Biology subjects

Wewer, V.

Publications and source records attributed to Wewer, V..

9 recordsLinked to original sources

bioRxiv2026

FE DEFICIENCY-INDUCED KELCH REPEAT PROTEIN 1 (FDK1) links coumarin metabolism and iron homeostasis during alkaline iron deficiency in Arabidopsis

Although iron (Fe) is abundant in soils, its low solubility, particularly under alkaline conditions, often limits plant Fe acquisition. Under these conditions, coumarin-mediated Fe mobilization becomes increasingly important. Arabidopsis thaliana FE DEFICIENCY-INDUCED KELCH REPEAT PROTEIN 1 (FDK1, AT3G07720) is strongly induced by Fe deficiency and regulated by the central transcription factor FIT, but its function is unknown. We investigated FDK1 using genetic, physiological, metabolite, and transcriptomic analyses. Loss of FDK1 altered root growth, whereas this phenotype was restored in the FDK1-Ox overexpression line. Under alkaline Fe deficiency, growth medium from FDK1-Ox contained strongly increased levels of the Fe-mobilizing coumarins fraxetin and esculetin compared with wild type, whereas their induction was attenuated in fdk1-1. RNA-seq analysis linked FDK1 abundance to coumarin biosynthesis and iron-homeostasis gene expression. FIT and many FIT-associated genes were highly expressed in FDK1-Ox, whereas several upstream iron-homeostasis regulators, including bHLH Ib factors, were highest in fdk1-1. These findings identify FDK1 as a component of the alkaline Fe-deficiency response that promotes iron-mobilizing coumarin accumulation and is associated with coordinated regulation of iron-homeostasis genes.

plant biology↗

bioRxiv2026

Metabolic profiling and genome-scale modelling uncover mechanistic drivers of microbiome stability in synthetic maize root community

Stability is a desirable property for agricultural microbiomes, but there is a poor understanding of the mechanisms that mediate microbial community stability. A representative bacterial synthetic community from maize roots has been proposed by Niu et al. (2017, PNAS, 114:E2450) as a model system to study microbiome stability. This SynCom assembles stably when all seven members are present, but community diversity collapses without the keystone E. ludwigii strain. In this study, we used complementary in vitro experiments and in silico metabolic modelling to assess the role of metabolites for the stability of this SynCom, by defining the metabolic niches occupied by each strain, as well as their cross-feeding phenotypes and B-vitamin dependencies. We show that the individual member strains occupy complementary metabolic niches, measured by the depletion of distinct metabolites in exometabolomic experiments, as well as contrasting growth phenotypes on diverse carbon substrates, patterns which are largely recapitulated by computational simulations. Minimal medium experiments show that the established seven-member community comprises a mixture of prototrophic and auxotrophic strains. Correspondingly, experimental and in silico cross-feeding phenotypes showed that spent media harvested from the prototrophic strains can sustain growth of two auxotrophs and let to the identification of B-vitamin dependencies. Altogether, this study highlights the complementary power of in vitro and in silico approaches and suggests that the metabolic mechanisms of this SynCom can serve as design principles to inform the rational assembly of stable plant-associated microbial communities.

microbiology↗

bioRxiv2026

A hidden T-DNA-linked inversion-duplication causes a pronounced light-dependent phenotype in Arabidopsis

T-DNA insertion mutants are widely used to disrupt genes and infer their functions, yet the insertions can also trigger unintended genomic changes that confound phenotypic interpretation. Here, we used T-DNA insertion mutants affecting the major mitochondrial malate dehydrogenase (MDH1) and the heterodimeric NAD-dependent malic enzymes (ME1 and ME2) to examine their functional coordination across photoperiods and irradiance regimes. Under short days, especially at low light intensity, mdh1xme2 mutants were markedly smaller than wild type and, unexpectedly, than the mdh1xme1xme2 triple mutant, and they showed a more pronounced reduction in photosynthetic capacity. ME1 was undetectable in mdh1xme2, implying that the double and triple mutants effectively lack heterodimeric ME and should therefore behave similarly, contrary to what we observed. Whole-genome analysis resolved this discrepancy by revealing that the MDH1 T-DNA insertion in mdh1xme2 is accompanied by a major rearrangement, a 137-kbp duplication downstream of the insertion site, which was absent in the mdh1xme1xme2 triple mutant. This duplication increased gene dosage and elevated transcript abundance across the duplicated interval, while proteomics detected 5 of the 38 encoded proteins, including PEPC1. mdh1xme2 accumulated oxaloacetate-derived amino acids and displayed an altered carbon/nitrogen balance, making PEPC1 a plausible contributor to the exacerbated mdh1xme2 phenotype. Together, our data indicate that a T-DNA-linked structural variant can amplify expression of dozens of genes and intensify phenotypes at specific conditions, thereby affecting the interpretation of genotype-phenotype relationships. Because Agrobacterium-mediated DNA transfer also underpins many genome-editing workflows, our findings argue that structural validation around insertion/editing loci should be considered essential when interpreting T-DNA-derived plant lines.

plant biology↗

bioRxiv2026

Quantification of Phytohormones in Plants - Optimized Extraction, Separation and Detection

Phytohormones are key players in the regulation of plant development and metabolism. The different phytohormone classes comprise numerous chemically very diverse compounds, which are often present at very low concentrations. The chemical properties of phytohormones range from acidic to basic and from polar to non-polar. Furthermore, concentration varies strongly among different phytohormones, between plant species, tissues and developmental stages. Challenges often arise when only small amounts of plant material are available and when plant species are investigated in which the phytohormone profile has not yet been characterized. To establish a method for comprehensive phytohormone analysis we addressed these challenges by choosing and optimizing a suitable extraction method followed by optimized HPLC separation. We compared the most widely-used mass spectrometric detection methods, multiple reaction monitoring (MRM) on a triple quad instrument with high-resolution mass spectrometry (HRMS) on a Q-TOF instrument, and discuss the advantages of both methods and their limitations. O_LIWe compared various methods described in literature for the extraction of six phytohormone classes by liquid-liquid extraction and solid phase extraction purification and describe our optimizations to the selected method. C_LIO_LIWe optimized HPLC separation for 50 different phytohormones. C_LIO_LIWe evaluated the application of MRM and HRMS detection strategies. C_LI

biochemistry↗

bioRxiv2026

NADP-malic enzyme 1 couples ABA signaling to ROS-auxin patterning to restrict Arabidopsis root growth

Abscisic acid (ABA) restricts primary root growth by reshaping reactive oxygen species (ROS) dynamics and hormone signaling at the root apex, yet how cellular reductant supply for redox homeostasis is integrated into this response remains unclear. Here, we show that the cytosolic NADP-dependent malic enzyme 1 (NADP-ME1) is required for full ABA inhibition of Arabidopsis primary root elongation after germination. Three independent me1 loss-of-function mutants retained significant elongation of primary roots under ABA compared with wild type. In wild type, ABA induced an asymmetric auxin response at the root tip, whereas me1 roots failed to establish this auxin asymmetry and instead accumulated superoxide, indicating disrupted ROS balance. Pharmacological perturbation of auxin transport and ethylene biosynthesis/signaling attenuated the mutant phenotype, linking NADP-ME1 function to auxin-ethylene interactions during ABA-regulated growth. NADP-ME1 loss amplifies ABA-dependent transcriptional rewiring, including induction of oxidative stress and depression of growth-associated hormone modules. Co-immunoprecipitation coupled with bimolecular fluorescence complementation identified ascorbate peroxidase 1 (APX1) and major latex protein-like 34 (MLP34) as NADP-ME1 interaction partners, suggesting functional coupling between NADPH production and ROS detoxification. Together, our results support a model in which NADP-ME1 shapes the superoxide/H2O2 balance to control auxin patterning at the root tip and thereby execute ABA-mediated growth inhibition.

plant biology↗

bioRxiv2024

From Flowering Time to High Temperature Resilience: PHOTOPERIOD 1 (PPD-H1) Controls Spike Fertility through Improving Stress Resistance and Energy Metabolism under High Ambient Temperatures

High ambient temperature (HT) impairs reproductive development and grain yield in temperate crops. To ensure reproductive success under HT, plants must maintain developmental stability. However, the mechanisms integrating plant development and temperature resilience are largely unknown. Here, we demonstrate that PHOTOPERIOD 1 (PPD-H1), homologous to PSEUDO RESPONSE REGULATOR genes of the Arabidopsis circadian clock, controls developmental stability in response to HT in barley. We analyzed HT responses in independent introgression lines with either the ancestral wild-type Ppd-H1 allele or the natural ppd-h1 variant, selected in spring varieties to delay flowering and enhance yield under favourable conditions. HT delayed inflorescence development and reduced grain number in ppd-h1 mutant lines, while the wild-type Ppd-H1 genotypes accelerated reproductive development and showed a stable grain set under HT. Using a CRISPR/Cas9-induced ppd-h1 mutant, we confirmed that the CCT domain of Ppd-H1 controls developmental stability, but not clock gene expression. Transcriptome and phytohormone analyses in developing leaves and inflorescences revealed increased stress gene expression and abscisic acid levels in the leaf and inflorescence of the natural and induced mutant ppd-h1 lines. Furthermore, the mutant ppd-h1 lines downregulated photosynthesis-and energy metabolism-related genes, and reduced auxin and cytokinin levels in the inflorescence, which impaired anther and pollen development. By contrast, in the wild-type Ppd-H1 plants, the transcriptome and phytohormone levels and anther and pollen development remained stable under HT. Our findings suggest that Ppd-H1 enhances stress resistance and energy metabolism, thereby stabilizing reproductive development, floret fertility and grain set under HT.

plant biology↗

bioRxiv2024

Drought resistance and improved yield result from modified malate metabolism in guard and vascular companion cells

Drought is a major threat to food security. Water loss through stomata is an inevitable consequence of CO2 uptake, and water deficit inhibits plant growth, making it challenging to develop drought-resistant strategies without compromising yield. Here, we generated tobacco plants expressing a maize NADP-dependent malate decarboxylating enzyme in stomata and vascular cells (ME plants), which show higher seed yield and faster maturation compared to wild-type (WT) plants under normal irrigation and after drought. While WT plants die after 45 days of drought, ME plants survive without any adverse effects on seed production. In addition, ME plants exhibit improved photosynthetic efficiency despite reduced stomatal conductance and changes in stem morphology, which are likely related to their ability to withstand drought. We propose that enhanced C4-like biochemistry in cells surrounding the vascular system and increased sugar export likely compensated for the reduced stomatal conductance in ME plants. The study demonstrates that cell-targeted metabolic modifications can avoid pleiotropic effects and facilitate the stacking of beneficial traits to improve crop design. Significance StatementDrought is one of the biggest threats to global food security, and its impact on crop yield is expected to worsen due to climate change. Traditionally, drought resistance has often come at the expense of yield, creating a negative trade-off. However, we present here a promising solution to this challenge. We have developed a novel approach that successfully uncouples the negative balance between drought resistance and yield. By introducing a maize enzyme into specific tobacco cells, we have created drought-resistant plants with faster growth and higher seed yield. Most importantly, after prolonged drought, while the wild type dies, the modified plants maintain their high yield. This technology paves the way for greater food security and resilience to climate change.

plant biology↗

bioRxiv2021

Metabolic analysis of a bacterial synthetic community from maize roots provides new mechanistic insights into microbiome stability

Stability is a desirable property for agricultural microbiomes, but there is a poor understanding of the mechanisms that mediate microbial community stability. Recently, a representative bacterial synthetic community from maize roots has been proposed as a model system to study microbiome stability (Niu 2017, PNAS, 114:E2450). This SynCom assembles stably when all seven members are present, but community diversity collapses without the keystone E. cloacae strain. The aim of this study was to assess the role of metabolites for the stability of this SynCom, by defining the metabolic niches occupied by each strain, as well as their cross-feeding phenotypes and B-vitamin dependencies. We show that the individual member strains occupy complementary metabolic niches, measured by the depletion of distinct metabolites in exometabolomic experiments, as well as contrasting growth phenotypes on diverse carbon substrates. Minimal medium experiments show that the established seven-member community comprises a mixture of prototrophic and auxotrophic strains. Correspondingly, experimental cross-feeding phenotypes showed that spent media harvested from the prototrophic strains can sustain growth of two auxotrophs. We suggest that the metabolic mechanisms exhibited by this SynCom could serve as design principles to inform the rational assembly of stable plant-associated microbial communities.

microbiology↗

bioRxiv2017

Lipid transfer from plants to arbuscular mycorrhiza fungi

Arbuscular mycorrhiza (AM) symbioses contribute to global carbon cycles as plant hosts divert up to 20% of photosynthate to the obligate biotrophic fungi. Previous studies suggested carbohydrates as the only form of carbon transferred to the fungi. However, de novo fatty acid (FA) synthesis has not been observed in AM fungi in absence of the plant. In a forward genetic approach, we identified two Lotus japonicus mutants defective in AM-specific paralogs of lipid biosynthesis genes (KASI and GPAT6). These mutants perturb fungal development and accumulation of emblematic fungal 16:1{omega}5 FAs. Using isotopolog profiling we demonstrate that 13C patterns of fungal FAs recapitulate those of wild-type hosts, indicating cross-kingdom lipid transfer from plants to fungi. This transfer of labelled FAs was not observed for the AM-specific lipid biosynthesis mutants. Thus, growth and development of beneficial AM fungi is not only fueled by sugars but depends on lipid transfer from plant hosts.

plant biology↗