Biology subjects

Krapp, A.

Publications and source records attributed to Krapp, A..

9 recordsLinked to original sources

bioRxiv2025

The Arabidopsis nucleoporins 98A/B are essential for NLP7 nuclear accumulation in response to nitrate

The nuclear compartment is an essential evolutionary gain in eukaryotes. Stimulus-induced nuclear accumulation of transcription factors allows rapid and reversible regulation of gene expression. Nitrate-regulated nuclear accumulation of the master transcriptional regulator NLP7, a member of the RWP-RK family of transcription factors, triggers a major gene expression cascade. Whether and how this process is regulated at the level of the nuclear pore remains elusive. Here we show that the mobile nucleoporin NUP98A and its close homolog NUP98B interact with NLP7 in the nucleus and that the nitrate-triggered nuclear accumulation of NLP7 is impaired in their absence. We also demonstrated that the simultaneous loss of NLP7 and NUP98A has a strong and specific effect on the expression of nitrate-regulated genes, resulting in a drastic reduction in plant growth. Our results indicate that plant NUP98 acts on nitrate use by plants through its interaction with the top-tier NLP7 transcription factor. Significance StatementNucleoporins (NUPs) are fundamental components of all eukaryotic cells. They are increasingly recognized not only as structural components of the nuclear pore complex but also as active regulators of gene expression and signaling pathways across eukaryotes. NUP98 proteins in mammals are multifunctional proteins with key roles beyond nucleocytoplasmic transport. The adaptation of plants to nitrogen availability is crucial for their development and yield. The master transcription factor NLP7 orchestrates early responses to nitrate supply and is regulated by a rapid nitrate-regulated nucleo-cytosolic shuttling. In this study, we demonstrate that the Arabidopsis nucleoporins 98A/B enable acclimation of Arabidopsis to N status by gating the nucleocytoplasmic trafficking of the nitrate sensor NLP7 transcription factor, enlarging their functional network. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/677877v2_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@1bae44corg.highwire.dtl.DTLVardef@e245bforg.highwire.dtl.DTLVardef@1513778org.highwire.dtl.DTLVardef@110cce2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

What Large Language Models Know About Plant Molecular Biology

Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MOBIPLANT, the first comprehensive benchmark for evaluating LLMs in this domain, developed by a consortium of 112 plant scientists across 19 countries. MOBIPLANT comprises 565 expert-curated multiple-choice questions and 1,075 synthetically generated questions, spanning core topics from gene regulation to plant-environment interactions. We benchmarked seven leading chat-based LLMs using both automated scoring and human evaluation of open-ended answers. Models performed well on multiple-choice tasks (exceeding 75% accuracy), although most of them exhibited a consistent bias towards option A. In contrast, expert reviews exposed persistent limitations, including factual misalignment, hallucinations, and low self-awareness. Critically, we found that model performance strongly correlated with the citation frequency of source literature, suggesting that LLM knowledge inherits the visibility distribution of the underlying scientific corpus. Consequently, models tend to be more reliable on consolidated topics and less reliable on under-cited or recently emerging ones. We also benchmarked agents equipped with web-search and additional tools in more complex tasks involving DNA sequence analysis. These agents were outperformed by domain specific models in sequence classification and regression tasks, indicating an opportunity for joint agentic systems that combine both the reasoning power of LLMs and the dedicated processing of DNA models. This understanding is key to guiding both the development of next-generation models and the informed use of current tools in the everyday work of plant researchers. MOBIPLANT is publicly available online in this link.

plant biology↗

bioRxiv2024

Nitrate activates a MKK3-dependent MAPK module via NLP transcription factors in Arabidopsis

Plant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via NIN-LIKE PROTEIN (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen-activated protein (MAP) kinase genes are among the early nitrate-responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen-depleted Arabidopsis (Arabidopsis thaliana) plants triggers, within minutes, a MAPK cascade that requires NLP-dependent transcriptional induction of MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 13 (MAP3K13) and MAP3K14. Importantly, nitrate reductase-deficient mutants exhibited nitrate-induced MAPK activities comparable to those observed in wild-type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate-stimulated gene expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that a MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency. Significance statementNitrate is an essential nutrient that also acts as a signaling molecule to regulate plant metabolism and development. We identified a specific MAPK cascade that is activated by nitrate and regulates several nitrate-dependent responses, such as senescence and nitrate transport.

plant biology↗

bioRxiv2024

Overexpressing NRT2.7 induces nitrate export from the vacuole and increases growth of Arabidopsis

Nitrogen nutrition is essential for crop yield but applying fertilizers has detrimental effects on the environment. Compartmenting nitrate into vacuoles is one of the options to develop Nitrogen-efficient crop adapted to less fertilizers. Only few proteins involved in nitrate transport on the tonoplast have been identified. CLCa is the major transporter involved in nitrate storage in Arabidopsis but it can also facilitate nitrate remobilization from the vacuole in guard cells. Several other nitrate transporters amongst NRT2.7 have been localized in this membrane. The transport mechanism of NRT2.7 has not yet been defined as this protein is present mainly in seed cells that are not easily amenable for electrophysiology analysis. Here, we investigated NRT2.7 function through its ectopic overexpression in a clca knock-out mutant. Although the growth diminution of clca on nitrogen sufficient medium was complemented, nitrate homeostasis was not restored by NRT2.7 activity. Moreover, NRT2.7 ectopic overexpression in wild-type background (WT) increased growth under limiting nitrogen supply, suggesting that NRT2.7 stimulates nitrate efflux from vacuoles. This hypothesis was demonstrated by electrophysiological nitrate flux measurements on isolated vacuoles. This discovery of NRT2.7 function and more largely the coupling of vacuolar nitrate fluxes with growth under low nitrate supply, will enable new strategies for engineering better NUE for a more sustainable agriculture. HighlightThe overexpression of the nitrate transporter NRT2.7 stimulates growth by increasing the export of nitrate from the vacuole, the main cell compartment for nitrate storage.

plant biology↗

bioRxiv2024

The MKK3 module integrates nitrate and light signals to modulate secondary dormancy in Arabidopsis thaliana

Seed dormancy corresponds to a reversible blockage of germination. Primary dormancy is established during seed maturation while secondary dormancy is set up on the dispersed seed, following an exposure to unfavourable factors. Both dormancies are relieved in response to environmental factors, such as light, nitrate and coldness. QTL analyses for preharvest sprouting identified MKK3 kinase in cereals as a player in dormancy control. Here, we showed that MKK3 also plays a role in secondary dormancy in Arabidopsis within a signalling module composed of MAP3K13/14/19/20, MKK3 and clade-C MAPKs. Seeds impaired in this module acquired heat-induced secondary dormancy more rapidly than WT seeds and this dormancy is less sensitive to nitrate, a signal able to release dormancy. We also demonstrated that MPK7 was strongly activated in the seed during dormancy release, especially in response to light and nitrate. This activation was greatly reduced in map3k13/14/19/20 and mkk3 mutants. Finally, we showed that the module was not regulated, and apparently did not regulate, the genes controlling ABA/GA hormone balance, one of the crucial mechanisms of seed dormancy control. Overall, our work identified a whole new MAPK module controlling seed germination and enlarged the panel of functions of the MKK3-related modules in plants.

plant biology↗

bioRxiv2024

The endophytic fungus Serendipita indica alters auxin distribution in Arabidopsis thaliana roots through alteration of auxin transport and conjugation to promote plant growth

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Co-colonization of Arabidopsis roots with S. indica significantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by which S. indica promotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant-fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 (GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.

plant biology↗

bioRxiv2023

BdNRT2A and BdNRT3.2 are the major components of the High-Affinity nitrate Transport System in Brachypodium distachyon

O_LIAn efficient nitrate uptake system contributes to the improvement of crop nitrogen use efficiency under low nitrogen availability. The High Affinity nitrate Transport System (HATS) in plants is active in low external nitrate and is mediated by a two-component system [high affinity transporters NRT2 associated to a partner protein NRT3 (NAR2)]. C_LIO_LIIn Brachypodium, the model plant for C3 cereals, we investigated the role of BdNRT2A and BdNRT3.2 through various experimental approaches including gene expression profiling, functional characterisation in heterologous system, intracellular localization by imaging, and reverse genetics via gene silencing. C_LIO_LIExpression of BdNRT2.A and BdNRT3.2 genes in response to nitrate availability fits with the characteristics of the HATS components. Co-expression of BdNRT2A and BdNRT3.2 is required for an effective nitrate transport in the heterologous expression system Xenopus oocytes. Functional interaction between BdNRT2A-GFP and BdNRT3.2-RFP fusion proteins has been observed at the plasma membrane in Arabidopsis protoplasts in transient expression experiments. BdNRT3.2 appeared to be necessary for the plasma membrane localization of BdNRT2A. 15Nitrate influx measurements with bdnrt2a mutants (two amiRNA mutants and one NaN3 induced mutant with a truncated NRT2A protein), confirmed that BdNRT2A is a major contributor of the HATS in Brachypodium. C_LIO_LIDirected mutagenesis in BdNRT2A of a conserved Ser residue (S461) specific to monocotyledons has been performed to mimic a non-phosphorylated S461A or a constitutively phosphorylated S461D, in order to evaluate its potential role in the BdNRT2A and BdNRT3.2 interaction leading to plasma membrane targeting. Interestingly, the phosphorylation status of S461 did not modify the interaction, suggesting on a more complex mechanism. C_LIO_LIIn conclusion, our data show that BdNRT2A and BdNRT3.2 are the main components of the nitrate HATS activity in Brachypodium (Bd21-3) and allow an optimal growth in low N conditions. C_LI

plant biology↗

bioRxiv2022

The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply

Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Ongoing work has identified several transcriptional regulators of nitrate signaling, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN 7 (NLP7), but additional regulators likely remain to be identified. Here, we characterized Arabidopsis NLP2 as a master upstream transcriptional regulator of early nitrate responses that interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, a DNA binding motif, and some target genes with NLP7. Additional genetic, genomic and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multi-tiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production. One-sentence summaryNLP2 and NLP7 orchestrate plant responses to nitrate supply and control nitrate- dependent regulation of carbon and energy metabolism.

plant biology↗

bioRxiv2019

Wounding and insect feeding trigger two independent MAPK pathways with distinct regulation and kinetics

Wounding is caused by abiotic and biotic factors and triggers complex short- and long-term responses at the local and systemic level. These responses are under the control of complex signaling pathways, which are still poorly understood. Here, we show that the rapid activation of MKK4/5-MPK3/6 by wounding is independent of jasmonic acid (JA) signaling and that, contrary to what happens in tobacco, this fast module does not control wound-triggered JA accumulation in Arabidopsis. We also demonstrate that a second MAPK module, constituted by MKK3 and the clade-C MAPKs MPK1/2/7, is activated by wounding in an independent manner. We provide evidence that the activation of this MKK3-MPK1/2/7 module occurs mainly through wound-induced JA production via the transcriptional regulation of upstream clade-III MAP3Ks and particularly MAP3K14. We show that mkk3 mutant plants are more susceptible to the larvae of the generalist lepidopteran herbivore Spodoptera littoralis, indicating that the MKK3-MPK1/2/7 module is involved in counteracting insect feeding. One sentence summaryWounding induces the parallel activation of a rapid signaling module (MKK4/5-MPK3/6) and a JA-dependent slow one (MAP3K14-MKK3-MPK1/2/7/14) to restrict insect feeding.

plant biology↗