Biology subjects

Dreyer, I.

Publications and source records attributed to Dreyer, I..

8 recordsLinked to original sources

bioRxiv2025

Universal modules for decoding amplitude and frequency of Ca2+ signals in plants

O_LICalcium signals are fundamental for plants and play a crucial role in long-term processes such as growth and development, as well as in rapid responses to environmental stimuli and stress factors. Nevertheless, the mechanisms involved in decoding calcium signal in plants are still largely unclear. C_LIO_LIHere, we have addressed the question of calcium signal decoding in a bottom-up modelling approach. We started with the thermodynamics of Ca2+ binding to a Ca2+ binding protein (CBP), e.g. via EF hands. Remarkably, Ca2+ binding properties of the EF hands do not coincide with the Ca2+ sensitivity of the protein containing these EF hands. C_LIO_LIIn analysing the next levels of complexity, we identified six universal fundamental Ca2+-decoding modules, in which Ca2+ either interacts directly with a target protein (TP) or modulates its activity via a CBP. These modules are the basic units that enable the amplitude and frequency of Ca2+ signals to be decoded. Representatives of these modules are omnipresent in plant cells. They straightforwardly explain the puzzling finding that Ca2+-dependent kinases exhibit different Ca2+-sensitivities when tested with different substrates. C_LIO_LIIn-depth analysis of the properties of the modules provides a fundamental theoretical basis for understanding Ca2+ signal decoding and may contribute to finding the "Rosetta Stone" for Ca2+ signals in plants. C_LI

plant biology↗

bioRxiv2024

Homeostats - the hidden rulers of ion homeostasis in plants

Ion homeostasis is a crucial process in plants that is closely linked to the efficiency of nutrient uptake, stress tolerance and overall plant growth and development. Nevertheless, our understanding of the fundamental processes of ion homeostasis is still incomplete and highly fragmented. Especially at the mechanistic level, we are still in the process of dissecting physiological systems to analyze the different parts in isolation. However, modeling approaches have shown that it is not individual transporters but rather transporter networks (homeostats) that control membrane transport and associated homeostatic processes in plant cells. To facilitate access to such theoretical approaches, the modeling of the potassium homeostat is explained here in detail to serve as a blueprint for other homeostats. Based on a few, elementary knowledge about the thermodynamics of the different transport processes, it is possible to draw fundamental conclusions about the properties and physiology of the transporter network.

plant biology↗

bioRxiv2024

An auxin homeostat allows plant cells to establish and control defined transmembrane auxin gradients

O_LIExtracellular auxin maxima and minima are important to control plant developmental programs. Auxin gradients are provided by the concerted action of proteins from the three major plasma membrane auxin transporter classes AUX1/LAX, PIN and ABCB transporters. But neither genetic nor biochemical nor modelling approaches have been able to reliably assign the individual roles and interplay of these transporter types. C_LIO_LIBased on the thermodynamic properties of the transporters, we show here by mathematical modeling and computational simulations that the concerted action of different auxin transporter types allow the adjustment of specific transmembrane auxin gradients. The dynamic flexibility of the "auxin homeostats" comes at the cost of an energy-consuming "auxin cycling" across the membrane. C_LIO_LIAn unexpected finding was that functional ABCB-PIN coupling appears to allow an optimization of the trade-off between the speed of auxin gradient adjustment on the one hand and ATP consumption and disturbance of general anion homeostasis on the other. C_LIO_LIIn conclusion, our analyses provide fundamental insights into the thermodynamic constraints and flexibility of transmembrane auxin transport in plants. C_LI Plain language summaryThe phytohormone auxin controls essentially plant development. Plant cells produce auxin and export it to establish patterns by local auxin minima and maxima. Although several transporter proteins are known to contribute to this process, the mechanism by which a defined auxin gradient can be produced is not clear. This study now uses mathematical modeling based on the thermodynamic features of the auxin transporters to illustrate in computational simulations the fundamental characteristics of an "auxin homeostat". The concerted interplay of different auxin transporters allows plant cells to establish defined transmembrane auxin gradients that are the indispensable basis for polarized auxin maxima and minima and auxin fluxes within tissues.

plant biology↗

bioRxiv2023

Mechanistic insight into substrate specificity of plant glucosinolate transporters

Plants depend on transport processes for correct allocation of specialized metabolites. This is important for optimal defense, avoidance of autotoxicity, connecting compartmented biosynthetic modules and more. Transport of a wide variety of specialized metabolites is mediated by transporters from the Nitrate and Peptide transporter Family (NPF), which belongs to the Major Facilitator Superfamily (MFS). However, the mechanism by which NPF members recognize and transport specialized metabolites remains unknown. Here we mutate eight residues to reciprocally swap the substrate-preference of two closely related glucosinolate transporters (GTRs). Seven of these residues assemble in a ring-like structure in all conformations of the transporters. We labeled the ring-like structure a selectivity filter and based on docking studies, we propose that the interaction between the selectivity filter and the glucosinolate side chain determines whether a given glucosinolate is recognized as a substrate. Besides partly explaining the distinct substrate preference of GTR1 (NPF2.10) and GTR3 (NPF2.9), this study proposes fundamental principles of substrate recognition in the NPF and establishes the GTR subclade as a novel model system for studying structure function relationships in the NPF.

molecular biology↗

bioRxiv2021

Vicia faba TPC1, a genetically encoded variant of the vacuole Two Pore Channel 1, is hyperexcitable

To fire action-potential-like electrical signals, the vacuole membrane requires the depolarization-activated two-pore channel TPC1, also called Slowly activating Vacuolar SV channel. The TPC1/SV channel, encoded by the TPC1 gene, functions as a voltage-dependent and Ca2+-regulated potassium channel. TPC1 currents are activated by a rise in cytoplasmic Ca2+ but inhibited by luminal Ca2+. In search for species-dependent functional TPC1 channel variants, we studied polymorphic amino acids contributing to luminal Ca2+ sensitivity. We found that the acidic residues E457, E605 and D606 of the Ca2+-sensitive Arabidopsis AtTPC1 channel were neutralized by either asparagine or alanine in Vicia faba and many other Fabaceae as well. When expressed in the Arabidopsis loss-of-AtTPC1 function background, the wild type VfTPC1 was hypersensitive to vacuole depolarization and insensitive to blocking luminal Ca2+. When AtTPC1 was mutated for the three VfTPC1-homologous polymorphic site residues, the Arabidopsis At-VfTPC1 channel mutant gained VfTPC1-like voltage and luminal Ca2+ insensitivity that together made vacuoles hyperexcitable. These findings indicate that natural TPC1 channel variants in plant families exist which differ in vacuole excitability and very likely respond to changes in environmental settings of their ecological niche. Significance statementVacuolar electrical excitability and stress-related Ca2+ signaling depends on the activity of the vacuolar cation channel TPC1. Until now, the regulatory features of AtTPC1 from the model plant Arabidopsis thaliana was believed to apply to the TPC1 channels of other species. However, here we now show that, surprisingly, the VfTPC1 channel of the economic broad bean, in contrast to AtTPC1, proves to be hyperactive and confers hyperexcitability to the vacuole. The different gating behavior is most likely related to an impaired Ca2+ sensor site in the vacuolar pore vestibule, rising the probability to open at more negative membrane voltages. These natural variants of the TPC1 channel could help the plant adapt and respond to environmental challenges.

plant biology↗

bioRxiv2021

Nutrient cycling is an important mechanism for homeostasis in plant cells

Homeostasis in living cells refers to the steady state of internal, physical, and chemical conditions. It is maintained by self-regulation of the dynamic cellular system. In order to gain insight into homeostatic mechanisms that keep cytosolic nutrient concentrations in plant cells within a homeostatic range, I performed computational cell biology experiments. Systems of membrane transporters were modelled mathematically followed by the simulation of their dynamics. The detailed analyses of what-if scenarios demonstrate that a single transporter type for a nutrient, irrespective whether it is a channel or a co-transporter, is not sufficient to set a desired cytosolic concentration. A cell cannot flexibly react on different external conditions. At least two different transporter types for the same nutrient are required, which are energized differently. The gain of flexibility in adjusting the nutrient concentration was accompanied by the establishment of energy-consuming nutrient cycles at the membrane suggesting that these sometimes called futile cycles are not as futile as they appear. This understanding may help in future to design new strategies for increasing nutrient use efficiency of crop plants taking into account the complex interplay of transporter networks at the cellular level. One sentence summaryFirst principles of membrane transport explain why the maintenance of a constant cytosolic nutrient concentration is often accompanied by the futile cycling of the nutrient across the membrane.

plant biology↗

bioRxiv2018

Extracellular Cation Binding Pocket Is Essential For Ion Conduction Of OsHKT2;2

HKT channels mediate sodium uniport or sodium and potassium symport in plants. Monocotyledons express a higher number of HKT proteins than dicotyledons, and it is only within this clade of HKT channels that cation symport mechanisms are found. The prevailing ion composition in the extracellular medium affects the transport abilities of various HKT channels by changing their selectivity or ion transport rates. How this mutual effect is achieved at the molecular level is still unknown. Here, we built a homology model of the monocotyledonous OsHKT2;2, which shows sodium and potassium symport activity, and performed molecular dynamics simulations in the presence of sodium and potassium ions. By analyzing ion-protein interactions, we identified a cation binding pocket on the extracellular protein surface, which is formed by residues P71, D75, D501 and K504. Proline and the two aspartate residues coordinate cations, while K504 forms salt bridges with D75 and D501 and may be involved in the forwarding of cations towards the pore entrance. Functional validation via electrophysiological experiments confirmed the biological relevance of the predicted ion binding pocket and identified K504 as a central key residue. Mutation of the cation coordinating residues affected the functionality of HKT only slightly. Additional in silico mutants and simulations of K504 supported experimental results.

plant biology↗

bioRxiv2018

The fungal root endophyte Serendipita indica modifies extracellular nucleotides to subvert plant immunity

One sentence abstractImmune modulation by metabolites in plant fungus interaction\n\nAbstractExtracellular adenosine 5'-triphosphate (eATP) is an essential signaling molecule that mediates different cellular processes through its interaction with membrane-associated receptor proteins in animals and plants. eATP regulates plant growth, development and responses to biotic and abiotic stresses. Its accumulation in the apoplast induces ROS production and cytoplasmic calcium increase mediating a defense response to invading microbes. We demonstrate that perception of eATP is important in plant-fungus interaction and that during colonization by the beneficial root endophyte Serendipita indica accumulation of eATP in the apoplast occurs at early symbiotic stages. We show by liquid chromatography-tandem mass spectrometry, cytological and functional analysis that S. indica subvert eATP host response by secreting SiE5NT, an enzymatically active ecto-5'nucleotidase capable of hydrolyzing eATP to adenosine. A. thaliana lines producing extracellular SiE5NT are signi?cantly better colonized and have reduced eATP levels and defense signaling, indicating that SiE5NT functions as a compatibility factor. Our data show that extracellular bioactive nucleotides play an important role in fungus-root interactions and that fungi can modify plant derived metabolites in the apoplast to modulate host immunity.

plant biology↗