Crystal Structure of an Ammonia-Permeable Aquaporin

Molecular mechanism of anion permeation through aquaporin 6

Aquaporins (AQPs) are recognized as transmembrane water channels that facilitate selective water permeation through their monomeric pores. Among the AQP family, AQP6 has an intriguing characteristic as an anion channel, which is allosterically controlled by pH conditions and is eliminated by a single amino acid mutation. However, the molecular mechanism of anion permeation through AQP6 remains unclear. Using molecular dynamics simulations in the presence of a transmembrane voltage utilizing an ion concentration gradient, we show that chloride ions permeate through the pore corresponding to the central axis of the AQP6 homotetramer. Under low pH conditions, a subtle opening of the hydrophobic selectivity filter (SF), located near the extracellular part of the central pore, becomes wetted and enables anion permeation. Our simulations also indicate that a single mutation (N63G) in human AQP6, located at the central pore, significantly reduces anion conduction, consistent with experimental data. Moreover, we demonstrate that the pH-sensing mechanism in which the protonation of H184 and H189 under low pH conditions allosterically triggers the gating of the SF region. These results suggest a unique pH-dependent allosteric anion permeation mechanism in AQP6 and could clarify the role of the central pore in some of the AQP tetramers.

A charged existence: A century of transmembrane ion transport in plants

If the past century marked the birth of membrane transport as a focus for research in plants, the past 50 years has seen the field mature from arcane interest to a central pillar of plant physiology. Ion transport across plant membranes accounts for roughly 30% of the metabolic energy consumed by a plant cell, and it underpins virtually every aspect of plant biology, from mineral nutrition, cell expansion, and development to auxin polarity, fertilization, plant pathogen defense, and senescence. The means to quantify ion flux through individual transporters, even single channel proteins, became widely available as voltage clamp methods expanded from giant algal cells to the fungus Neurospora crassa in the 1970s and the cells of angiosperms in the 1980s. Here, I touch briefly on some key aspects of the development of modern electrophysiology with a focus on the guard cells of stomata, now without dispute the premier plant cell model for ion transport and its regulation. Guard cells have proven to be a crucible for many technical and conceptual developments that have since emerged into the mainstream of plant science. Their study continues to provide fundamental insights and carries much importance for the global challenges that face us today.

TIP aquaporins in Cyperus esculentus: genome-wide identification, expression profiles, subcellular localizations, and interaction patterns

BACKGROUND

Tonoplast intrinsic proteins (TIPs), which typically mediate water transport across vacuolar membranes, play an essential role in plant growth, development, and stress responses. However, their characterization in tigernut (Cyperus esculentus L.), an oil-bearing tuber plant of the Cyperaceae family, is still in the infancy.

RESULTS

In this study, a first genome-wide characterization of the TIP subfamily was conducted in tigernut, resulting in ten members representing five previously defined phylogenetic groups, i.e., TIP1-5. Although the gene amounts are equal to that present in two model plants Arabidopsis and rice, the group composition and/or evolution pattern were shown to be different. Except for CeTIP1;3 that has no counterpart in both Arabidopsis and rice, complex orthologous relationships of 1:1, 1:2, 1:3, 2:1, and 2:2 were observed. Expansion of the CeTIP subfamily was contributed by whole-genome duplication (WGD), transposed, and dispersed duplications. In contrast to the recent WGD-derivation of CeTIP3;1/-3;2, synteny analyses indicated that TIP4 and - 5 are old WGD repeats of TIP2, appearing sometime before monocot-eudicot divergence. Expression analysis revealed that CeTIP genes exhibit diverse expression profiles and are subjected to developmental and diurnal fluctuation regulation. Moreover, when transiently overexpressed in tobacco leaves, CeTIP1;1 was shown to locate in the vacuolar membrane and function in homo/heteromultimer, whereas CeTIP2;1 is located in the cell membrane and only function in heteromultimer. Interestingly, CeTIP1;1 could mediate the tonoplast-localization of CeTIP2;1 via protein interaction, implying complex regulatory patterns.

CONCLUSIONS

Our findings provide a global view of CeTIP genes, which provide valuable information for further functional analysis and genetic improvement through manipulating key members in tigernut.

Enhanced Stomatal Conductance Supports Photosynthesis in Wheat to Improved NH4+ Tolerance

The impact of ammonium (NH4+) stress on plant growth varies across species and cultivars, necessitating an in-depth exploration of the underlying response mechanisms. This study delves into elucidating the photosynthetic responses and differences in tolerance to NH4+ stress by investigating the effects on two wheat (Triticum aestivum L.) cultivars, Xumai25 (NH4+-less sensitive) and Yangmai20 (NH4+-sensitive). The cultivars were grown under hydroponic conditions with either sole ammonium nitrogen (NH4+, AN) or nitrate nitrogen (NO3-, NN) as the nitrogen source. NH4+ stress exerted a profound inhibitory effect on seedling growth and photosynthesis in wheat. However, these effects were less pronounced in Xumai25 than in Yangmai20. Dynamic photosynthetic analysis revealed that the suppression in photosynthesis was primarily attributed to stomatal limitation associated with a decrease in leaf water status and osmotic potential. Compared to Yangmai20, Xumai25 exhibited a significantly higher leaf K+ concentration and TaAKT1 upregulation, leading to a stronger stomatal opening and, consequently, a better photosynthetic performance under NH4+ stress. In conclusion, our study suggested stomatal limitation as the primary factor restricting photosynthesis under NH4+ stress. Furthermore, we demonstrated that improved regulation of osmotic substances contributed to higher stomatal conductance and enhanced photosynthetic performance in Xumai25.

Barley Nodulin 26-like intrinsic protein permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Aquaporins can facilitate the passive movement of water, small polar molecules, and some ions. Here, we examined solute selectivity for the barley Nodulin 26-like Intrinsic Protein (HvNIP2;1) embedded in liposomes and examined through stopped-flow light scattering spectrophotometry and Xenopus laevis oocyte swelling assays. We found that HvNIP2;1 permeates water, boric and germanic acids, sucrose, and lactose but not d-glucose or d-fructose. Other saccharides, such as neutral (d-mannose, d-galactose, d-xylose, d-mannoheptaose) and charged (N-acetyl d-glucosamine, d-glucosamine, d-glucuronic acid) aldoses, disaccharides (cellobiose, gentiobiose, trehalose), trisaccharide raffinose, and urea, glycerol, and acyclic polyols, were permeated to a much lower extent. We observed apparent permeation of hydrated KCl and MgSO4 ions, while CH3COONa and NaNO3 permeated at significantly lower rates. Our experiments with boric acid and sucrose revealed no apparent interaction between solutes when permeated together, and AgNO3 or H[AuCl4] blocked the permeation of all solutes. Docking of sucrose in HvNIP2;1 and spinach water-selective SoPIP2;1 aquaporins revealed the structural basis for sucrose permeation in HvNIP2;1 but not in SoPIP2;1, and defined key residues interacting with this permeant. In a biological context, sucrose transport could constitute a novel element of plant saccharide-transporting machinery. Phylogenomic analyses of 164 Viridiplantae and 2993 Archaean, bacterial, fungal, and Metazoan aquaporins rationalized solute poly-selectivity in NIP3 sub-clade entries and suggested that they diversified from other sub-clades to acquire a unique specificity of saccharide transporters. Solute specificity definition in NIP aquaporins could inspire developing plants for food production.

Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales

Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae-Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon-intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.

Aquaporins and CO2 diffusion across biological membrane

Despite the physiological significance of effective CO₂ diffusion across biological membranes, the underlying mechanism behind this process is not yet resolved. Particularly debatable is the existence of CO₂-permeable aquaporins. The lipophilic characteristic of CO₂ should, according to Overton's rule, result in a rapid flux across lipid bilayers. However, experimental evidence of limited membrane permeability poses a challenge to this idea of free diffusion. In this review, we summarized recent progress with regard to CO₂ diffusion, and discussed the physiological effects of altered aquaporin expression, the molecular mechanisms of CO₂ transport via aquaporins, and the function of sterols and other membrane proteins in CO₂ permeability. In addition, we highlight the existing limits in measuring CO₂ permeability and end up with perspectives on resolving such argument either by determining the atomic resolution structure of CO₂ permeable aquaporins or by developing new methods for measuring permeability.

Vacuolar MATE/DTX protein-mediated cucurbitacin C transport is co-regulated with bitterness biosynthesis in cucumber

Membrane-localized transporters constitute important components for specialized metabolism in plants. However, due to the vast array of specialized metabolites produced by plants, and the large families of transporter genes, knowledge about the intracellular and intercellular transport of plant metabolites is still in its infancy. Cucurbitacins are bitter and defensive triterpenoids produced mainly in the cucurbits. Using a comparative genomics and multi-omics approach, a MATE gene (CsMATE1), physically clustered with cucurbitacin C (CuC) biosynthetic genes, was identified and functionally shown to sequester CuC in cucumber leaf mesophyll cells. Notably, the CuC transport process is strictly co-regulated with CuC biosynthesis. CsMATE1 clustering with bitterness biosynthesis genes may provide benefits and a basis for this feedback regulation on CuC sequestration and biosynthesis. Identification of transport systems for plant-specialized metabolites can accelerate the metabolic engineering of high-value-added compounds by simplifying their purification process.

Molecular membrane separation: plants inspire new technologies

Plants draw up their surrounding soil solution to gain water and nutrients required for growth, development and reproduction. Obtaining adequate water and nutrients involves taking up both desired and undesired elements from the soil solution and separating resources from waste. Desirable and undesirable elements in the soil solution can share similar chemical properties, such as size and charge. Plants use membrane separation mechanisms to distinguish between different molecules that have similar chemical properties. Membrane separation enables distribution or retention of resources and efflux or compartmentation of waste. Plants use specialised membrane separation mechanisms to adapt to challenging soil solution compositions and distinguish between resources and waste. Coordination and regulation of these mechanisms between different tissues, cell types and subcellular membranes supports plant nutrition, environmental stress tolerance and energy management. This review considers membrane separation mechanisms in plants that contribute to specialised separation processes and highlights mechanisms of interest for engineering plants with enhanced performance in challenging conditions and for inspiring the development of novel industrial membrane separation technologies. Knowledge gained from studying plant membrane separation mechanisms can be applied to developing precision separation technologies. Separation technologies are needed for harvesting resources from industrial wastes and transitioning to a circular green economy.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Photorespiration - Rubisco's repair crew

The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O₂ as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO₂ fixation in the Calvin cycle. However, the CO₂-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO₂ and can also use O₂ in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO₂. This disadvantageous feature can be suppressed by CO₂-concentrating mechanisms, such as those that evolved in C₄ plants thirty million years ago, which enhance CO₂ fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C₄ plants, C₃-C₄ intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.

Protein Structure and Modification of Aquaporins

Aquaporins (AQPs) allow water molecules and other small, neutral solutes to quickly pass through membrane. The protein structures of AQPs solved by crystallographic methods or cryo-electron microscopy technology show that AQP monomer consists of six membrane-spanning alpha-helices that form the central water-transporting pore. AQP monomers assemble to form tetramers, forming the functional units in the membrane, to transport water or other small molecules. The biological functions of AQPs are regulated by posttranslational modifications, e.g., phosphorylation, ubiquitination, glycosylation, subcellular distribution, degradation and protein interactions. Modifications of AQP combined with structural properties contribute to a better functional mechanism of AQPs. Insight into the molecular mechanisms responsible for AQP modifications as well as gating and transport properties proved to be fundamental to the development of new therapeutic targets or reliable diagnostic and prognostic biomarkers.

High-resolution structure of a fish aquaporin reveals a novel extracellular fold

The structural and functional characterization of a fish AQP reveals a water-specific AQP with unique structural features that may have implications for channel gating in response to osmotic changes.

Aquaporins are protein channels embedded in the lipid bilayer in cells from all organisms on earth that are crucial for water homeostasis. In fish, aquaporins are believed to be important for osmoregulation; however, the molecular mechanism behind this is poorly understood. Here, we present the first structural and functional characterization of a fish aquaporin; cpAQP1aa from the fresh water fish climbing perch (Anabas testudineus), a species that is of high osmoregulatory interest because of its ability to spend time in seawater and on land. These studies show that cpAQP1aa is a water-specific aquaporin with a unique fold on the extracellular side that results in a constriction region. Functional analysis combined with molecular dynamic simulations suggests that phosphorylation at two sites causes structural perturbations in this region that may have implications for channel gating from the extracellular side.

PIPs from Fragaria vesca: A structural analysis of native and mutated protein

Aquaporins are an ancient family of membrane channel proteins present in all eukaryotes and most prokaryotes, and apart from water, allow the transport of neutral solutes and organic compounds through the pore. These proteins are essential role differentially expressed during ripening in Fragaria vesca fruits. Fv PIP2-1a is intensively expressed in fruits, inclusive several other proteins member are differentially expressed in fruit but also in other plant tissues. Phylogenetic analysis shows that Fv PIP2-1a grouped with other Fragaria proteins and far apart from other F. vesca PIP proteins. A structural model for Fv PIP2-1a protein was built by comparative modelling methodology, which was validated and refined by molecular dynamics simulation. Fv PIP2-1a structure consists of 6 transmembrane regions and two NPA domains. The mobilization of water was analyzed by molecular docking simulations in wildtype and two mutants. Interestingly, the mutant FvPIP2-1a_H214G allowed the prediction of an increment in the flux of water molecules. On contrary, structural analysis predicted that H214E mutation blocked passage of water associated to constriction of the pore.

Phosphorylation of a wheat aquaporin at two sites enhances both plant growth and defense

Eukaryotic aquaporins share the characteristic of functional multiplicity in transporting distinct substrates and regulating various processes, but the underlying molecular basis for this is largely unknown. Here, we report that the wheat (Triticum aestivum) aquaporin TaPIP2;10 undergoes phosphorylation to promote photosynthesis and productivity and to confer innate immunity against pathogens and a generalist aphid pest. In response to elevated atmospheric CO₂ concentrations, TaPIP2;10 is phosphorylated at the serine residue S280 and thereafter transports CO₂ into wheat cells, resulting in enhanced photosynthesis and increased grain yield. In response to apoplastic H₂O₂ induced by pathogen or insect attacks, TaPIP2;10 is phosphorylated at S121 and this phosphorylated form transports H₂O₂ into the cytoplasm, where H₂O₂ intensifies host defenses, restricting further attacks. Wheat resistance and grain yield could be simultaneously increased by TaPIP2;10 overexpression or by expressing a TaPIP2;10 phosphomimic with aspartic acid substitutions at S121 and S280, thereby improving both crop productivity and immunity.

Effects of vapor pressure deficit combined with different N levels on tomato seedling anatomy, photosynthetic performance, and N uptake

Vapor pressure difference (VPD) is the main driving force of plant transpiration and the main factor of greenhouse environment regulation. Nitrogen is the main element of crop growth and development. It is significant to explore the regulation of VPD on nitrogen absorption and its effect on tomato photosynthesis. In this paper, using tomato as material, using an artificial climate chamber, the effect of VPD and nitrogen level coupling on nitrogen absorption and distribution, hydraulic characteristics, and photosynthetic characteristics of tomato was studied and analyzed. The optimal regulation of VPD and nitrogen was analyzed. Studies have shown that appropriately reducing the VPD can promote the absorption of nitrogen by plants. The increased surface area and volume of tomato roots and the increased activity of nitrogen assimilation-related enzymes were beneficial to nitrogen absorption and assimilation. Compared with high VPD (HVPD) plants, the leaf thickness and spongy tissue thickness of low VPD (LVPD) plants decreased, and the palisade/spongy tissue thickness ratio (P/S) increased; Leaf water conductance (K_leaf) increased with the increase of nitrogen level. The K_leaf at normal and high nitrogen plants increased by 4.00 % and 33.93 %, respectively, compared with HVPD plants of the same nitrogen level (significant difference at high nitrogen level) but significantly decreased at low nitrogen level. The decrease of spongy tissue thickness, the increase of palisade/sponge tissue, and the up-regulation of aquaporin expression were all beneficial to increasing K_leaf. Decreasing VPD and increasing nitrogen application under LVPD both increased specific leaf area (SLA). Compared with HVPD treatment, the photosynthetic rate of LVPD-treated plants increased by 7.06 % and 30.48 % at normal and high nitrogen levels, respectively.

Cadmium promotes the absorption of ammonium in hyperaccumulator Solanum nigrum L. mediated by ammonium transporters and aquaporins

Cadmium (Cd) is a toxic heavy metal affecting the normal growth of plants. Nitrate (NO₃^-) and ammonium (NH₄⁺) are the primary forms of inorganic nitrogen (N) absorbed by plants. However, the mechanism of N absorption and regulation under Cd stress remains unclear. This study found that: (1) Cd treatment affected the biomass, root length, and Cd²⁺ flux in Solanum nigrum seedling roots. Specifically, 50 μM Cd significantly inhibited NO₃^- influx while increased NH₄⁺ influx compared with 0 and 5 μM Cd treatments measured by non-invasive micro-test technology. (2) qRT-PCR analysis showed that 50 μM Cd inhibited the expressions of nitrate transporter genes, SnNRT2;4 and SnNRT2;4-like, increased the expressions of ammonium transporter genes, SnAMT1;2 and SnAMT1;3, in the roots. (3) Under NH₄⁺ supply, 50 μM Cd significantly induced the expressions of the aquaporin genes, SnPIP1;5, SnPIP2;7, and SnTIP2;1. Our results showed that 50 μM Cd stress promoted NH₄⁺ absorption by up-regulating the gene expressions of NH₄⁺ transporter and aquaporins, suggesting that high Cd stress can affect the preference of N nutrition in S. nigrum.

Aquaporin Gating: A New Twist to Unravel Permeation through Water Channels

Aquaporins (AQPs) are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their presence has been extensively reported in the biological membranes of almost all living organisms. Although their discovery is much more recent than ion transport systems, different biophysical approaches have contributed to confirm that permeation through each monomer is consistent with closed and open states, introducing the term gating mechanism into the field. The study of AQPs in their native membrane or overexpressed in heterologous systems have experimentally demonstrated that water membrane permeability can be reversibly modified in response to specific modulators. For some regulation mechanisms, such as pH changes, evidence for gating is also supported by high-resolution structures of the water channel in different configurations as well as molecular dynamics simulation. Both experimental and simulation approaches sustain that the rearrangement of conserved residues contributes to occlude the cavity of the channel restricting water permeation. Interestingly, specific charged and conserved residues are present in the environment of the pore and, thus, the tetrameric structure can be subjected to alter the positions of these charges to sustain gating. Thus, is it possible to explore whether the displacement of these charges (gating current) leads to conformational changes? To our knowledge, this question has not yet been addressed at all. In this review, we intend to analyze the suitability of this proposal for the first time.

Characterization of the Aquaporin-9 Inhibitor RG100204 In Vitro and in db/db Mice

Aquaporin-9 (AQP9) is a facilitator of glycerol and other small neutral solute transmembrane diffusion. Identification of specific inhibitors for aquaporin family proteins has been difficult, due to high sequence similarity between the 13 human isoforms, and due to the limited channel surface areas that permit inhibitor binding. The few AQP9 inhibitor molecules described to date were not suitable for in vivo experiments. We now describe the characterization of a new small molecule AQP9 inhibitor, RG100204 in cell-based calcein-quenching assays, and by stopped-flow light-scattering recordings of AQP9 permeability in proteoliposomes. Moreover, we investigated the effects of RG100204 on glycerol metabolism in mice. In cell-based assays, RG100204 blocked AQP9 water permeability and glycerol permeability with similar, high potency (~5 × 10-8 M). AQP9 channel blocking by RG100204 was confirmed in proteoliposomes. After oral gavage of db/db mice with RG100204, a dose-dependent elevation of plasma glycerol was observed. A blood glucose-lowering effect was not statistically significant. These experiments establish RG100204 as a direct blocker of the AQP9 channel, and suggest its use as an experimental tool for in vivo experiments on AQP9 function.

Structure and function of a silicic acid channel Lsi1

Silicon is a beneficial element for plant growth and production, especially in rice. Plant roots take up silicon in the form of silicic acid. Silicic acid channels, which belong to the NIP subfamily of aquaporins, are responsible for silicic acid uptake. Accumulated experimental results have deepened our understanding of the silicic acid channel for its uptake mechanism, physiological function, localization, and other aspects. However, how the silicic acid channel efficiently and selectively permeates silicic acid remains to be elucidated. Recently reported crystal structures of the silicic acid channel enabled us to discuss the mechanism of silicic acid uptake by plant roots at an atomic level. In this mini-review, we focus on the crystal structures of the silicic acid channel and provide a detailed description of the structural determinants of silicic acid permeation and its transport mechanism, which are crucial for the rational creation of secure and sustainable crops.

The Hidden Intricacies of Aquaporins: Remarkable Details in a Common Structural Scaffold

Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of four representatives, key aspects of AQP stability, gating, selectivity, pore geometry, and oligomerization, with a potential impact on channel functionality, are identified. The general view of AQPs possessing a continuous open water pore is challenged and it is depicted that AQPs' selectivity is not exclusively shaped by pore-lining residues but also by the relative arrangement of transmembrane helices. Moreover, this analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, a numbering scheme of the conserved AQP scaffold is established, facilitating direct comparison of, for example, disease-causing mutations and prediction of potential structural consequences. Additionally, the results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.

Diversification of the aquaporin family in geographical isolated oyster species promote the adaptability to dynamic environments

BACKGROUND

The diversified aquaporin (AQP) family that was derived from gene duplication and subsequent functional differentiation play critical roles in multiple physiological processes and in adaptation to the dynamic environments during the evolutionary process. Oysters are a group of bivalve fauna in Mollusca that were widely distributed around the world and show extraordinary adaptation to harsh environments. However, knowledge is lacking with the diversity and evolution of the AQP family in oysters, even in molluscs.

RESULTS

Here, we performed a comprehensive analysis of the AQP family in three geographical isolated oyster species that are native to different environments. Genome distribution and phylogenetic analysis revealed that the expansion of the AQP family in oysters were attributed to tandem duplication. Synteny analysis indicated that large-scale inversions lead to the independent duplication or deletion of the AQPs after speciation. As a consequence, these independent duplication events contributed to the diversification of the AQP family in different oysters. Pore pattern analysis suggested that the duplicated AQPs in oysters were highly diversified in inner surface profiles, implying the subsequent functional differentiation. The comparison conducted based on the transcriptome data demonstrated that the functional differentiated AQP family members in oysters may play critical roles in maintaining the balance between the stationary homeostasis and dynamic environments.

CONCLUSIONS

Our observation provides evidence for the correlation between the duplicated and functional differentiated AQP family and the adaptation to stationary life under dynamic environments in oysters. Additionally, it also broadens our knowledge of the evolution of AQP family in molluscs.

Outstanding Questions on the Beneficial Role of Silicon in Crop Plants

Silicon (Si) is widely accepted as a beneficial element for plants. Despite the substantial progress made in understanding Si transport mechanisms and modes of action in plants, several questions remain unanswered. In this review, we discuss such outstanding questions and issues commonly encountered by biologists studying the role of Si in plants in relation to Si bioavailability. In recent years, advances in our understanding of the role of Si-solubilizing bacteria and the efficacy of Si nanoparticles have been made. However, there are many unknown aspects associated with structural and functional features of Si transporters, Si loading into the xylem, and the role of specialized cells like silica cells and compounds preventing Si polymerization in plant tissues. In addition, despite several 1,000 reports showing the positive effects of Si in high as well as low Si-accumulating plant species, the exact roles of Si at the molecular level are yet to be understood. Some evidence suggests that Si regulates hormonal pathways and nutrient uptake, thereby explaining various observed benefits of Si uptake. However, how Si modulates hormonal pathways or improves nutrient uptake remains to be explained. Finally, we summarize the knowledge gaps that will provide a roadmap for further research on plant silicon biology, leading to an exploration of the benefits of Si uptake to enhance crop production.

Duplication and subsequent functional diversification of aquaporin family in Pacific abalone Haliotis discus hannai

Aquaporins (AQPs) are a group of proteins that evolved to mediate specific permeation of water and other small solutes, playing important roles in osmoregulation and nutrition, especially for aquatic animals. Genome-wide characterization of the AQP family in a typical mollusc, Pacific abalone, suggested that tandem duplication and retroduplication led to the dramatic expansion and diversification of AQP genes. Structural analysis indicated that tandem duplicated AQPs showed abnormal characteristics. The conserved amino acids in the key site of the Ar/R region were replaced by the others. These substitutions altered the pore diameter and properties of the inner surface and could accommodate the pass through of other molecules except water. Functional analysis indicated that abnormal Ar/R region of the tandemly adjacent members led to the different permeability, suggesting the neofunctionalization of tandemly duplicated genes. Mutation analysis indicated that at the key site of Ar/R region, just a single amino acid substitute could alter the permeability of HdAQPs, further explaining the mechanism of neofunctionalization between the tandem duplicated HdAQPs. Our observations provided strong evidence that duplication and subsequent neofunctionalization have led to structural and functional diversity of AQPs in Pacific abalone, providing insights into the evolution of AQPs in molluscs.

Scattering versus fluorescence self-quenching: more than a question of faith for the quantification of water flux in large unilamellar vesicles?

The endeavors to understand the determinants of water permeation through membrane channels, the effect of the lipid or polymer membrane on channel function, the development of specific water flow inhibitors, the design of artificial water channels and aquaporins for the use in industrial water filtration applications all rely on accurate ways to quantify water permeabilities (P f). A commonly used method is to reconstitute membrane channels into large unilamellar vesicles (LUVs) and to subject these vesicles to an osmotic gradient in a stopped-flow device. Fast recordings of either scattered light intensity or fluorescence self-quenching signals are taken as a readout for vesicle volume change, which in turn can be recalculated to accurate P f values. By means of computational and experimental data, we discuss the pros and cons of using scattering versus self-quenching experiments or subjecting vesicles to hypo- or hyperosmotic conditions. In addition, we explicate for the first time the influence of the LUVs size distribution, channel distribution between vesicles and remaining detergent after protein reconstitution on P f values. We point out that results such as the single channel water permeability (p f) depend on the membrane matrix or on the direction of the applied osmotic gradient may be direct results of the measurement and analysis procedure.

Structural basis for high selectivity of a rice silicon channel Lsi1

Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.

The rice Lsi1 aquaporin mediates uptake of silicic acid via the roots. Here the authors show the crystal structure of rice Lsi1 and characterize a unique five residue hydrophilic selectivity filter providing a structural basis for the highly selective activity of Lsi1 in Si uptake.

Structural Basis for Silicic Acid Uptake by Higher Plants

Many of the world's most important food crops such as rice, barley and maize accumulate silicon (Si) to high levels, resulting in better plant growth and crop yields. The first step in Si accumulation is the uptake of silicic acid by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins, also named metalloid porins. Here, we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). The OsNIP2;1 channel is closed in the crystal structure by the cytoplasmic loop D, which is known to regulate channel opening in classical plant aquaporins. The structure further reveals a novel, five-residue extracellular selectivity filter with a large diameter. Unbiased molecular dynamics simulations show a rapid opening of the channel and visualise how silicic acid interacts with the selectivity filter prior to transmembrane diffusion. Our results will enable detailed structure-function studies of metalloid porins, including the basis of their substrate selectivity.

Functional modulation of an aquaporin to intensify photosynthesis and abrogate bacterial virulence in rice

Plant aquaporins are a recently noted biological resource with a great potential to improve crop growth and defense traits. Here, we report the functional modulation of the rice (Oryza sativa) aquaporin OsPIP1;3 to enhance rice photosynthesis and grain production and to control bacterial blight and leaf streak, the most devastating worldwide bacterial diseases in the crop. We characterize OsPIP1;3 as a physiologically relevant CO₂ -transporting facilitator, which supports 30% of rice photosynthesis on average. This role is nullified by interaction of OsPIP1;3 with the bacterial protein Hpa1, an essential component of the Type III translocon that supports translocation of the bacterial Type III effectors PthXo1 and TALi into rice cells to induce leaf blight and streak, respectively. Hpa1 binding shifts OsPIP1;3 from CO₂ transport to effector translocation, aggravates bacterial virulence, and blocks rice photosynthesis. On the contrary, the external application of isolated Hpa1 to rice plants effectively prevents OsPIP1;3 from interaction with Hpa1 secreted by the bacteria that are infecting the plants. Blockage of the OsPIP1;3-Hpa1 interaction reverts OsPIP1;3 from effector translocation to CO₂ transport, abrogates bacterial virulence, and meanwhile induces defense responses in rice. These beneficial effects can combine to enhance photosynthesis by 29-30%, reduce bacterial disease by 58-75%, and increase grain yield by 11-34% in different rice varieties investigated in small-scale field trials conducted during the past years. Our results suggest that crop productivity and immunity can be coordinated by modulating the physiological and pathological functions of a single aquaporin to break the growth-defense tradeoff barrier.

Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

Aquaporins in regulation of plant protective responses to drought

Plasmolemma permeability is an integral indicator of the functional state of plant cells under stress. Aquaporins (AQPs), specialized transmembrane proteins that form water channels and play an important role in the adaptation of plants to adverse conditions and, in particular, to lack or excess of water, are involved in the formation of the response to drought. The main function of AQPs is to facilitate the movement of water across cell membranes and maintain aqueous cell homeostasis. Under stressful conditions, there is both an increase and decrease in the expression of individual aquaporin genes. Analysis of the data revealed differences in the expression of AQPs genes in stable and sensitive plant genotypes. It turned out that aquaporins in different stress-resistant varieties of the same species also respond differently to drought. The review provides brief information on the history of the discovery of aquaporins, the structure and function of these proteins, summarizes the latest information on the role of aquaporins in the regulation of metabolism and the response of plants to stressors, with particular emphasis on aquaporins in drought protection. The discovery and study of AQPs expands the possibilities of using genetic engineering methods for the selection of new plant species, in particular, more resistant to drought and salinization of the soil, as well as to increase their productivity. The use of aquaporins in biotechnology to improve drought resistance of various species has many prospects.

The Cerebral Effect of Ammonia in Brain Aging: Blood-Brain Barrier Breakdown, Mitochondrial Dysfunction, and Neuroinflammation

Aging occurs along with multiple pathological problems in various organs. The aged brain, especially, shows a reduction in brain mass, neuronal cell death, energy dysregulation, and memory loss. Brain aging is influenced by altered metabolites both in the systemic blood circulation and the central nervous system (CNS). High levels of ammonia, a natural by-product produced in the body, have been reported as contributing to inflammatory responses, energy metabolism, and synaptic function, leading to memory function in CNS. Ammonia levels in the brain also increase as a consequence of the aging process, ultimately leading to neuropathological problems in the CNS. Although many researchers have demonstrated that the level of ammonia in the body alters with age and results in diverse pathological alterations, the definitive relationship between ammonia and the aged brain is not yet clear. Thus, we review the current body of evidence related to the roles of ammonia in the aged brain. On the basis of this, we hypothesize that the modulation of ammonia level in the CNS may be a critical clinical point to attenuate neuropathological alterations associated with aging.

Adaptable and Multifunctional Ion-Conducting Aquaporins

Aquaporins function as water and neutral solute channels, signaling hubs, disease virulence factors, and metabolon components. We consider plant aquaporins that transport ions compared to some animal counterparts. These are candidates for important, as yet unidentified, cation and anion channels in plasma, tonoplast, and symbiotic membranes. For those individual isoforms that transport ions, water, and gases, the permeability spans 12 orders of magnitude. This requires tight regulation of selectivity via protein interactions and posttranslational modifications. A phosphorylation-dependent switch between ion and water permeation in AtPIP2;1 might be explained by coupling between the gates of the four monomer water channels and the central pore of the tetramer. We consider the potential for coupling between ion and water fluxes that could form the basis of an electroosmotic transducer. A grand challenge in understanding the roles of ion transporting aquaporins is their multifunctional modes that are dependent on location, stress, time, and development.

Grapevine aquaporins: Diversity, cellular functions, and ecophysiological perspectives

High-scored premium wines are typically produced under moderate drought stress, suggesting that the water status of grapevine is crucial for wine quality. Aquaporins greatly influence the plant water status by facilitating water diffusion across the plasma membrane in a tightly regulated manner. They adjust the hydraulic conductance of the plasma membrane rapidly and reversibly, which is essential in specific physiological events, including adaptation to soil water scarcity. The comprehension of the sophisticated plant-water relations at the molecular level are thus important to optimize agricultural practices or to assist plant breeding programs. This review explores the recent progresses in understanding the water transport in grapevine at the cellular level through aquaporins and its regulation. Important aspects, including aquaporin structure, diversity, cellular localization, transport properties, and regulation at the cellular and whole plant level are addressed. An ecophysiological perspective about the roles of grapevine aquaporins in plant response to drought stress is also provided.

Plant transporters involved in combating boron toxicity: beyond 3D structures

Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.

Aquaporins - Expression, purification and characterization

Aquaporin water channels facilitate the bi-directional flow of water and small, neutral solutes down an osmotic gradient in all kingdoms of life. Over the last two decades, the availability of high-quality protein has underpinned progress in the structural and functional characterization of these water channels. In particular, recombinant protein technology has guaranteed the supply of aquaporin samples that were of sufficient quality and quantity for further study. Here we review the features of successful expression, purification and characterization strategies that have underpinned these successes and that will drive further breakthroughs in the field. Overall, Escherichia coli is a suitable host for prokaryotic isoforms, while Pichia pastoris is the most commonly-used recombinant host for eukaryotic variants. Generally, a two-step purification procedure is suitable after solubilization in glucopyranosides and most structures are determined by X-ray following crystallization.

Foliar Application of Boron Nanoencapsulated in Almond Trees Allows B Movement Within Tree and Implements Water Uptake and Transport Involving Aquaporins

Nanotechnology brings to agriculture new forms of fertilizer applications, which could be used to reduce environmental contamination and increase efficiency. In this study, foliar fertilization with nanoencapsulated boron (B) was studied in comparison to an ionic B (non-encapsulated) application in young B-deficient almond trees grown under a controlled environment. B movement within the plant in relation to the leaf gas exchange, water relations parameters, and root hydraulic conductance was measured. Also, the expression of aquaporins (AQPs) [plasma membrane intrinsic protein (PIP) and tonoplast intrinsic protein (TIP)] was studied in relation to water uptake and transport parameters to establish the effectiveness of the different B treatments. The obtained results were associated with a high concentration of observed B with nanoencapsulated B, provided by the higher permeability of carrier nanovesicles, which allowed B to reach the cell wall more efficiently. The increases in water uptake and transport obtained in these plants could be related to the role that this element played in the cell wall and the relationship that it could have in the regulation of the expression of AQPs and their involvement in water relations. Also, an increase in the expression of PIPs (mainly PIP2.2) to the applied nanoencapsulated B could be related to the need for B and water transport, and fine regulation of TIP1.1 in relation to B concentration in tissues provides an important feature in the remobilization of B within the cell.

Genome-wide analysis of the aquaporin genes in melon (Cucumis melo L.)

Melon (Cucumis melo L.) is a very important crop throughout the world and has great economic importance, in part due to its nutritional properties. It prefers well-drained soil with low acidity and has a strong demand for water during fruit set. Therefore, a correct water balance—involving aquaporins—is necessary to maintain the plants in optimal condition. This manuscript describes the identification and comparative analysis of the complete set of aquaporins in melon. 31 aquaporin genes were identified, classified and analysed according to the evolutionary relationship of melon with related plant species. The individual role of each aquaporin in the transport of water, ions and small molecules was discussed. Finally, qPCR revealed that almost all melon aquaporins in roots and leaves were constitutively expressed. However, the high variations in expression among them point to different roles in water and solute transport, providing important features as that CmPIP1;1 is the predominant isoform and CmTIP1;1 is revealed as the most important osmoregulator in the tonoplast under optimal conditions. The results of this work pointing to the physiological importance of each individual aquaporin of melon opening a field of knowledge that deserves to be investigated.

Understanding aquaporin transport system in highly stress-tolerant and medicinal plant species Jujube (Ziziphus jujuba Mill.)

Jujube (Ziziphus jujubaMill.), a deciduous tree, is well known for its medicinal and nutritional values. Being an extremophile, it has an excellent capability to survive under arid conditions with limited water availability. In this regard, studying the role of water transport regulating proteins such as Aquaporins (AQPs) in jujube is of great importance. Aquaporins, channel-forming proteins are known to have a significant role in the transport of water and many other small solutes in plants. In the present study, computational approaches have identified 36 AQPs, which comprised of 12 NIPs (Nodulin 26-like intrinsic proteins), 10 PIPs (Plasma membrane intrinsic proteins), 10 TIPs (Tonoplast intrinsic proteins), 3 SIPs (Small intrinsic proteins), and 1 XIP (uncharacterized intrinsic protein). Conserved features of AQPs like asparagines-proline-alanine (NPA) amino acid motifs, aromatic/arginine (ar/R) selectivity filters, and Frogger's residues, having a significant role in solute specificity and transport, were also predicted. Homology-based tertiary (3D) structures of AQP_S were also resolved using various tools, and subsequently, pore-lining residues have been identified using the 3D structures. The information of pore morphology, along with the conserved features provided through this work, will be helpful to predict solute specificity of AQPs. Analysis of transcriptomic data revealed the tissue-specific or ubiquitous expression of several AQPs in different tissues of jujube. Interestingly, TIP3-1 was found to have fruit specific expression whereas most of the AQPs have a relatively low expression. Based on the present study and previous reports, TIP3s seems to have a significant role in seed desiccation processes. The findings presented here provide pivotal insights into the functions of extremophile specific AQPs, to better understand the role of AQPs and, subsequently, the stress tolerance mechanism in jujube.

Insights into the Selectivity Mechanisms of Grapevine NIP Aquaporins

Nodulin 26-like intrinsic proteins (NIPs) of the plant aquaporin family majorly facilitate the transport of physiologically relevant solutes. The present study intended to investigate how substrate selectivity in grapevine NIPs is influenced by the aromatic/arginine (ar/R) selectivity filter within the pore and the possible underlying mechanisms. A mutational approach was used to interchange the ar/R residues between grapevine NIPs (VvTnNIP1;1 with VvTnNIP6;1, and VvTnNIP2;1 with VvTnNIP5;1). Their functional characterization by stopped-flow spectroscopy in Saccharomyces cerevisiae revealed that mutations in residues of H2/H5 helices in VvTnNIP1;1 and VvTnNIP6;1 caused a general decline in membrane glycerol permeability but did not impart the expected substrate conductivity in the mutants. This result suggests that ar/R filter substitution could alter the NIP channel activity, but it was not sufficient to interchange their substrate preferences. Further, homology modeling analyses evidenced that variations in the pore radius combined with the differences in the channel's physicochemical properties (hydrophilicity/hydrophobicity) may drive substrate selectivity. Furthermore, yeast growth assays showed that H5 residue substitution alleviated the sensitivity of VvTnNIP2;1 and VvTnNIP5;1 to As, B, and Se, implying importance of H5 sequence for substrate selection. These results contribute to the knowledge of the overall determinants of substrate selectivity in NIPs.

The intersection of nitrogen nutrition and water use in plants: new paths toward improved crop productivity

Water and nitrogen availability limit crop productivity globally more than most other environmental factors. Plant availability of macronutrients such as nitrate is, to a large extent, regulated by the amount of water available in the soil, and, during drought episodes, crops can become simultaneously water and nitrogen limited. In this review, we explore the intricate relationship between water and nitrogen transport in plants, from transpiration-driven mass flow in the soil to uptake by roots via membrane transporters and channels and transport to aerial organs. We discuss the roles of root architecture and of suberized hydrophobic root barriers governing apoplastic water and nitrogen movement into the vascular system. We also highlight the need to identify the signalling cascades regulating water and nitrogen transport, as well as the need for targeted physiological analyses of plant traits influencing water and nitrogen uptake. We further advocate for incorporation of new phenotyping technologies, breeding strategies, and agronomic practices to improve crop yield in water- and nitrogen-limited production systems.

Evolutionary and Predictive Functional Insights into the Aquaporin Gene Family in the Allotetraploid Plant Nicotiana tabacum

Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the membrane diffusion of water and other small solutes. Nicotiana tabacum is an important model plant, and its allotetraploid genome has recently been released, providing us with the opportunity to analyze the AQP gene family and its evolution. A total of 88 full-length AQP genes were identified in the N. tabacum genome, and the encoding proteins were assigned into five subfamilies: 34 plasma membrane intrinsic proteins (PIPs); 27 tonoplast intrinsic proteins (TIPs); 20 nodulin26-like intrinsic proteins (NIPs); 3 small basic intrinsic proteins (SIPs); 4 uncharacterized X intrinsic proteins (XIPs), including two splice variants. We also analyzed the genomes of two N. tabacum ancestors, Nicotiana tomentosiformis and Nicotiana sylvestris, and identified 49 AQP genes in each species. Functional prediction, based on the substrate specificity-determining positions (SDPs), revealed significant differences in substrate specificity among the AQP subfamilies. Analysis of the organ-specific AQP expression levels in the N. tabacum plant and RNA-seq data of N. tabacum bright yellow-2 suspension cells indicated that many AQPs are simultaneously expressed, but differentially, according to the organs or the cells. Altogether, these data constitute an important resource for future investigations of the molecular, evolutionary, and physiological functions of AQPs in N. tabacum.

Molecular Modeling of Aquaporins from Leishmania major

Aquaporins are membrane proteins responsible for permeating water, ions, dissolved gases, and other small molecular weight compounds through the protective cell membranes of living organisms. These proteins have been gaining increased importance as targets for treating a variety of parasitic diseases, since they control key physiological processes in the life cycle of parasitic protozoans, such as the uptake of nutrients, release of metabolites, and alleviation of osmotic stress. In this work, we use homology modeling to build three-dimensional structures for the four main aquaporins encoded and expressed by Leishmania major, a protozoan that causes leishmaniasis and affects millions of people worldwide. Physico-chemical properties of the proposed models for LmAQP1, LmAQPα, LmAQPβ, and LmAQPγ are then investigated using molecular dynamics simulations and the reference interaction site model (RISM) molecular theory of solvation. Pore characteristics, water permeation, and potential of mean force across the AQP channels for water, methanol, urea, ammonia, and carbon dioxide are examined and compared with results obtained for a protozoan (Plasmodium falciparum) aquaporin for which a crystal structure is available.

Genome-wide identification and characterisation of Aquaporins in Nicotiana tabacum and their relationships with other Solanaceae species

BACKGROUND

Cellular membranes are dynamic structures, continuously adjusting their composition, allowing plants to respond to developmental signals, stresses, and changing environments. To facilitate transmembrane transport of substrates, plant membranes are embedded with both active and passive transporters. Aquaporins (AQPs) constitute a major family of membrane spanning channel proteins that selectively facilitate the passive bidirectional passage of substrates across biological membranes at an astonishing 108 molecules per second. AQPs are the most diversified in the plant kingdom, comprising of five major subfamilies that differ in temporal and spatial gene expression, subcellular protein localisation, substrate specificity, and post-translational regulatory mechanisms; collectively providing a dynamic transportation network spanning the entire plant. Plant AQPs can transport a range of solutes essential for numerous plant processes including, water relations, growth and development, stress responses, root nutrient uptake, and photosynthesis. The ability to manipulate AQPs towards improving plant productivity, is reliant on expanding our insight into the diversity and functional roles of AQPs.

RESULTS

We characterised the AQP family from Nicotiana tabacum (NtAQPs; tobacco), a popular model system capable of scaling from the laboratory to the field. Tobacco is closely related to major economic crops (e.g. tomato, potato, eggplant and peppers) and itself has new commercial applications. Tobacco harbours 76 AQPs making it the second largest characterised AQP family. These fall into five distinct subfamilies, for which we characterised phylogenetic relationships, gene structures, protein sequences, selectivity filter compositions, sub-cellular localisation, and tissue-specific expression. We also identified the AQPs from tobacco's parental genomes (N. sylvestris and N. tomentosiformis), allowing us to characterise the evolutionary history of the NtAQP family. Assigning orthology to tomato and potato AQPs allowed for cross-species comparisons of conservation in protein structures, gene expression, and potential physiological roles.

CONCLUSIONS

This study provides a comprehensive characterisation of the tobacco AQP family, and strengthens the current knowledge of AQP biology. The refined gene/protein models, tissue-specific expression analysis, and cross-species comparisons, provide valuable insight into the evolutionary history and likely physiological roles of NtAQPs and their Solanaceae orthologs. Collectively, these results will support future functional studies and help transfer basic research to applied agriculture.

Versatile roles of aquaporin in physiological processes and stress tolerance in plants

Aquaporins are pore-forming transmembrane proteins that facilitate the movement of water and many other small neutral solutes across the cells and intracellular compartments. Plants exhibits high diversity in aquaporin isoforms and broadly classified into five different subfamilies on the basis of phylogenetic distribution and subcellular occurrence: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like proteins (NIPs), small basic intrinsic proteins (SIPs) and uncharacterized intrinsic proteins (XIPs). The gating mechanism of aquaporin channels is tightly regulated by post-translational modifications such as phosphorylation, methylation, acetylation, glycosylation, and deamination. Aquaporin expression and transport functions are also modulated by the various phytohormones-mediated signalling in plants. Combined physiology and transcriptome analysis revealed the role of aquaporins in regulating hydraulic conductance in roots and leaves. The present review mainly focused on aquaporin functional activity during solute transport, plant development, abiotic stress response, and plant-microbe symbiosis. Genetically modified plants overexpressing aquaporin-encoding genes display improved agronomic and abiotic stress tolerance.

Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study

Formate/nitrite transporters (FNTs) selectively transport monovalent anions and are found in prokaryotes and lower eukaryotes. They play a significant role in bacterial growth and act against the defense mechanism of infected hosts. Because FNTs do not occur in higher animals, they are attractive drug targets for many bacterial diseases. Phylogenetic analysis revealed that they can be classified into eight subgroups, two of which belong to the uncharacterized YfdC-α and YfdC-β groups. Experimentally determined structures of FNTs belonging to different phylogenetic groups adopt the unique aquaporin-like hourglass helical fold. We considered the formate channel from Vibrio cholerae, the hydrosulphide channel from Clostridium difficile, and the uncharacterized channel from Escherichia coli (EcYfdC) to investigate the mechanism of transport and selectivity. Using equilibrium molecular dynamics and umbrella sampling studies, we determined temporal channel radius profiles, permeation events, and potential of mean force profiles of different substrates with the conserved central histidine residue in protonated or neutral form. Unlike the formate channel from V. cholerae and the hydrosulphide channel from C. difficile, molecular dynamics studies showed that the formate substrate was unable to enter the vestibule region of EcYfdC. Absence of a conserved basic residue and presence of acidic residues in the vestibule regions, conserved only in YfdC-α, were found to be responsible for high energy barriers for the anions to enter EcYfdC. Potential of mean force profiles generated for ammonia and ammonium ion revealed that EcYfdC can transport neutral solutes and could possibly be involved in the transport of cations analogous to the mechanism proposed for ammonium transporters. Although YfdC members belong to the FNT family, our studies strongly suggest that EcYfdC is not an anion channel. Absence or presence of specific charged residues at particular positions makes EcYfdC selective for neutral or possibly cationic substrates. Further experimental studies are needed to get a definitive answer to the question of the substrate selectivity of EcYfdC. This provides an example of membrane proteins from the same family transporting substrates of different chemical nature.

SLC4A11 function: evidence for H+(OH-) and NH3-H+ transport

Whether SLC4A11 transports ammonia and its potential mode of ammonia transport (NH4+, NH₃, or NH₃-2H⁺ transport have been proposed) are controversial. In the absence of ammonia, whether SLC4A11 mediates significant conductive H⁺(OH^-) transport is also controversial. The present study was performed to determine the mechanism of human SLC4A11 ammonia transport and whether the transporter mediates conductive H⁺(OH^-) transport in the absence of ammonia. We quantitated H⁺ flux by monitoring changes in intracellular pH (pH_i) and measured whole cell currents in patch-clamp studies of HEK293 cells expressing the transporter in the absence and presence of NH₄Cl. Our results demonstrate that SLC4A11 mediated conductive H⁺(OH^-) transport that was stimulated by raising the extracellular pH (pH_e). Ammonia-induced HEK293 whole cell currents were also stimulated by an increase in pH_e. In studies using increasing NH₄Cl concentrations with equal NH4+ extracellular and intracellular concentrations, the shift in the reversal potential (E_rev) due to the addition of ammonia was compatible with NH₃-H⁺ transport competing with H⁺(OH^-) rather than NH₃-nH⁺ (n ≥ 2) transport. The increase in equivalent H⁺(OH^-) flux observed in the presence of a transcellular H⁺ gradient was also compatible with SLC4A11-mediated NH₃-H⁺ flux. The NH₃ versus E_rev data fit a theoretical model suggesting that NH₃-H⁺ and H⁺(OH^-) competitively interact with the transporter. Studies of mutant SLC4A11 constructs in the putative SLC4A11 ion coordination site showed that both H⁺(OH^-) transport and ammonia-induced whole cell currents were blocked suggesting that the H⁺(OH^-) and NH₃-H⁺ transport processes share common features involving the SLC4A11 transport mechanism.

Roles of membrane transporters: connecting the dots from sequence to phenotype

BACKGROUND

Plant membrane transporters are involved in diverse cellular processes underpinning plant physiology, such as nutrient acquisition, hormone movement, resource allocation, exclusion or sequestration of various solutes from cells and tissues, and environmental and developmental signalling. A comprehensive characterization of transporter function is therefore key to understanding and improving plant performance.

SCOPE AND CONCLUSIONS

In this review, we focus on the complexities involved in characterizing transporter function and the impact that this has on current genomic annotations. Specific examples are provided that demonstrate why sequence homology alone cannot be relied upon to annotate and classify transporter function, and to show how even single amino acid residue variations can influence transporter activity and specificity. Misleading nomenclature of transporters is often a source of confusion in transporter characterization, especially for people new to or outside the field. Here, to aid researchers dealing with interpretation of large data sets that include transporter proteins, we provide examples of transporters that have been assigned names that misrepresent their cellular functions. Finally, we discuss the challenges in connecting transporter function at the molecular level with physiological data, and propose a solution through the creation of new databases. Further fundamental in-depth research on specific transport (and other) proteins is still required; without it, significant deficiencies in large-scale data sets and systems biology approaches will persist. Reliable characterization of transporter function requires integration of data at multiple levels, from amino acid residue sequence annotation to more in-depth biochemical, structural and physiological studies.

Involvement of aquaporins on nitrogen-acquisition strategies of juvenile and adult plants of an epiphytic tank-forming bromeliad

Depending on the N source and plant ontogenetic state, the epiphytic tank-forming bromeliad Vriesea gigantea can modulate aquaporin expression to maximize the absorption of the most available nitrogen source. Epiphytic bromeliads frequently present a structure formed by the overlapping of leaf bases where water and nutrients can be accumulated and absorbed, called tank. However, this structure is not present during the juvenile ontogenetic phase, leading to differences in nutrient acquisition strategies. Recent studies have shown a high capacity of the bromeliad Vriesea gigantea, an epiphytic tank-forming bromeliad, to absorb urea by their leaves. Since plant aquaporins can facilitate the diffusion of urea through the membranes, we cloned three foliar aquaporin genes, VgPIP1;1, VgPIP1;2 and VgTIP2;1 from V. gigantea plants. Through functional studies, we observed that besides water, VgTIP2;1 was capable of transporting urea while VgPIP1;2 may facilitate ammonium/ammonia diffusion. Moreover, aiming at identifying urea and ammonium-induced changes in aquaporin expression in leaves of juvenile and adult-tank plants, we showed that VgPIP1;1 and VgPIP1;2 transcripts were up-regulated in response to either urea or ammonium only in juvenile plants, while VgTIP2;1 was up-regulated in response to urea only in adult-tank plants. Thereby, an ontogenetic shift from juvenile to adult-tank-forming-plant appears to occur with metabolic changes regarding nitrogen metabolism regulation. Investigating urea metabolism in wild species that naturally cope with organic N sources, such as V. gigantea, may provide the knowledge to modify nitrogen use efficiency of crop plants.