Gating of the two-pore cation channel AtTPC1 in the plant vacuole is based on a single voltage-sensing domain

Coordinating activation of endo-lysosomal two-pore channels and TRP mucolipins

Two-pore channels and TRP mucolipins are ubiquitous endo-lysosomal cation channels of pathophysiological relevance. Both are Ca2+-permeable and regulated by phosphoinositides, principally PI(3,5)P2. Accumulating evidence has uncovered synergistic channel activation by PI(3,5)P2 and endogenous metabolites such as the Ca2+ mobilizing messenger NAADP, synthetic agonists including approved drugs and physical cues such as voltage and osmotic pressure. Here, we provide an overview of this coordination.

Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels

To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca2+. In our search for species-dependent functional TPC1 channel variants with different luminal Ca2+ sensitivity, we found in total three acidic residues present in Ca2+ sensor sites 2 and 3 of the Ca2+-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca2+. When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca2+ sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca2+ sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.

TPC1 vacuole SV channel gains further shape - voltage priming of calcium-dependent gating

Across phyla, voltage-gated ion channels (VGICs) allow excitability. The vacuolar two-pore channel AtTPC1 from the tiny mustard plant Arabidopsis thaliana has emerged as a paradigm for deciphering the role of voltage and calcium signals in membrane excitation. Among the numerous experimentally determined structures of VGICs, AtTPC1 was the first to be revealed in a closed and resting state, fueling speculation about structural rearrangements during channel activation. Two independent reports on the structure of a partially opened AtTPC1 channel protein have led to working models that offer promising insights into the molecular switches associated with the gating process. We review new structure-function models and also discuss the evolutionary impact of two-pore channels (TPCs) on K⁺ homeostasis and vacuolar excitability.

PI(3,5)P2 and NAADP: Team players or lone warriors? - New insights into TPC activation modes

NAADP (nicotinic acid adenine dinucleotide phosphate) is a second messenger, releasing Ca²⁺ from acidic calcium stores such as endosomes and lysosomes. PI(3,5)P₂ (phosphatidylinositol 3,5-bisphosphate) is a phospho-inositide, residing on endolysosomal membranes and likewise releasing Ca²⁺ from endosomes and lysosomes. Both compounds have been shown to activate endolysosomal two-pore channels (TPCs) in mammalian cells. However, their effects on ion permeability as demonstrated specifically for TPC2 differ. While PI(3,5)P₂ elicits predominantly Na⁺-selective currents, NAADP increases the Ca²⁺ permeability of the channel. What happens when both compounds are applied simultaneously was unclear until recently.

TPC1-Type Channels in Physcomitrium patens: Interaction between EF-Hands and Ca2

Two-pore channels (TPCs) are members of the superfamily of ligand-gated and voltage-sensitive ion channels in the membranes of intracellular organelles of eukaryotic cells. The evolution of ordinary plant TPC1 essentially followed a very conservative pattern, with no changes in the characteristic structural footprints of these channels, such as the cytosolic and luminal regions involved in Ca²⁺ sensing. In contrast, the genomes of mosses and liverworts encode also TPC1-like channels with larger variations at these sites (TPC1b channels). In the genome of the model plant Physcomitrium patens we identified nine non-redundant sequences belonging to the TPC1 channel family, two ordinary TPC1-type, and seven TPC1b-type channels. The latter show variations in critical amino acids in their EF-hands essential for Ca²⁺ sensing. To investigate the impact of these differences between TPC1 and TPC1b channels, we generated structural models of the EF-hands of PpTPC1 and PpTPC1b channels. These models were used in molecular dynamics simulations to determine the frequency with which calcium ions were present in a coordination site and also to estimate the average distance of the ions from the center of this site. Our analyses indicate that the EF-hand domains of PpTPC1b-type channels have a lower capacity to coordinate calcium ions compared with those of common TPC1-like channels.

Structure, Function, and Applications of Soybean Calcium Transporters

Glycine max is a calcium-loving crop. The external application of calcium fertilizer is beneficial to the increase of soybean yield. Indeed, calcium is a vital nutrient in plant growth and development. As a core metal ion in signaling transduction, calcium content is maintained in dynamic balance under normal circumstances. Now, eight transporters were found to control the uptake and efflux of calcium. Though these calcium transporters have been identified through genome-wide analysis, only a few of them were functionally verified. Therefore, in this study, we summarized the current knowledge of soybean calcium transporters in structural features, expression characteristics, roles in stress response, and prospects. The above results will be helpful in understanding the function of cellular calcium transport and provide a theoretical basis for elevating soybean yield.

Major vacuolar TPC1 channel in stress signaling: what matters, K+, Ca2+ conductance or an ion-flux independent mechanism?

Two-pore cation channel, TPC1, is ubiquitous in the vacuolar membrane of terrestrial plants and mediates the long distance signaling upon biotic and abiotic stresses. It possesses a wide pore, which transports small mono- and divalent cations. K+ is transported more than 10-fold faster than Ca2+, which binds with a higher affinity within the pore. Key pore residues, responsible for Ca2+ binding, have been recently identified. There is also a substantial progress in the mechanistic and structural understanding of the plant TPC1 gating by membrane voltage and cytosolic and luminal Ca2+. Collectively, these gating factors at resting conditions strongly reduce the potentially lethal Ca2+ leak from the vacuole. Such tight control is impressive, bearing in mind high unitary conductance of the TPC1 and its abundance, with thousands of active channel copies per vacuole. But it remains a mystery how this high threshold is overcome upon signaling, and what type of signal is emitted by TPC1, whether it is Ca2+ or electrical one, or a transduction via protein conformational change, independent on ion conductance. Here we discuss non-exclusive scenarios for the TPC1 integration into Ca2+, ROS and electrical signaling.

Molecular basis of multistep voltage activation in plant two-pore channel 1

Despite decades of biophysical and structural research, little is understood about how voltage-gated ion channels (VGICs) activate during membrane depolarization, and less is known about how VGICs can be modulated by lipids and other ligands. We identify multiple functional states of the voltage- and Ca²⁺-gated ion channel TPC1 from Arabidopsis thaliana (AtTPC1), which confers electrical excitability to the plant vacuole. Here, we show how a voltage-sensing domain (VSD) functions during electrical activation and the mechanism of inhibition by vacuolar Ca²⁺. We show that the VSD undergoes large-scale, domain-wide structural changes during activation that involves Ca²⁺-dependent in-membrane plane rotation, subsequent charge transfer, and a Ca²⁺-dependent gate in the pore mouth that is allosterically coupled to the VSD.

Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge–bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca²⁺ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.

Molecular Evolution of Calcium Signaling and Transport in Plant Adaptation to Abiotic Stress

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca2+) signaling is characterized by the spatiotemporal pattern of Ca2+ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca2+ signaling remains elusive in green plants. We review mechanisms of Ca2+ membrane transporters and intracellular Ca2+ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca2+ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca2+ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca2+ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca2+ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway

Two Pore Channels (TPCs) are cation-selective voltage- and ligand-gated ion channels in membranes of intracellular organelles of eukaryotic cells. In plants, the TPC1 subtype forms the slowly activating vacuolar (SV) channel, the most dominant ion channel in the vacuolar membrane. Controversial reports about the permeability properties of plant SV channels fueled speculations about the physiological roles of this channel type. TPC1 is thought to have high Ca²⁺ permeability, a conclusion derived from relative permeability analyses using the Goldman–Hodgkin–Katz (GHK) equation. Here, we investigated in computational analyses the properties of the permeation pathway of TPC1 from Arabidopsis thaliana. Using the crystal structure of AtTPC1, protein modeling, molecular dynamics (MD) simulations, and free energy calculations, we identified a free energy minimum for Ca²⁺, but not for K⁺, at the luminal side next to the selectivity filter. Residues D269 and E637 coordinate in particular Ca²⁺ as demonstrated in in silico mutagenesis experiments. Such a Ca²⁺-specific coordination site in the pore explains contradicting data for the relative Ca²⁺/K⁺ permeability and strongly suggests that the Ca²⁺ permeability of SV channels is largely overestimated from relative permeability analyses. This conclusion was further supported by in silico electrophysiological studies showing a remarkable permeation of K⁺ but not Ca²⁺ through the open channel.

Recent Advances in the Physiology of Ion Channels in Plants

Our knowledge of plant ion channels was significantly enhanced by the first application of the patch-clamp technique to isolated guard cell protoplasts over 35 years ago. Since then, research has demonstrated the importance of ion channels in the control of gas exchange in guard cells, their role in nutrient uptake in roots, and the participation of calcium-permeable cation channels in the regulation of cell signaling affected by the intracellular concentrations of this second messenger. In recent years, through the employment of reverse genetics, mutant proteins, and heterologous expression systems, research on ion channels has identified mechanisms that modify their activity through protein-protein interactions or that result in activation and/or deactivation of ion channels through posttranslational modifications. Additional and confirmatory information on ion channel functioning has been derived from the crystallization and molecular modeling of plant proteins that, together with functional analyses, have helped to increase our knowledge of the functioning of these important membrane proteins that may eventually help to improve crop yield. Here, an update on the advances obtained in plant ion channel function during the last few years is presented.

Application of naturally occurring mechanical forces in in vitro plant tissue culture and biotechnology

Cues and signals of the environment in nature can be either beneficial or detrimental from the growth and developmental perspectives. Plants, despite their limited spatial mobility, have developed advanced strategies to overcome the various and changing environmental impacts including stresses. In vitro plantlets, tissues and cells are constantly exposed to the influence of their environment that is well controlled. Light has a widely known morphogenetic effect on plants; however, other physical cues and signals are at least as important but were often neglected. In this review, I summarize our knowledge about the role of the mechanical stimuli, like sound, ultrasound, touch, or wounding in in vitro plant cultures. I summarize the molecular, biochemical, physiological, growth, and developmental changes they cause and how these processes are controlled; moreover, how their regulating or stimulating roles are applied in various plant biotechnological applications. Recent studies revealed that mechanical forces can be used for affecting the plant development and growth in plant tissue culture efficiently, and for increasing the efficacy of other plant biotechnological methods, like genetic transformation and secondary metabolite production.

How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution

Phylogenetic analysis can be a powerful tool for generating hypotheses regarding the evolution of physiological processes. Here, we provide an updated view of the evolution of the main cation channels in plant electrical signalling: the Shaker family of voltage-gated potassium channels and the two-pore cation (K⁺) channel (TPC1) family. Strikingly, the TPC1 family followed the same conservative evolutionary path as one particular subfamily of Shaker channels (K_out) and remained highly invariant after terrestrialisation, suggesting that electrical signalling was, and remains, key to survival on land. We note that phylogenetic analyses can have pitfalls, which may lead to erroneous conclusions. To avoid these in the future, we suggest guidelines for analyses of ion channel evolution in plants.

Resting state structure of the hyperdepolarization activated two-pore channel 3

Voltage-gated ion channels endow membranes with excitability and the means to propagate action potentials that form the basis of all neuronal signaling. We determined the structure of a voltage-gated sodium channel, two-pore channel 3 (TPC3), which generates ultralong action potentials. TPC3 is distinguished by activation only at extreme membrane depolarization (V₅₀ ∼ +75 mV), in contrast to other TPCs and Na_V channels that activate between -20 and 0 mV. We present electrophysiological evidence that TPC3 voltage activation depends only on voltage sensing domain 2 (VSD2) and that each of the three gating arginines in VSD2 reduces the activation threshold. The structure presents a chemical basis for sodium selectivity, and a constricted gate suggests a closed pore consistent with extreme voltage dependence. The structure, confirmed by our electrophysiology, illustrates the configuration of a bona fide resting state voltage sensor, observed without the need for any inhibitory ligand, and independent of any chemical or mutagenic alteration.

Voltage-dependent gating of SV channel TPC1 confers vacuole excitability

In contrast to the plasma membrane, the vacuole membrane has not yet been associated with electrical excitation of plants. Here, we show that mesophyll vacuoles from Arabidopsis sense and control the membrane potential essentially via the K⁺-permeable TPC1 and TPK channels. Electrical stimuli elicit transient depolarization of the vacuole membrane that can last for seconds. Electrical excitability is suppressed by increased vacuolar Ca²⁺ levels. In comparison to wild type, vacuoles from the fou2 mutant, harboring TPC1 channels insensitive to luminal Ca²⁺, can be excited fully by even weak electrical stimuli. The TPC1-loss-of-function mutant tpc1-2 does not respond to electrical stimulation at all, and the loss of TPK1/TPK3-mediated K⁺ transport affects the duration of TPC1-dependent membrane depolarization. In combination with mathematical modeling, these results show that the vacuolar K⁺-conducting TPC1 and TPK1/TPK3 channels act in concert to provide for Ca²⁺- and voltage-induced electrical excitability to the central organelle of plant cells.

Role of auxin (IAA) in the regulation of slow vacuolar (SV) channels and the volume of red beet taproot vacuoles

BACKGROUND

Auxin (IAA) is a central player in plant cell growth. In contrast to the well-established function of the plasma membrane in plant cell expansion, little is known about the role of the vacuolar membrane (tonoplast) in this process.

RESULTS

It was found that under symmetrical 100 mM K⁺ and 100 μM cytoplasmic Ca²⁺ the macroscopic currents showed a typical slow activation and a strong outward rectification of the steady-state currents. The addition of IAA at a final concentration of 1 μM to the bath medium stimulated the SV currents, whereas at 0.1 and 10 μM slight inhibition of SV currents was observed. The time constant, τ, decreased in the presence of this hormone. When single channels were analyzed, an increase in their activity was recorded with IAA compared to the control. The single-channel recordings that were obtained in the presence of IAA showed that auxin increased the amplitude of the single-channel currents. Interestingly, the addition of IAA to the bath medium with the same composition as the one that was used in the patch-clamp experiments showed that auxin decreased the volume of the vacuoles.

CONCLUSIONS

It is suggested that the SV channels and the volume of red beet taproot vacuoles are modulated by auxin (IAA).

Structure and Function of TPC1 Vacuole SV Channel Gains Shape

Plants and animals in endosomes operate TPC1/SV-type cation channels. All plants harbor at least one TPC1 gene. Although the encoded SV channel was firstly discovered in the plant vacuole membrane two decades ago, its biological function has remained enigmatic. Recently, the structure of a plant TPC1/SV channel protein was determined. Insights into the 3D topology has now guided site-directed mutation approaches, enabling structure-function analyses of TPC1/SV channels to shed new light on earlier findings. Fou2 plants carrying a hyperactive mutant form of TPC1 develop wounding stress phenotypes. Recent studies with fou2 and mutants that lack functional TPC1 have revealed atypical features in local and long-distance stress signaling, providing new access to the previously mysterious biology of this vacuolar cation channel type in planta.

Two-pore cation (TPC) channel: not a shorthanded one

Two-pore cation (TPC) channels form functional dimers in membranes, delineating acidic intracellular compartments such as vacuoles in plants and lysosomes in animals. TPC1 is ubiquitously expressed in thousands of copies per vacuole in terrestrial plants, where it is known as slow vacuolar (SV) channel. An SV channel possesses high permeability for Na+, K+, Mg2+, and Ca2+, but requires high (tens of μM) cytosolic Ca2+ and non-physiological positive voltages for its full activation. Its voltage dependent activation is negatively modulated by physiological concentrations of vacuolar Ca2+, Mg2+and H+. Double control of the SV channel activity from cytosolic and vacuolar sides keeps its open probability at a minimum and precludes a potentially harmful global Ca2+ release. But this raises the question of what such' inactive' channel could be good for? One possibility is that it is involved in ultra-local Ca2+ signalling by generating 'hotspots' - microdomains of extremely high cytosolic Ca2+. Unexpectedly, recent studies have demonstrated the essential role of the TPC1 in the systemic Ca2+ signalling, and the crystal structure of plant TPC1, which became available this year, unravels molecular mechanisms underlying voltage and Ca2+ gating. This review emphasises the significance of these ice-breaking findings and sets a new perspective for the TPC1-based Ca2+ signalling.

On the structure and mechanism of two-pore channels

In eukaryotes, two-pore channels (TPC1-3) comprise a family of ion channels that regulate the conductance of Na⁺ and Ca²⁺ ions across cellular membranes. TPC1-3 form endolysosomal channels, but TPC3 can also function in the plasma membrane. TPC1/3 are voltage-gated channels, but TPC2 opens in response to binding endolysosome-specific lipid phosphatidylinositol-3,5-diphosphate (PI(3,5)P₂ ). Filoviruses, such as Ebola, exploit TPC-mediated ion release as a means of escape from the endolysosome during infection. Antagonists that block TPC1/2 channel conductance abrogate filoviral infections. TPC1/2 form complexes with the mechanistic target of rapamycin complex 1 (mTORC1) at the endolysosomal surface that couple cellular metabolic state and cytosolic nutrient concentrations to the control of membrane potential and pH. We determined the X-ray structure of TPC1 from Arabidopsis thaliana (AtTPC1) to 2.87Å resolution-one of the two first reports of a TPC channel structure. Here, we summarize these findings and the implications that the structure may have for understanding endolysosomal control mechanisms and their role in human health.

Vacuolar ion channels in the liverwort Marchantia polymorpha: influence of ion channel inhibitors

Potassium-permeable slow activating vacuolar channels (SV) and chloride-permeable channels in the vacuole of the liverwort Marchantia polymorpha were characterized in respect to calcium dependence, selectivity, and pharmacology. The patch-clamp method was used in the study of ion channel activity in the vacuoles from the liverwort Marchantia polymorpha. The whole-vacuole recordings allowed simultaneous observation of two types of currents-predominant slow activated currents recorded at positive voltages and fast activated currents recorded at negative voltages. Single-channel recordings carried out in the gradient of KCl indicated that slow activated currents were carried by potassium-permeable slowly activating vacuolar channels (SV) and fast activated currents-by chloride-permeable channels. Both types of the channels were dependent in an opposite way on calcium, since elimination of this ion from the cytoplasmic side caused inhibition of SV channels, but the open probability of chloride-permeable channels even increased. The dependence of the activity of both channels on different types of ion channel inhibitors was studied. SV channels exhibited different sensitivity to potassium channel inhibitors. These channels were insensitive to 3 mM Ba²⁺, but were blocked by 3 mM tetraethyl ammonium (TEA). Moreover, the activity of the channels was modified in a different way by calcium channel inhibitors. 200 µM Gd³⁺ was an effective blocker, but 50 µM ruthenium red evoked bursts of the channel activity resulting in an increase in the open probability. Different effectiveness of anion channel inhibitors was observed in chloride-permeable channels. After the application of 100 µM Zn²⁺, a decrease in the open probability was recorded but the channels were still active. 50 µM DIDS was more effective, as it completely blocked the channels.