrient availability facilitate the emergence of early successional species with high resource utilization traits. As the ecosystem evolved toward a climax community, the soil and vegetation exhibit increased stability. Furthermore, soil enzyme activities displayed dynamic patterns that corresponded with changes in soil nutrient content, directly influencing the regeneration and diversity of plant communities. Importantly, our study documented a transition in the influence of soil properties on community stability from direct positive effects in initial recovery phases to negative impacts in later stages, while indirect benefits accrue through increased species diversity and enzyme activity. Vegetation composition and structure changed dynamically with recovery time during community succession. Plant nutrient absorption and accumulation affected nutrient dynamics in the soil, influencing plant regeneration, distribution, and diversity. Our results underscore the complex interactions between soil and vegetation that drive the recovery dynamics post-wildfire, highlighting the resilience of forest ecosystems to fire disturbances. This study contributes to the understanding of post-fire recovery processes and offers valuable insights for the management and restoration of fire-affected forest ecosystems.

Improvement of morphophysiological and anatomical attributes of plants under abiotic stress conditions using plant growth-promoting bacteria and safety treatments.

Drought and salinity are the major abiotic stress factors negatively affecting the morphophysiological, biochemical, and anatomical characteristics of numerous plant species worldwide. The detrimental effects of these environmental factors can be seen in leaf and stem anatomical structures including the decrease in thickness of cell walls, palisade and spongy tissue, phloem and xylem tissue. Also, the disintegration of grana staking, and an increase in the size of mitochondria were observed under salinity and drought conditions. Drought and salt stresses can significantly decrease plant height, number of leaves and branches, leaf area, fresh and dry weight, or plant relative water content (RWC%) and concentration of photosynthetic pigments. On the other hand, stress-induced lipid peroxidation and malondialdehyde (MDA) production, electrolyte leakage (EL%), and production of reactive oxygen species (ROS) can increase under salinity and drought conditions. Antioxidant defense systems such as catalase, peroxidase, glutathione reductase, ascorbic acid, and gamma-aminobutyric acid are essential components under drought and salt stresses to protect the plant organelles from oxidative damage caused by ROS. The application of safe and eco-friendly treatments is a very important strategy to overcome the adverse effects of drought and salinity on the growth characteristics and yield of plants. It is shown that treatments with plant growth-promoting bacteria (PGPB) can improve morphoanatomical characteristics under salinity and drought stress. It is also shown that yeast extract, mannitol, proline, melatonin, silicon, chitosan, α-Tocopherols (vitamin E), and biochar alleviate the negative effects of drought and salinity stresses through the ROS scavenging resulting in the improvement of plant attributes and yield of the stressed plants. This review discusses the role of safety and eco-friendly treatments in alleviating the harmful effects of salinity and drought associated with the improvement of the anatomical, morphophysiological, and biochemical features in plants.

The role of CBL-CIPK signaling in plant responses to biotic and abiotic stresses.

Plants have a variety of regulatory mechanisms to perceive, transduce, and respond to biotic and abiotic stress. One such mechanism is the calcium-sensing CBL-CIPK system responsible for the sensing of specific stressors, such as drought or pathogens. CBLs perceive and bind Calcium (Ca2+) in response to stress and then interact with CIPKs to form an activated complex. This leads to the phosphorylation of downstream targets, including transporters and ion channels, and modulates transcription factor levels and the consequent levels of stress-associated genes. This review describes the mechanisms underlying the response of the CBL-CIPK pathway to biotic and abiotic stresses, including regulating ion transport channels, coordinating plant hormone signal transduction, and pathways related to ROS signaling. Investigation of the function of the CBL-CIPK pathway is important for understanding plant stress tolerance and provides a promising avenue for molecular breeding.

Ascorbic acid metabolism and functions.

This Special Issue was assembled to mark the 25th anniversary of the proposal of the d -mannose/ l -galactose (Smirnoff-Wheeler) ascorbate biosynthesis pathway in plants ( Wheeler et al., 1998 ). The issue aims to assess the current state of knowledge and to identify outstanding questions about ascorbate metabolism and functions in plants.

The "plant neurobiology" revolution.

The 21st-century "plant neurobiology" movement is an amalgam of scholars interested in how "neural processes", broadly defined, lead to changes in plant behavior. Integral to the movement (now called plant behavioral biology) is a triad of historically marginalized subdisciplines, namely plant ethology, whole plant electrophysiology and plant comparative psychology, that set plant neurobiology apart from the mainstream. A central tenet held by these "triad disciplines" is that plants are exquisitely sensitive to environmental perturbations and that destructive experimental manipulations rapidly and profoundly affect plant function. Since destructive measurements have been the norm in plant physiology, much of our "textbook knowledge" concerning plant physiology is unrelated to normal plant function. As such, scientists in the triad disciplines favor a more natural and holistic approach toward understanding plant function. By examining the history, philosophy, sociology and psychology of the triad disciplines, this paper refutes in eight ways the criticism that plant neurobiology presents nothing new, and that the topics of plant neurobiology fall squarely under the purview of mainstream plant physiology. It is argued that although the triad disciplines and mainstream plant physiology share the common goal of understanding plant function, they are distinct in having their own intellectual histories and epistemologies.

Modulation of plant immunity and biotic interactions under phosphate deficiency.

Phosphorus (P) is an essential macronutrient for plant life and growth. P is primarily acquired in the form of inorganic phosphate (Pi) from soil. To cope with Pi deficiency, plants have evolved an elaborate system to improve Pi acquisition and utilization through an array of developmental and physiological changes, termed Pi starvation response (PSR). Plants also assemble and manage mutualistic microbes to enhance Pi uptake, through integrating PSR and immunity signaling. A trade-off between plant growth and defense favors the notion that plants lower a cellular state of immunity to accommodate host-beneficial microbes for nutrition and growth at the cost of infection risk. However, the existing data indicate that plants selectively activate defense responses against pathogens, but do not or less against non-pathogens, even under nutrient deficiency. In this review, we highlight recent advances in the principles and mechanisms with which plants balance immunity and growth-related processes to optimize their adaptation to Pi deficiency.

Impact of vegetation composition and seasonality on sensitivity of modelled CO2 exchange in temperate raised bogs.

Encroachment of vascular plants (VP) in temperate raised bogs, as a consequence of altered hydrological conditions and nutrient input, is widely observed. Effects of such vegetation shift on water and carbon cycles are, however, largely unknown and identification of responsible plant physiological traits is challenging. Process-based modelling offers the opportunity of gaining insights into ecosystem functioning beyond observations, and to infer decisive trait shifts of plant functional groups. We adapted the Soil-Vegetation-Atmosphere Transfer model pyAPES to a temperate raised bog site by calibration against measured peat temperature, water table and surface CO2 fluxes. We identified the most important traits determining CO2 fluxes by conducting Morris sensitivity analysis (MSA) under changing conditions throughout the year and simulated VP encroachment. We further investigated transferability of results to other sites by extending MSA to parameter ranges derived from literature review. We found highly variable intra-annual plant traits importance determining ecosystem CO2 fluxes, but only a partial shift of importance of photosynthetic processes from moss to VP during encroachment. Ecosystem respiration was dominated by peat respiration. Overall, carboxylation rate, base respiration rate and temperature sensitivity (Q10) were most important for determining bog CO2 balance and parameter ranking was robust even under the extended MSA.

Odorant receptors for floral- and plant-derived volatiles in the yellow fever mosquito, Aedes aegypti (Diptera: Culicidae).

Adult mosquitoes require regular sugar meals, including nectar, to survive in natural habitats. Both males and females locate potential sugar sources using sensory proteins called odorant receptors (ORs) activated by plant volatiles to orient toward flowers or honeydew. The yellow fever mosquito, Aedes aegypti (Linnaeus, 1762), possesses a large gene family of ORs, many of which are likely to detect floral odors. In this study, we have uncovered ligand-receptor pairings for a suite of Aedes aegypti ORs using a panel of environmentally relevant, plant-derived volatile chemicals and a heterologous expression system. Our results support the hypothesis that these odors mediate sensory responses to floral odors in the mosquito's central nervous system, thereby influencing appetitive or aversive behaviors. Further, these ORs are well conserved in other mosquitoes, suggesting they function similarly in diverse species. This information can be used to assess mosquito foraging behavior and develop novel control strategies, especially those that incorporate mosquito bait-and-kill technologies.

Potential strategies for phytoremediation of heavy metals from wastewater with circular bioeconomy approach.

Water pollution is an inextricable problem that stems from natural and human-related factors. Unfortunately, with rapid industrialization, the problem has escalated to alarming levels. The pollutants that contribute to water pollution include heavy metals (HMs), chemicals, pesticides, pharmaceuticals, and other industrial byproducts. Numerous methods are used for treating HMs in wastewater, like ion exchange, membrane filtration, chemical precipitation, adsorption, and electrochemical treatment. But the remediation through the plant, i.e., phytoremediation is the most sustainable approach to remove the contaminants from wastewater. Aquatic plants illustrate the capacity to absorb excess pollutants including organic and inorganic compounds, HMs, and pharmaceutical residues present in agricultural, residential, and industrial discharges. The extensive exploitation of these hyperaccumulator plants can be attributed to their abundance, invasive mechanisms, potential for bioaccumulation, and biomass production. Post-phytoremediation, plant biomass can be toxic to both water bodies and soil. Therefore, the circular bioeconomy approach can be applied to reuse and repurpose the toxic plant biomass into different circular bioeconomy byproducts such as biochar, biogas, bioethanol, and biodiesel is essential. In this regard, the current review highlights the potential strategies for the phytoremediation of HMs in wastewater and various strategies to efficiently reuse metal-enriched biomass material and produce commercially valuable products. The implementation of circular bioeconomy practices can help overcome significant obstacles and build a new platform for an eco-friendlier lifestyle.

Integrated Full-Length Transcriptomics and Metabolomics Reveal Glycosyltransferase Involved in the Biosynthesis of Flavonol Glycosides in Laportea bulbifera.

Many species of the Urticaceae family are important cultivated fiber plants that are known for their economic and industrial values. However, their secondary metabolite profiles and associated biosynthetic mechanisms have not been well-studied. Using Laportea bulbifera as a model, we conducted widely targeted metabolomics, which revealed 523 secondary metabolites, including a unique accumulation of flavonol glycosides in bulblet. Through full-length transcriptomic and RNA-seq analyses, the related genes in the flavonoid biosynthesis pathway were identified. Finally, weighted gene correlation network analysis and functional characterization revealed four LbUGTs, including LbUGT78AE1, LbUGT72CT1, LbUGT71BX1, and LbUGT71BX2, can catalyze the glycosylation of flavonol aglycones (kaempferol, myricetin, gossypetin, and quercetagetin) using UDP-Gal and UDP-Glu as the sugar donors. LbUGT78AE1 and LbUGT72CT1 showed substrate promiscuity, whereas LbUGT71BX1 and LbUGT71BX2 exhibited different substrate and sugar donor selectivity. These results provide a genetic resource for studying Laportea in the Urticaceae family, as well as key enzymes responsible for the metabolism of valuable flavonoid glycosides.

Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals.

BACKGROUND: In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. RESULTS: A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. CONCLUSION: Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.

Assessing the High Temperature Effects on Stomatal Production.

The production of stomata, the epidermal pores of plants, is influenced by diverse environmental signals including high temperature. To assess its impact on stomatal formation, researchers need to grow plants in a carefully designed regime under controlled conditions and capture clear, microscopic views of the epidermis. Here, we describe a procedure to study the effect of high temperature on stomatal formation. This method can generate high-quality epidermal images of cotyledons, leaves, and hypocotyl of young Arabidopsis seedlings, which allow the determination of the pattern, density, and index of stomata on these tissues. Besides temperature, the protocol can serve as a general approach to examine stomatal phenotype and the effect of other external signals on stomatal formation.

Investigating the Effects of Temperature on Pathogen Propagation in Arabidopsis.

Temperature is one of the most prominent environmental factors that influence plant immunity. Depending on the plant-pathogen system, increased temperature may inhibit or enhance disease resistance or immunity in plants. Measuring the effect of temperature on plant immunity is the first step toward revealing climate effects on plant-pathogen interactions and molecular regulators of temperature sensitivity of plant immunity. Quantification of plant disease resistance or susceptibility under different temperatures can be accomplished by assessing pathogen growth over time in infected plants or tissues. Here, we present a protocol for quantifying pathogen growth in the most studied system of Arabidopsis thaliana and Pseudomonas syringae pathovar tomato (Pst) DC3000. We discuss important factors to consider for assaying pathogen growth in plants under different temperatures. This protocol can be used to assess temperature sensitivity of resistance in different plant genotypes and to various pathovars.

Climate, litter quality and radiation duration jointly regulate the net effect of UV radiation on litter decomposition.

Photodegradation via ultraviolet (UV) radiation is an important factor driving plant litter decomposition. Despite increasing attention to the role of UV photodegradation in litter decomposition, the specific impact of UV radiation on the plant litter decomposition stage within biogeochemical cycles remains unclear at regional and global scales. To clarify the variation rules of magnitude of UV effect on plant litter decomposition and their regulatory factors, we conducted a meta-analysis based on 54 published papers. Our results indicated that UV significantly promoted the mass loss of litter by facilitating decay of carbonaceous fractions and release of nitrogen and phosphorus. The promotion effect varied linearly or non-linearly with the time that litter exposed to UV, and with climatic factors. The UV effect on litter decomposition decreased first than increased on precipitation and temperature gradients, reaching its minimum in the area with a precipitation of 400-600 mm, and a temperature of 15-20 °C. This trend might be attributed to a potential equilibrium between the photofacilitation and photo-inhibition effects of UV under this condition. This variation in UV effect on precipitation gradient was in agreement with the fact that UV photodegradation effect was weakest in grassland ecosystems compared to that in forest and desert ecosystems. In addition, initial litter quality significantly influenced the magnitude of UV effect, but had no influence on the correlation between UV effect and climate gradient. Litter with lower initial nitrogen and lignin content shown a greater photodegradation effect, whereas those with higher hemicellulose and cellulose content had a greater photodegradation effect. Our study provides a comprehensive understanding of photodegradation effect on plant litter decomposition, indicates potentially substantial impacts of global enhancements of litter decomposition by UV, and highlights the necessity to quantify the contribution of photochemical minerallization pathway and microbial degradation pathway in litter decomposition.