Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants?

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.

Two pyridoxal phosphate homeostasis proteins are essential for management of the coenzyme pyridoxal 5'-phosphate in Arabidopsis

Coenzyme management is important for homeostasis of the pool of active metabolic enzymes. The coenzyme pyridoxal 5'-phosphate (PLP) is involved in diverse enzyme reactions including amino acid and hormone metabolism. Regulatory proteins that contribute to PLP homeostasis remain to be explored in plants. Here, we demonstrate the importance of proteins annotated as PLP homeostasis proteins (PLPHPs) for controlling PLP in Arabidopsis (Arabidopsis thaliana). A systematic analysis indicates that while most organisms across kingdoms have a single PLPHP homolog, Angiosperms have two. PLPHPs from Arabidopsis bind PLP and exist as monomers, in contrast to reported PLP-dependent enzymes, which exist as multimers. Disrupting the function of both PLPHP homologs perturbs vitamin B6 (pyridoxine) content, inducing a PLP deficit accompanied by light hypersensitive root growth, unlike PLP biosynthesis mutants. Micrografting studies show that the PLP deficit can be relieved distally between shoots and roots. Chemical treatments probing PLP-dependent reactions, notably those for auxin and ethylene, provide evidence that PLPHPs function in the dynamic management of PLP. Assays in vitro show that Arabidopsis PLPHP can coordinate PLP transfer and withdrawal from other enzymes. This study thus expands our knowledge of vitamin B6 biology and highlights the importance of PLP coenzyme homeostasis in plants.

Next generation plant biostimulants & genome sequencing strategies for sustainable agriculture development

The best environment for plant growth and development contains certain essential metabolites. A broad category of metabolites known as "plant biostimulants" (PBs) includes biomolecules such as proteins, carbohydrates, lipids, and other secondary metabolites related to groups of terpenes, specific nitrogen-containing compounds, and benzene ring-conjugated compounds. The formation of biomolecules depends on both biotic and abiotic factors, such as the release of PB by plants, animals, and microorganisms, or it can result from the control of temperature, humidity, and pressure in the atmosphere, in the case of humic substances (HSs). Understanding the genomic outputs of the concerned organism (may be plants or others than them) becomes crucial for identifying the underlying behaviors that lead to the synthesis of these complex compounds. For the purposes of achieving the objectives of sustainable agriculture, detailed research on PBs is essential because they aid in increasing yield and other growth patterns of agro-economic crops. The regulation of homeostasis in the plant-soil-microbe system for the survival of humans and other animals is mediated by the action of plant biostimulants, as considered essential for the growth of plants. The genomic size and gene operons for functional and regulation control have so far been revealed through technological implementations, but important gene annotations are still lacking, causing a delay in revealing the information. Next-generation sequencing techniques, such as nanopore, nanoball, and Illumina, are essential in troubleshooting the information gaps. These technical advancements have greatly expanded the candidate gene openings. The secondary metabolites being important precursors need to be studied in a much wider scale for accurate calculations of biochemical reactions, taking place inside and outside the synthesized living cell. The present review highlights the sequencing techniques to provide a foundation of opportunity generation for agricultural sustainability.

B Vitamins: An Update on Their Importance for Plant Homeostasis

B vitamins are a source of coenzymes for a vast array of enzyme reactions, particularly those of metabolism. As metabolism is the basis of decisions that drive maintenance, growth, and development, B vitamin-derived coenzymes are key components that facilitate these processes. For over a century, we have known about these essential compounds and have elucidated their pathways of biosynthesis, repair, salvage, and degradation in numerous organisms. Only now are we beginning to understand their importance for regulatory processes, which are becoming an important topic in plants. Here, I highlight and discuss emerging evidence on how B vitamins are integrated into vital processes, from energy generation and nutrition to gene expression, and thereby contribute to the coordination of growth and developmental programs, particularly those that concern maintenance of a stable state, which is the foundational tenet of plant homeostasis.

'From metabolism to metabolism': holistic considerations on B-vitamin interactions, biofortification, and deficiencies

In the post-Green Revolution era, disparities in dietary access, rising obesity rates, demographic shifts, adoption of plant-based diets, and the impact of climate change collectively contribute to a progressive decline in dietary nutritional value, exacerbating B vitamin deficiencies across both low- and high-income countries. While the prevailing focus of biofortification has been on three micronutrients - provitamin A, iron, and zinc - utilizing conventional breeding, it is imperative to diversify biofortification strategies to combat micronutrient malnutrition. Metabolic engineering, facilitated by biotechnological tools, presents a promising avenue, contingent upon advances in fundamental knowledge, technological innovation, regulatory updates, and sustained public funding. Recognizing the intricate metabolic interplay of B vitamins in plants and humans, a comprehensive 'from metabolism to metabolism' approach is crucial for designing effective biofortification strategies that target multiple vitamins. This holistic perspective also extends beyond individual crops to encompass the entire food chain, a complex socioeconomic ecosystem that necessitates a paradigm shift, prioritizing quality over quantity.

Unravelling the biostimulant activity of a protein hydrolysate in lettuce plants under optimal and low N availability: a multi-omics approach

The application of protein hydrolysates (PH) biostimulants is considered a promising approach to promote crop growth and resilience against abiotic stresses. Nevertheless, PHs bioactivity depends on both the raw material used for their preparation and the molecular fraction applied. The present research aimed at investigating the molecular mechanisms triggered by applying a PH and its fractions on plants subjected to nitrogen limitations. To this objective, an integrated transcriptomic-metabolomic approach was used to assess lettuce plants grown under different nitrogen levels and treated with either the commercial PH Vegamin® or its molecular fractions PH1(>10 kDa), PH2 (1-10 kDa) and PH3 (<1 kDa). Regardless of nitrogen provision, biostimulant application enhanced lettuce biomass, likely through a hormone-like activity. This was confirmed by the modulation of genes involved in auxin and cytokinin synthesis, mirrored by an increase in the metabolic levels of these hormones. Consistently, PH and PH3 upregulated genes involved in cell wall growth and plasticity. Furthermore, the accumulation of specific metabolites suggested the activation of a multifaceted antioxidant machinery. Notwithstanding, the modulation of stress-response transcription factors and genes involved in detoxification processes was observed. The coordinated action of these molecular entities might underpin the increased resilience of lettuce plants against nitrogen-limiting conditions. In conclusion, integrating omics techniques allowed the elucidation of mechanistic aspects underlying PH bioactivity in crops. Most importantly, the comparison of PH with its fraction PH3 showed that, except for a few peculiarities, the effects induced were equivalent, suggesting that the highest bioactivity was ascribable to the lightest molecular fraction.

Physiological and Transcriptomic Analyses Reveal the Mechanisms Underlying Methyl Jasmonate-Induced Mannitol Stress Resistance in Banana

Exogenous methyl jasmonate (MeJA) application has shown promising effects on plant defense under diverse abiotic stresses. However, the mechanisms underlying MeJA-induced stress resistance in bananas are unclear. Therefore, in this study, we treated banana plants with 100 μM MeJA before inducing osmotic stress using mannitol. Plant phenotype and antioxidant enzyme activity results demonstrated that MeJA improved osmotic stress resistance in banana plants. Thereafter, to explore the molecular mechanisms underlying MeJA-induced osmotic stress resistance in banana seedlings, we conducted high-throughput RNA sequencing (RNA-seq) using leaf and root samples of "Brazilian" banana seedlings treated with MeJA for 0 h and 8 h. RNA-seq analysis showed that MeJA treatment upregulated 1506 (leaf) and 3341 (root) genes and downregulated 1768 (leaf) and 4625 (root) genes. Then, we performed gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses on the differentially expressed genes. We noted that linoleic acid metabolism was enriched in both root and leaf samples, and the genes of this pathway exhibited different expression patterns; 9S-LOX genes were highly induced by MeJA in the leaves, whereas 13S-LOX genes were highly induced in the roots. We also identified the promoters of these genes, as the differences in response elements may contribute to tissue-specific gene expression in response to MeJA application in banana seedlings. Overall, the findings of this study provide insights into the mechanisms underlying abiotic stress resistance in banana that may aid in the improvement of banana varieties relying on molecular breeding.

Exogenous riboflavin (vitamin B2) application enhances salinity tolerance through the activation of its biosynthesis in rice seedlings under salinity stress

Salinity stress triggers the accumulation of reactive oxygen species (ROS), leading to impaired plant growth. Riboflavin (RIB; vitamin B2) is synthesized by plants, fungi, and microorganisms and is a precursor of the coenzymes, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), which are important for cellular metabolism. In this study, we aimed to elucidate the mechanistic basis of the RIB-mediated alleviation of salinity stress in rice. We observed higher biomass accumulation and lower concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in RIB-pretreated seedlings under salinity stress. In vitro assays showed that H2O2 was scavenged as the RIB concentration increased, implying that RIB may function as a non-enzymatic antioxidant in ROS detoxification. RIB-pretreated seedlings accumulated more Na+ in the roots than in the leaf blades because of the contributions of OsHKT2;1, OsNHX1, and OsHKT1;4 in the roots and leaf sheaths, respectively. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis revealed increased RIB concentration in roots and shoots and upregulation of key genes (OsRIBA1, OsGCHI, OsLS, and OsRS) involved in RIB biosynthesis in the roots of RIB-pretreated seedlings. Taken together, our findings suggest that RIB pretreatment ameliorates salinity stress in rice by improving (1) oxidative stress tolerance, as increased RIB concentration may function as a non-enzymatic antioxidant, and (2) ionic stress tolerance, as RIB pretreatment limits Na+ accumulation in the leaf blades and maintains a favorable Na+/K+ balance.

Glutamate decarboxylase-1 is essential for efficient acclimation of Arabidopsis thaliana to nutritional phosphorus deprivation

Glutamate decarboxylase (GAD) is a Ca2+ -calmodulin-activated, cytosolic enzyme that produces γ-aminobutyrate (GABA) as the committed step of the GABA shunt. This pathway bypasses the 2-oxoglutarate to succinate reactions of the tricarboxylic acid (TCA) cycle. GABA also accumulates during many plant stresses. We tested the hypothesis that AtGAD1 (At5G17330) facilitates Arabidopsis acclimation to Pi deprivation. Quantitative RT-PCR and immunoblotting revealed that AtGAD1 transcript and protein expression is primarily root-specific, but inducible at lower levels in shoots of Pi-deprived (-Pi) plants. Pi deprivation reduced levels of the 2-oxoglutarate dehydrogenase (2-OGDH) cofactor thiamine diphosphate (ThDP) in shoots and roots by > 50%. Growth of -Pi atgad1 T-DNA mutants was significantly attenuated relative to wild-type plants. This was accompanied by: (i) an > 60% increase in shoot and root GABA levels of -Pi wild-type, but not atgad1 plants, and (ii) markedly elevated anthocyanin and reduced free and total Pi levels in leaves of -Pi atgad1 plants. Treatment with 10 mM GABA reversed the deleterious development of -Pi atgad1 plants. Our results indicate that AtGAD1 mediates GABA shunt upregulation during Pi deprivation. This bypass is hypothesized to circumvent ThDP-limited 2-OGDH activity to facilitate TCA cycle flux and respiration by -Pi Arabidopsis.

Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange

Vitamin B1 (thiamin) is a vital nutrient for most cells in nature, including marine plankton. Early and recent experiments show that B1 degradation products instead of B1 can support the growth of marine bacterioplankton and phytoplankton. However, the use and occurrence of some degradation products remains uninvestigated, namely N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), which has been a focus of plant oxidative stress research. We investigated the relevance of FAMP in the ocean. Experiments and global ocean meta-omic data indicate that eukaryotic phytoplankton, including picoeukaryotes and harmful algal bloom species, use FAMP while bacterioplankton appear more likely to use deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine. Measurements of FAMP in seawater and biomass revealed that it occurs at picomolar concentrations in the surface ocean, heterotrophic bacterial cultures produce FAMP in the dark-indicating non-photodegradation of B1 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton produce intracellular FAMP. Our results require an expansion of thinking about vitamin degradation in the sea, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange of the compound within the networks of plankton. IMPORTANCE Results of this collaborative study newly show that a vitamin B1 degradation product, N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), can be used by diverse marine microbes (bacteria and phytoplankton) to meet their vitamin B1 demands instead of B1 and that FAMP occurs in the surface ocean. FAMP has not yet been accounted for in the ocean and its use likely enables cells to avoid B1 growth deficiency. Additionally, we show FAMP is formed in and out of cells without solar irradiance-a commonly considered route of vitamin degradation in the sea and nature. Altogether, the results expand thinking about oceanic vitamin degradation, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as its generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange within networks of plankton.

Harnessing enzyme cofactors and plant metabolism: an essential partnership

Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.

Transcriptome and targeted metabolomic integrated analysis reveals mechanisms of B vitamin accumulation in Areca catechu nut development

Areca catechu is well known as a medicinal plant that has high nutritional and medicinal benefits. However, the metabolism and regulatory mechanism of B vitamins during areca nut development remain largely unclear. In this study, we obtained the metabolite profiles of six B vitamins during different areca nut developmental stages by targeted metabolomics. Furthermore, we obtained a panoramic expression profile of genes related to the biosynthetic pathway of B vitamins in areca nuts at different developmental stages using RNA-seq. In total, 88 structural genes related to B vitamin biosynthesis were identified. Furthermore, the integrated analysis of B vitamin metabolism data and RNA-seq data showed the key transcription factors regulating thiamine and riboflavin accumulation in areca nuts, including AcbZIP21, AcMYB84, and AcARF32. These results lay the foundation for understanding metabolite accumulation and the molecular regulatory mechanisms of B vitamins in A. catechu nut.

RNA sequencing-based exploration of the effects of far-red light on microRNAs involved in the shade-avoidance response of D. officinale

Dendrobium officinale (D. officinale) has remarkable medicinal functions and high economic value. The shade-avoidance response to far-red light importantly affects the D. officinale productivity. However, the regulatory mechanism of miRNAs involved in the far-red light-avoidance response is unknown. Previous studies have found that, in D. officinale, 730 nm (far-red) light can promote the accumulation of plant metabolites, increase leaf area, and accelerate stem elongation. Here, the effects of far-red light on D. officinale were analysed via RNA-seq. KEGG analysis of miRNA target genes revealed various far-red light response pathways, among which the following played central roles: the one-carbon pool by folate; ascorbate and aldarate; cutin, suberine and wax biosynthesis; and sulfur metabolism. Cytoscape analysis of DE miRNA targets showed that novel_miR_484 and novel_miR_36 were most likely involved in the effects of far-red light on the D. officinale shade avoidance. Content verification revealed that far-red light promotes the accumulation of one-carbon compounds and ascorbic acid. Combined with qPCR validation results, the results showed that miR395b, novel_miR_36, novel_miR_159, novel_miR_178, novel_miR_405, and novel_miR_435 may participate in the far-red light signalling network through target genes, regulating the D. officinale shade avoidance. These findings provide new ideas for the efficient production of D. officinale.

B vitamin supply in plants and humans: the importance of vitamer homeostasis

B vitamins are a group of water-soluble micronutrients that are required in all life forms. With the lack of biosynthetic pathways, humans depend on dietary uptake of these compounds, either directly or indirectly, from plant sources. B vitamins are frequently given little consideration beyond their role as enzyme accessory factors and are assumed not to limit metabolism. However, it should be recognized that each individual B vitamin is a family of compounds (vitamers), the regulation of which has dedicated pathways. Moreover, it is becoming increasingly evident that individual family members have physiological relevance and should not be sidelined. Here, we elaborate on the known forms of vitamins B₁ , B₆ and B₉ , their distinct functions and importance to metabolism, in both human and plant health, and highlight the relevance of vitamer homeostasis. Research on B vitamin metabolism over the past several years indicates that not only the total level of vitamins but also the oft-neglected homeostasis of the various vitamers of each B vitamin is essential to human and plant health. We briefly discuss the potential of plant biology studies in supporting human health regarding these B vitamins as essential micronutrients. Based on the findings of the past few years we conclude that research should focus on the significance of vitamer homeostasis - at the organ, tissue and subcellular levels - which could improve the health of not only humans but also plants, benefiting from cross-disciplinary approaches and novel technologies.

Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development

Riboflavin is the precursor of essential cofactors for diverse metabolic processes. Unlike animals, plants can de novo produce riboflavin through an ancestrally conserved pathway, like bacteria and fungi. However, the mechanism by which riboflavin regulates seed development is poorly understood. Here, we report a novel maize (Zea mays L.) opaque mutant o18, which displays an increase in lysine accumulation, but impaired endosperm filling and embryo development. O18 encodes a rate-limiting bifunctional enzyme ZmRIBA1, targeted to plastid where to initiate riboflavin biosynthesis. Loss of function of O18 specifically disrupts respiratory complexes I and II, but also decreases SDH1 flavinylation, and in turn shifts the mitochondrial tricarboxylic acid (TCA) cycle to glycolysis. The deprivation of cellular energy leads to cell-cycle arrest at G1 and S phases in both mitosis and endoreduplication during endosperm development. The unexpected up-regulation of cell-cycle genes in o18 correlates with the increase of H3K4me3 levels, revealing a possible H3K4me-mediated epigenetic back-up mechanism for cell-cycle progression under unfavourable circumstances. Overexpression of O18 increases riboflavin production and confers osmotic tolerance. Altogether, our results substantiate a key role of riboflavin in coordinating cellular energy and cell cycle to modulate maize endosperm development.

Thiamin stimulates growth, yield quality and key biochemical processes of cauliflower (Brassica oleracea L. var. Botrytis) under arid conditions

Thiamin is a crucial vitamin with a vast variety of anti-oxidative and physiological roles in plants subjected to abiotic stresses. We examined the efficiency of foliar-applied thiamin (50 and 100 mM) on growth, yield quality and key-biochemical characteristics of two cultivars (FD1 and FD3) of cauliflower (Brassica oleracea L.) under water-deficit stress. Water stress at the rate of 50% field capacity (F.C.) markedly decreased the plant biomass, leaf total phenolics and ascorbic acid (AsA) contents. In contrast, drought-induced increase was noted in the leaf [hydrogen peroxide (H2O2), AsA, proline, malondialdehyde (MDA), glycinebetaine (GB), total soluble proteins and oxidative defense system in terms of high activities of peroxidase (POD), and catalase (CAT) enzymes] and the inflorescence (total phenolics, proline, GB, MDA, H2O2, and activities of SOD and CAT enzymes) characteristics of cauliflower. However, foliar-applied thiamin significantly improved growth and physio-biochemical attributes except leaf and inflorescence MDA and H2O2 contents of both cauliflower cultivars under water stress. Overall, application of thiamin enhanced the plant growth may be associated with suppressed reactive oxygen species (ROS) and upregulated antioxidants defense system of cauliflower.

Natural Variation in Vitamin B1 and Vitamin B6 Contents in Rice Germplasm

Insufficient dietary intake of micronutrients contributes to the onset of deficiencies termed hidden hunger-a global health problem affecting approximately 2 billion people. Vitamin B1 (thiamine) and vitamin B6 (pyridoxine) are essential micronutrients because of their roles as enzymatic cofactors in all organisms. Metabolic engineering attempts to biofortify rice endosperm-a poor source of several micronutrients leading to deficiencies when consumed monotonously-have led to only minimal improvements in vitamin B1 and B6 contents. To determine if rice germplasm could be exploited for biofortification of rice endosperm, we screened 59 genetically diverse accessions under greenhouse conditions for variation in vitamin B1 and vitamin B6 contents across three tissue types (leaves, unpolished and polished grain). Accessions from low, intermediate and high vitamin categories that had similar vitamin levels in two greenhouse experiments were chosen for in-depth vitamer profiling and selected biosynthesis gene expression analyses. Vitamin B1 and B6 contents in polished seeds varied almost 4-fold. Genes encoding select vitamin B1 and B6 biosynthesis de novo enzymes (THIC for vitamin B1, PDX1.3a-c and PDX2 for vitamin B6) were differentially expressed in leaves across accessions contrasting in their respective vitamin contents. These expression levels did not correlate with leaf and unpolished seed vitamin contents, except for THIC expression in leaves that was positively correlated with total vitamin B1 contents in polished seeds. This study expands our knowledge of diversity in micronutrient traits in rice germplasm and provides insights into the expression of genes for vitamin B1 and B6 biosynthesis in rice.

Using continuous directed evolution to improve enzymes for plant applications

Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt ("plantize") enzymes from prokaryotes-especially exotic prokaryotes-to function well in mild, plant-like conditions.

A Core Metabolome Response of Maize Leaves Subjected to Long-Duration Abiotic Stresses

Abiotic stresses reduce crop growth and yield in part by disrupting metabolic homeostasis and triggering responses that change the metabolome. Experiments designed to understand the mechanisms underlying these metabolomic responses have usually not used agriculturally relevant stress regimes. We therefore subjected maize plants to drought, salt, or heat stresses that mimic field conditions and analyzed leaf responses at metabolome and transcriptome levels. Shared features of stress metabolomes included synthesis of raffinose, a compatible solute implicated in tolerance to dehydration. In addition, a marked accumulation of amino acids including proline, arginine, and γ-aminobutyrate combined with depletion of key glycolysis and tricarboxylic acid cycle intermediates indicated a shift in balance of carbon and nitrogen metabolism in stressed leaves. Involvement of the γ-aminobutyrate shunt in this process is consistent with its previously proposed role as a workaround for stress-induced thiamin-deficiency. Although convergent metabolome shifts were correlated with gene expression changes in affected pathways, patterns of differential gene regulation induced by the three stresses indicated distinct signaling mechanisms highlighting the plasticity of plant metabolic responses to abiotic stress.

Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O₂-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O₂ at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O₂-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

The Thiamin-Requiring 3 Mutation of Arabidopsis 5-Deoxyxylulose-Phosphate Synthase 1 Highlights How the Thiamin Economy Impacts the Methylerythritol 4-Phosphate Pathway

The thiamin-requiring mutants of Arabidopsis have a storied history as a foundational model for biochemical genetics in plants and have illuminated the central role of thiamin in metabolism. Recent integrative genetic and biochemical analyses of thiamin biosynthesis and utilization imply that leaf metabolism normally operates close to thiamin-limiting conditions. Thus, the mechanisms that allocate thiamin-diphosphate (ThDP) cofactor among the diverse thiamin-dependent enzymes localized in plastids, mitochondria, peroxisomes, and the cytosol comprise an intricate thiamin economy. Here, we show that the classical thiamin-requiring 3 (th3) mutant is a point mutation in plastid localized 5-deoxyxylulose synthase 1 (DXS1), a key regulated enzyme in the methylerythritol 4-phosphate (MEP) isoprene biosynthesis pathway. Substitution of a lysine for a highly conserved glutamate residue (E323) located at the subunit interface of the homodimeric enzyme conditions a hypomorphic phenotype that can be rescued by supplying low concentrations of thiamin in the medium. Analysis of leaf thiamin vitamers showed that supplementing the medium with thiamin increased total ThDP content in both wild type and th3 mutant plants, supporting a hypothesis that the mutant DXS1 enzyme has a reduced affinity for the ThDP cofactor. An unexpected upregulation of a suite of biotic-stress-response genes associated with accumulation of downstream MEP intermediate MEcPP suggests that th3 causes mis-regulation of DXS1 activity in thiamin-supplemented plants. Overall, these results highlight that the central role of ThDP availability in regulation of DXS1 activity and flux through the MEP pathway.

Metabolomics Analysis in Different Development Stages on SP0 Generation of Rice Seeds After Spaceflight

Spaceflight is a special abiotic stress condition. In recent years, it has been confirmed that the spaceflight caused the stress response of rice seeds, and the protein level, transcription level, and methylation level will change during the planting process after returning to the ground. However, the changes at the metabolome level are not very clear. In this study, two kinds of rice seeds, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the ShiJian-10 retractable satellite (SJ-10) for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the spaceflight caused the stress response of rice. The TLP and TS of DN3 identified 110 and 57 different metabolites, respectively, while the TLP and TS of DN6 identified 104 and 74 different metabolites, respectively. These metabolites included amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the tricarboxylic acid cycle (TCA) and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggested that the response mechanisms of the two different rice strains to spaceflight stress are different, and these differences may be reflected in energy consumption and compound biosynthesis of rice in different growth and development stages. This study provided new insights for further exploring the effects of spaceflight.

Perspective: Practical Approach to Preventing Subclinical B12 Deficiency in Elderly Population

Vitamin B12 (also known as cobalamin) is an essential water-soluble vitamin that plays a pivotal role for several physiologic functions during one's lifespan. Only certain microorganisms are able to synthetize B12, thus humans obtain cobalamin exclusively from their diet, specifically from animal-derived foods. Specific sub-group populations are at risk of vitamin B12 subclinical deficiency due to different factors including poor intake of animal source foods and age-dependent decrease in the capacity of intestinal B12 uptake. Consumption of animal products produces some negative health issues and negatively impacts sustainability while a plant-based diet increases the risk of B12 deficiency. Taking a cue from the aforementioned considerations, this narrative review aims to summarize facts about B12 deficiency and the burden of inadequate dietary intake in elderly population, as well as to discuss sustainable approaches to vitamin B12 deficiency in aging population.

Thiamin stimulates growth and secondary metabolites in turnip (Brassica rapa L.) leaf and root under drought stress

Thiamin, an important member of the vitamin B family, is believed to play a significant role in mitigating environmental stresses including drought stress. In turnip, drought stress causes a reduced growth, biomass yield, pigment content, total phenolics and ascorbic acid (AsA), particularly at 50% field capacity (F.C.) in the two cultivars (cv) studied. However, a significant enhancement was observed in the contents of leaf proline, glycinebetaine (GB), malondialdehyde (MDA), hydrogen peroxide (H₂ O₂ ) and the activities of catalase (CAT) and superoxide dismutase (SOD) as well as root proline, GB, total phenolics, AsA, H₂ O₂ , MDA and the activities of peroxidase (POD) and SOD. However, foliar-applied thiamin significantly improved (particularly 100 mM) all the growth attributes, photosynthetic pigments, leaf and root osmoprotectants (GB and proline), AsA, total phenolics and the activities of enzymatic antioxidants such as SOD and POD as well as root CAT in both turnip cultivars under drought stress conditions. Foliar application of thiamin was effective in decreasing the leaf and root H₂ O₂ and MDA content in both cultivars particularly at 50% F.C. Thiamin-induced growth of both turnip cultivars, particularly of cv. Purple Top, was found to be associated with increased photosynthetic pigments, proline and GB contents and antioxidant capacity, but reduced levels of reactive oxygen species (ROS) under water deficit conditions. So, it is suggested that exogenous application of thiamin can be effective in improving drought tolerance of plants.

Biostimulants Application: A Low Input Cropping Management Tool for Sustainable Farming of Vegetables

Biostimulants, are a diverse class of compounds including substances or microorganism which have positive impacts on plant growth, yield and chemical composition as well as boosting effects to biotic and abiotic stress tolerance. The major plant biostimulants are hydrolysates of plant or animal protein and other compounds that contain nitrogen, humic substances, extracts of seaweeds, biopolymers, compounds of microbial origin, phosphite, and silicon, among others. The mechanisms involved in the protective effects of biostimulants are varied depending on the compound and/or crop and mostly related with improved physiological processes and plant morphology aspects such as the enhanced root formation and elongation, increased nutrient uptake, improvement in seed germination rates and better crop establishment, increased cation exchange, decreased leaching, detoxification of heavy metals, mechanisms involved in stomatal conductance and plant transpiration or the stimulation of plant immune systems against stressors. The aim of this review was to provide an overview of the application of plant biostimulants on different crops within the framework of sustainable crop management, aiming to gather critical information regarding their positive effects on plant growth and yield, as well as on the quality of the final product. Moreover, the main limitations of such practice as well as the future prospects of biostimulants research will be presented.

Of clocks and coenzymes in plants: intimately connected cycles guiding central metabolism?

Plant fitness is a measure of the capacity of a plant to survive and reproduce in its particular environment. It is inherently dependent on plant health. Molecular timekeepers like the circadian clock enhance fitness due to their ability to coordinate biochemical and physiological processes with the environment on a daily basis. Central metabolism underlies these events and it is well established that diel metabolite adjustments are intimately and reciprocally associated with the genetically encoded clock. Thus, metabolic pathway activities are time-of-day regulated. Metabolite rhythms are driven by enzymes, a major proportion of which rely on organic coenzymes to facilitate catalysis. The B vitamin complex is the key provider of coenzymes in all organisms. Emerging evidence suggests that B vitamin levels themselves undergo daily oscillations in animals but has not been studied in any depth in plants. Moreover, it is rarely considered that daily rhythmicity in coenzyme levels may dictate enzyme activity levels and therefore metabolite levels. Here we put forward the proposal that B-vitamin-derived coenzyme rhythmicity is intertwined with metabolic and clock derived rhythmicity to achieve a tripartite homeostasis integrated into plant fitness.

Benefiting others and self: Production of vitamins in plants

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

Pure Organic Active Compounds Against Abiotic Stress: A Biostimulant Overview

Biostimulants (BSs) are probably one of the most promising alternatives nowadays to cope with yield losses caused by plant stress, which are intensified by climate change. Biostimulants comprise many different compounds with positive effects on plants, excluding pesticides and chemical fertilisers. Usually mixtures such as lixiviates from proteins or algal extracts have been used, but currently companies are interested in more specific compounds that are capable of increasing tolerance against abiotic stress. Individual application of a pure active compound offers researchers the opportunity to better standarise formulations, learn more about the plant defence process itself and assist the agrochemical industry in the development of new products. This review attempts to summarise the state of the art regarding various families of organic compounds and their mode/mechanism of action as BSs, and how they can help maximise agricultural yields under stress conditions aggravated by climate change.

Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest

Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions.

Comparative metabolomic responses of low- and high-cadmium accumulating genotypes reveal the cadmium adaptive mechanism in Brassica napus

Recently, oilseed rape has gathered interest for its ability to withstand elevated metal contents in plant, a key feature for remediation of contaminated soils. In this study, comparative and functional metabolomic analyses using liquid chromatography/mass spectrometry were undertaken to explore the metabolic basis of this attribute under cadmium (Cd) stress. Results revealed both conserved and differential metabolomic responses between genotype CB671 (tolerant Cd-accumulating) and its sensitive counterpart ZD622. CB671 responded to Cd stress by rearranging carbon flux towards production of compatible solutes, sugar storage forms and ascorbate, as well as jasmonates, ethylene and vitamin B6. Intriguingly, IAA abundance was reduced by 1.91-fold, which was in connection with tryptophan funnelling into serotonin (3.48-fold rise). In ZD622 by contrast, Cd provoked drastic depletion of carbohydrates and vitamins, but subtle hormones alteration. A striking accumulation of unsaturated fatty acids and oxylipins in CB671, paralleled by glycerophospholipids build-up and induction of inositol-derived signalling metabolites (up to 5.41-fold) suggested ability for prompt triggering of detoxifying mechanisms. Concomitantly, phytosteroids, monoterpenes and carotenoids were induced, denoting fine-tuned mechanisms for membrane maintenance, which was not evident in ZD622. Further, ZD622 markedly accumulated phenolics from upstream sub-classes of flavonoids; in CB671 however, a distinct phenolic wiring was activated, prioritizing anthocyanins and lignans instead. Along with cell wall (CW) saccharides, the activation of lignans evoked CW priming in CB671. Current results have demonstrated existence of notable metabolomic-based strategies for Cd tolerance in metal-accumulating oilseed rapes, and provided a holistic view of metabolites potentially contributing to Cd tolerance in this species.

The Barley S-Adenosylmethionine Synthetase 3 Gene HvSAMS3 Positively Regulates the Tolerance to Combined Drought and Salinity Stress in Tibetan Wild Barley

Drought and salinity are two of the most frequently co-occurring abiotic stresses. Despite recent advances in the elucidation of the effects of these stresses individually during the vegetative stage of plants, significant gaps exist in our understanding of the combined effects of these two frequently co-occurring stresses. Here, Tibetan wild barley XZ5 (drought tolerant), XZ16 (salt tolerant), and cultivated barley cv. CM72 (salt tolerant) were subjected to drought (D), salinity (S), or a combination of both treatments (D+S). Protein synthesis is one of the primary activities of the green part of the plant. Therefore, leaf tissue is an important parameter to evaluate drought and salinity stress conditions. Sixty differentially expressed proteins were identified by mass spectrometry (MALDI-TOF/TOF) and classified into 9 biological processes based on Gene Ontology annotation. Among them, 21 proteins were found to be expressed under drought or salinity alone; however, under D+S, 7 proteins, including S-adenosylmethionine synthetase 3 (SAMS3), were exclusively upregulated in drought-tolerant XZ5 but not in CM72. HvSAMS3 carries both N-terminal and central domains compared with Arabidopsis and activates the expression of several ethylene (ET)-responsive transcription factors. HvSAMS3 is mainly expressed in the roots and stems, and HvSAMS3 is a secretory protein located in the cell membrane and cytoplasm. Barley stripe mosaic virus-based virus-induced gene silencing (BSMV-VIGS) of HvSAMS3 in XZ5 severely compromised its tolerance to D+S and significantly reduced plant growth and K+ uptake. The reduced tolerance to the combined stress was associated with the inhibition of polyamines such as spermidine and spermine, polyamine oxidase, ethylene, biotin, and antioxidant enzyme activities. Furthermore, the exogenous application of ethylene and biotin improved the tolerance to D+S in BSMV-VIGS:HvSAMS3-inoculated plants. Our findings highlight the significance of HvSAMS3 in the tolerance to D+S in XZ5.

Construction and applications of a B vitamin genetic resource for investigation of vitamin-dependent metabolism in maize

The B vitamins provide essential co-factors for central metabolism in all organisms. In plants, B vitamins have surprising emerging roles in development, stress tolerance and pathogen resistance. Hence, there is a paramount interest in understanding the regulation of vitamin biosynthesis as well as the consequences of vitamin deficiency in crop species. To facilitate genetic analysis of B vitamin biosynthesis and functions in maize, we have mined the UniformMu transposon resource to identify insertional mutations in vitamin pathway genes. A screen of 190 insertion lines for seed and seedling phenotypes identified mutations in biotin, pyridoxine and niacin biosynthetic pathways. Importantly, isolation of independent insertion alleles enabled genetic confirmation of genotype-to-phenotype associations. Because B vitamins are essential for survival, null mutations often have embryo lethal phenotypes that prevent elucidation of subtle, but physiologically important, metabolic consequences of sub-optimal (functional) vitamin status. To circumvent this barrier, we demonstrate a strategy for refined genetic manipulation of vitamin status based on construction of heterozygotes that combine strong and hypomorphic mutant alleles. Dosage analysis of pdx2 alleles in endosperm revealed that endosperm supplies pyridoxine to the developing embryo. Similarly, a hypomorphic bio1 allele enabled analysis of transcriptome and metabolome responses to incipient biotin deficiency in seedling leaves. We show that systemic pipecolic acid accumulation is an early metabolic response to sub-optimal biotin status highlighting an intriguing connection between biotin, lysine metabolism and systemic disease resistance signaling. Seed-stocks carrying insertions for vitamin pathway genes are available for free, public distribution via the Maize Genetics Cooperation Stock Center.

Metabolomic Dynamics Reveals Oxidative Stress in Spongy Tissue Disorder During Ripening of Mangifera indica L. Fruit

Spongy tissue disorder, a mesocarp specific malady, severely affects the flavor and pulp characters of Alphonso mango fruit reducing its consumer acceptability. Here, we investigated comparative metabolomic changes that occur during ripening in healthy and spongy tissue-affected fruits using high resolution mass spectrometric analysis. During the spongy tissue formation, 46 metabolites were identified to be differentially accumulated. These putative metabolites belong to various primary and secondary metabolic pathways potentially involved in maintaining the quality of the fruit. Analysis revealed metabolic variations in tricarboxylic acid cycle and gamma amino butyric acid shunt generating reactive oxygen species, which causes stressed conditions inside the mesocarp. Further, reduced levels of antioxidants and enzymes dissipating reactive oxygen species in mesocarp deteriorate the fruit physiology. This oxidative stress all along affects the level of amino acids, sugars and enzymes responsible for flavor generation in the fruit. Our results provide metabolic insights into spongy tissue development in ripening Alphonso mango fruit.

Rethinking the PDH Bypass and GABA Shunt as Thiamin-Deficiency Workarounds

The PDH bypass and the GABA shunt serve to maintain mainline metabolic fluxes during episodes of organellar thiamin diphosphate deficiency.

Differential regulation of defence pathways in aromatic and non-aromatic indica rice cultivars towards fluoride toxicity

Excessive bioaccumulation of fluoride in IR-64 caused low abscisic acid level, inhibition of polyamine biosynthesis and ascorbate-glutathione cycle but not in Gobindobhog which had higher antioxidant activity. The current study presents regulation of diverse metabolic and molecular defence pathways during fluoride stress in non-aromatic rice variety, IR-64 and aromatic rice variety, Gobindobhog (GB). Increasing concentration of fluoride affected fresh weight, dry weight, vigour index and relative water content to a lesser extent in GB compared to IR-64. GB exhibited lower methylglyoxal accumulation and lipoxygenase activity compared to IR-64 during stress. The level of osmolytes (proline, amino acids and glycine-betaine) increased in both the stressed varieties. The biosynthesis of higher polyamines was stimulated in stressed GB. IR-64 accumulated higher amount of putrescine due to degradation of higher polyamines as supported by gene expression analysis. Unlike IR-64, GB efficiently maintained the ascorbate-glutathione cycle due to much lower fluoride bioaccumulation, compared to IR-64. GB adapted to fluoride stress by strongly inducing guaiacol peroxidase, phenylalanine ammonia lyase and a novel isozyme of superoxide dismutase. While GB accumulated higher abscisic acid (ABA) level during stress, IR-64 exhibited slow ABA degradation which enabled induction of associated osmotic stress-responsive genes. Unlike GB, ABA-independent DREB2A was downregulated in stressed IR-64. The research illustrates varietal differences in the defence machinery of the susceptible variety, IR-64, and the well adapted cultivar, GB, on prolonged exposure to increasing concentrations of fluoride.

Enhancement of vitamin B6 levels in rice expressing Arabidopsis vitamin B6 biosynthesis de novo genes

Vitamin B₆ (pyridoxine) is vital for key metabolic reactions and reported to have antioxidant properties in planta. Therefore, enhancement of vitamin B₆ content has been hypothesized to be a route to improve resistance to biotic and abiotic stresses. Most of the current studies on vitamin B₆ in plants are on eudicot species, with monocots remaining largely unexplored. In this study, we investigated vitamin B₆ biosynthesis in rice, with a view to examining the feasibility and impact of enhancing vitamin B₆ levels. Constitutive expression in rice of two Arabidopsis thaliana genes from the vitamin B₆ biosynthesis de novo pathway, AtPDX1.1 and AtPDX2, resulted in a considerable increase in vitamin B₆ in leaves (up to 28.3-fold) and roots (up to 12-fold), with minimal impact on general growth. Rice lines accumulating high levels of vitamin B₆ did not display enhanced tolerance to abiotic stress (salt) or biotic stress (resistance to Xanthomonas oryzae infection). While a significant increase in vitamin B₆ content could also be achieved in rice seeds (up to 3.1-fold), the increase was largely due to its accumulation in seed coat and embryo tissues, with little enhancement observed in the endosperm. However, seed yield was affected in some vitamin B₆ -enhanced lines. Notably, expression of the transgenes did not affect the expression of the endogenous rice PDX genes. Intriguingly, despite transgene expression in leaves and seeds, the corresponding proteins were only detectable in leaves and could not be observed in seeds, possibly pointing to a mode of regulation in this organ.

mRNA transcription profile of potato (Solanum tuberosum L.) exposed to ultrasound during different stages of in vitro plantlet development

KEY MESSAGE

In response to an ultrasound pulse, several hundred DEGs, including in response to stress, were up- or down-regulated in in vitro potato plantlets. Despite this abiotic stress, plantlets survived. Ultrasound (US) can influence plant growth and development. To better understand the genetic mechanism underlying the physiological response of potato to US, single-node segments of four-week-old in vitro plantlets were subjected to US at 35 kHz for 20 min. Following mRNA purification, 10 cDNA libraries were assessed by RNA-seq. Significantly differentially expressed genes (DEGs) were categorized by gene ontology or Kyoto Encyclopedia of Genes and Genomes identifiers. The expression intensity of 40,430 genes was studied. Several hundred DEGs associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, and response to stress, and which were expressed mainly in the extracellular region, nucleus, and plasma membrane, were either up- or down-regulated in response to US. RT-qPCR was used to validate RNA-seq data of 10 highly up- or down-regulated DEGs, and both Spearman and Pearson correlations between SeqMonk LFC and RT-qPCR LFC were highly positive (0.97). This study examines how some processes evolved over time (0 h, 24 h, 48 h, 1 week and 4 weeks) after an abiotic stress (US) was imposed on in vitro potato explants, and provides clues to the temporal dynamics in DEG-based enzyme functions in response to this stress. Despite this abiotic stress, plantlets survived.

Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity

In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.

Redesigning thiamin synthesis: Prospects and potential payoffs

Thiamin is essential for plant growth but is short-lived in vivo and energetically very costly to produce - a combination that makes thiamin biosynthesis a prime target for improvement by redesign. Thiamin consists of thiazole and pyrimidine moieties. Its high biosynthetic cost stems from use of the suicide enzyme THI4 to form the thiazole and the near-suicide enzyme THIC to form the pyrimidine. These energetic costs lower biomass yield potential and are likely compounded by environmental stresses that destroy thiamin and hence increase the rate at which it must be made. The energy costs could be slashed by refactoring the thiamin biosynthesis pathway to eliminate the suicidal THI4 and THIC reactions. To substantiate this design concept, we first document the energetic costs of the THI4 and THIC steps in the pathway and explain how cutting these costs could substantially increase crop biomass and grain yields. We then show that a refactored pathway must produce thiamin itself rather than a stripped-down analog because the thiamin molecule cannot be simplified without losing biological activity. Lastly, we consider possible energy-efficient alternatives to the inefficient natural THI4- and THIC-mediated steps.

Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis

Almost all cells require thiamin, vitamin B1 (B1), which is synthesized via the coupling of thiazole and pyrimidine precursors. Here we demonstrate that 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET) is a useful in vivo B1 precursor for representatives of ubiquitous marine picoeukaryotic phytoplankton and Escherichia coli – drawing attention to cHET as a valuable exogenous micronutrient for microorganisms with ecological, industrial, and biomedical value. Comparative utilization experiments with the terrestrial plant Arabidopsis thaliana revealed that it can also use exogenous cHET, but notably, picoeukaryotic marine phytoplankton and E. coli were adapted to grow on low (picomolar) concentrations of exogenous cHET. Our results call for the modification of the conventional B1 biosynthesis model to incorporate cHET as a key precursor for B1 biosynthesis in two domains of life, and for consideration of cHET as a microbial micronutrient currency modulating marine primary productivity and community interactions in human gut-hosted microbiomes.

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño

BACKGROUND

Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.

METHODS

Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.

RESULTS

A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.

DISCUSSION

Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.

A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis

The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate into the diphosphate can also very efficiently convert free HMP into the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2, that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins and ThiD2 fusion domains are small (∼130 residues) and do not belong to any previously known protein family. Genetic and biochemical analyses showed that representative standalone and fused ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogs and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases, ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover.

The Pseudoenzyme PDX1.2 Sustains Vitamin B6 Biosynthesis as a Function of Heat Stress

Plants sense temperature changes and respond by altering growth and metabolic activity to acclimate to the altered environmental conditions. The B vitamins give rise to vital coenzymes that are indispensable for growth and development but their inherent reactive nature renders them prone to destruction especially under stress conditions. Therefore, plant survival strategies would be expected to include mechanisms to sustain B vitamin supply under demanding circumstances. Here, using the example of vitamin B₆, we investigate the regulation of biosynthesis across eudicot and monocot species under heat stress. Most eudicots carry a pseudoenzyme PDX1.2 that is a noncatalytic homolog of the PDX1 subunit of the vitamin B₆ biosynthesis protein machinery, PYRIDOXINE BIOSYNTHESIS PROTEIN1. Using Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) as models, we show that PDX12 is transcriptionally regulated by the HSFA1 transcription factor family. Monocots only carry catalytic PDX1 homologs that do not respond to heat stress as demonstrated for rice (Oryza sativa) and maize (Zea mays), suggesting fundamental differences in the regulation of vitamin B₆ biosynthesis across the two lineages. Investigation of the molecular mechanism of PDX12 transcription reveals two alternative transcriptional start sites, one of which is exclusive to heat stress. Further data suggest that PDX1.2 leads to stabilization of the catalytic PDX1s under heat stress conditions, which would serve to maintain vitamin B₆ homeostasis in times of need in eudicots that carry this gene. Our analyses indicate an important abiotic stress tolerance strategy in several eudicots, which has not been evolutionarily adapted (or is not required) by monocots such as grasses.