A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots

Protein kinase SnRK2.4 is a key regulator of aquaporins and root hydraulics in Arabidopsis

Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever-changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; Lpr ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to Lpr . Using recombinant lines from a biparental cross (Cvi-0 x Col-0), we show that the gene encoding class 2 Sucrose-Non-Fermenting Protein kinase 2.4 (SnRK2.4) in Col-0 contributes to >30% of Lpr by enhancing aquaporin-dependent water transport. At variance with the inactive and possibly unstable Cvi-0 SnRK2.4 form, the Col-0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col-0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long-term (>3 h) inhibition of Lpr by ABA possibly involves a SnRK2.4-independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA-induced inhibition of primary root growth. The study identifies a key component of Lpr and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA-dependent or independent SnRK2s.

CRK12: A Key Player in Regulating the Phaseolus vulgaris-Rhizobium tropici Symbiotic Interaction

Cysteine-rich receptor-like kinases (CRKs) are a type of receptor-like kinases (RLKs) that are important for pathogen resistance, extracellular reactive oxygen species (ROS) signaling, and programmed cell death in plants. In a previous study, we identified 46 CRK family members in the Phaseolus vulgaris genome and found that CRK12 was highly upregulated under root nodule symbiotic conditions. To better understand the role of CRK12 in the Phaseolus-Rhizobia symbiotic interaction, we functionally characterized this gene by overexpressing (CRK12-OE) and silencing (CRK12-RNAi) it in a P. vulgaris hairy root system. We found that the constitutive expression of CRK12 led to an increase in root hair length and the expression of root hair regulatory genes, while silencing the gene had the opposite effect. During symbiosis, CRK12-RNAi resulted in a significant reduction in nodule numbers, while CRK12-OE roots showed a dramatic increase in rhizobial infection threads and the number of nodules. Nodule cross sections revealed that silenced nodules had very few infected cells, while CRK12-OE nodules had enlarged infected cells, whose numbers had increased compared to controls. As expected, CRK12-RNAi negatively affected nitrogen fixation, while CRK12-OE nodules fixed 1.5 times more nitrogen than controls. Expression levels of genes involved in symbiosis and ROS signaling, as well as nitrogen export genes, supported the nodule phenotypes. Moreover, nodule senescence was prolonged in CRK12-overexpressing roots. Subcellular localization assays showed that the PvCRK12 protein localized to the plasma membrane, and the spatiotemporal expression patterns of the CRK12-promoter::GUS-GFP analysis revealed a symbiosis-specific expression of CRK12 during the early stages of rhizobial infection and in the development of nodules. Our findings suggest that CRK12, a membrane RLK, is a novel regulator of Phaseolus vulgaris-Rhizobium tropici symbiosis.

Isolation of Plasmodesmata Membranes for Lipidomic and Proteomic Analysis

Plasmodesmata (PD) are membranous intercellular nanochannels crossing the plant cell wall to connect adjacent cells in plants. Our understanding of PD function heavily relies on the identification of their molecular components, these being proteins or lipids. In that regard, proteomic and lipidomic analyses of purified PD represent a crucial strategy in the field. Here we describe a simple two-step purification procedure that allows isolation of pure PD-derived membranes from Arabidopsis suspension cells suitable for "omic" approaches. The first step of this procedure consists on isolating pure cell walls containing intact PD, followed by a second step which involves an enzymatic degradation of the wall matrix to release PD membranes. The PD-enriched fraction can then serve to identify the lipid and protein composition of PD using lipidomic and proteomic approaches, which we also describe in this method article.

Inferring the genetic responses to acute drought stress across an ecological gradient

BACKGROUND

How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in many non-model organisms has yet to be explored. We investigated this question in Mentzelia section Bartonia (Loasaceae), which occurs throughout western North America, including arid lands. To better understand the genetic responses to drought stress among species that occur in different habitats, the gene expression levels of three species from Mentzelia were compared across a precipitation gradient. Two de novo reference transcriptomes were generated and annotated. Leaf and root tissues were collected from control and drought shocked plants and compared to one another for differential expression. A target-gene approach was also implemented to better understand how drought-related genes from model and crop species function in non-model systems.

RESULTS

When comparing the drought-shock treatment plants to their respective control plants, we identified 165 differentially expressed clusters across all three species. Differentially expressed genes including those associated with water movement, photosynthesis, and delayed senescence. The transcriptome profiling approach was coupled with a target genes approach that measured expression of 90 genes associated with drought tolerance in model organisms. Comparing differentially expressed genes with a ≥ 2 log-fold value between species and tissue types showed significant differences in drought response. In pairwise comparisons, species that occurred in drier environments differentially expressed greater genes in leaves when drought shocked than those from wetter environments, but expression in the roots mostly produced opposite results.

CONCLUSIONS

Arid-adapted species mount greater genetic responses compared to the mesophytic species, which has likely evolved in response to consistent annual drought exposure across generations. Drought responses also depended on organ type. Xerophytes, for example, mounted a larger response in leaves to downregulate photosynthesis and senescence, while mobilizing carbon and regulating water in the roots. The complexity of drought responses in Mentzelia suggest that whole organism responses need to be considered when studying drought and, in particular, the physiological mechanisms in which plants regulate water, carbon, cell death, metabolism, and secondary metabolites.

RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis

Rab proteins are small GTPases that are important in the regulation of vesicle trafficking. Through data mining, we identified RabA2b to be stress responsive, though little is known about the involvement of RabA in plant responses to abiotic stresses. Analysis of the RabA2b native promoter showed strong activity during osmotic stress, which required the stress hormone Abscisic acid (ABA) and was restricted to the vasculature. Sequence analysis of the promoter region identified predicted binding motifs for several ABA-responsive transcription factors. We cloned RabA2b and overexpressed it in Arabidopsis. The resulting transgenic plants were strikingly drought resistant. The reduced water loss observed in detached leaves of the transgenic plants could not be explained by stomatal aperture or density, which was similar in all the genotypes. Subcellular localization studies detected strong colocalization between RabA2b and the plasma membrane (PM) marker PIP2. Further studies of the PM showed, for the first time, a distinguished alteration in the PM proteome as a result of RabA2b overexpression. Proteomic analysis of isolated PM fractions showed enrichment of stress-coping proteins as well as cell wall/cuticle modifiers in the transgenic lines. Finally, the cuticle permeability of transgenic leaves was significantly reduced compared to the wild type, suggesting that it plays a role in its drought resistant properties. Overall, these data provide new insights into the roles and modes of action of RabA2b during water stresses, and indicate that increased RabA2b mediated PM trafficking can affect the PM proteome and increase drought tolerance.

Targeting aquaporins to alleviate hazardous metal(loid)s imposed stress in plants

Uptake of hazardous metal(loid)s adversely affects plants and imposes a threat to the entire food chain. Here, the role of aquaporins (AQPs) providing tolerance against hazardous metal(loid)s in plants is discussed to provide a perspective on the present understanding, knowledge gaps, and opportunities. Plants adopt complex molecular and physiological mechanisms for better tolerance, adaptability, and survival under metal(loid)s stress. Water conservation in plants is one such primary strategies regulated by AQPs, a family of channel-forming proteins facilitating the transport of water and many other solutes. The strategy is more evident with reports suggesting differential expression of AQPs adopted by plants to cope with the heavy metal stress. In this regard, numerous studies showing enhanced tolerance against hazardous elements in plants due to AQPs activity are discussed. Consequently, present understanding of various aspects of AQPs, such as tertiary-structure, transport activity, solute-specificity, differential expression, gating mechanism, and subcellular localization, are reviewed. Similarly, various tools and techniques are discussed in detail aiming at efficient utilization of resources and knowledge to combat metal(loid)s stress. The scope of AQP transgenesis focusing on heavy metal stresses is also highlighted. The information provided here will be helpful to design efficient strategies for the development of metal(loid)s stress-tolerant crops.

Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective

Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H⁺-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.

Two aquaporins, SIP1;1 and PIP1;2, mediate water transport for pollen hydration in the Arabidopsis pistil

Pollination is the crucial initial step that brings together the male and female gametophytes, and occurs at the surface of the stigmatic papilla cell in Arabidopsis thaliana. After pollen recognition, pollen hydration is initiated as a second critical step to activate desiccated mature pollen grains for germination, and thus water transport from pistil to pollen is essential for this process. In this study, we report a novel aquaporin-mediated water transport process in the papilla cell as a control mechanism for pollen hydration. Coupled with a time-series imaging analysis of pollination and a reverse genetic analysis using T-DNA insertion Arabidopsis mutants, we found that two aquaporins, the ER-bound SIP1;1 and the plasma membrane-bound PIP1;2, are key players in water transport from papilla cell to pollen during pollination. In wild type plant, hydration speed reached its maximal value within 5 min after pollination, remained high until 10-15 min. In contrast, sip1;1 and pip1;2 mutants showed no rapid increase of hydration speed, but instead a moderate increase during ∼25 min after pollination. Pollen of sip1;1 and pip1;2 mutants had normal viability without any functional defects for pollination, indicating that decelerated pollen hydration is due to a functional defect on the female side in sip1;1 and pip1;2 mutants. In addition, sip1;1 pip1;2 double knockout mutant showed a similar impairment of pollen hydration to individual single mutants, suggesting that their coordinated regulation is critical for proper water transport, in terms of speed and amount, in the pistil to accomplish successful pollen hydration.

Chlorophyll fluorescence, dark respiration and metabolomic analysis of Halodule pinifolia reveal potential heat responsive metabolites and biochemical pathways under ocean warming

Seagrasses are submerged marine angiosperms often prone to various biotic and abiotic stress factors in the marine environment. Our study investigated the response, adaptation and underlying tolerance mechanism of tropical seagrass Halodule pinifolia upon temperature stress (24°, 29°, 37°, and 45 °C) and evaluated the effect of temperature stress on net photosynthesis (ΔF/F'_m) and dark respiration (F_v/F_m). In this study, metabolomic analysis of seagrass H. pinifolia upon heat stress has been performed using GC-MS based omics approach. As a result, the net photosynthetic efficiency (ΔF/F'_m) was found significantly decreased upon heat stress, while the dark respiration rate was increased to 2.903 mg O₂/g FW h^-1 and 3.87 mg O₂/g FW h^-1 as compared to the control (24 °C), respectively. Metabolomic analysis showed heat stress could cause large metabolite variations with respect to sugar, amino acids and organic acids. Interestingly, three thermo-protective metabolites such as trehalose (sugar), glycine betaine (amino acid) and methyl vinyl ketone (organic acid) were profiled from H. pinifolia (45 °C) and is the first report on the occurrence of glycine betaine and methyl vinyl ketone from seagrasses and other aquatic species so far. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated H. pinifolia exposed to heat stress lead to intense biochemical changes and caused significant variations in the heat responsive metabolic pathways. The present findings would facilitate the further research on identifying gene to metabolite networks for an effective management of seagrass conservation by genetic manipulation.

NRT2.1 C-terminus phosphorylation prevents root high affinity nitrate uptake activity in Arabidopsis thaliana

In Arabidopsis thaliana, NRT2.1 codes for a main component of the root nitrate high-affinity transport system. Previous studies revealed that post-translational regulation of NRT2.1 plays an important role in the control of root nitrate uptake and that one mechanism could correspond to NRT2.1 C-terminus processing. To further investigate this hypothesis, we produced transgenic plants with truncated forms of NRT2.1. This revealed an essential sequence for NRT2.1 activity, located between the residues 494 and 513. Using a phospho-proteomic approach, we found that this sequence contains one phosphorylation site, at serine 501, which can inactivate NRT2.1 function when mimicking the constitutive phosphorylation of this residue in transgenic plants. This phenotype could neither be explained by changes in abundance of NRT2.1 and NAR2.1, a partner protein of NRT2.1, nor by a lack of interaction between these two proteins. Finally, the relative level of serine 501 phosphorylation was found to be increased by ammonium nitrate in wild-type plants, leading to the inactivation of NRT2.1 and to a decrease in high affinity nitrate transport into roots. Altogether, these observations reveal a new and essential mechanism for the regulation of NRT2.1 activity.

Detergent Resistant Membrane Domains in Broccoli Plasma Membrane Associated to the Response to Salinity Stress

Detergent-resistant membranes (DRMs) microdomains, or “raft lipids”, are key components of the plasma membrane (PM), being involved in membrane trafficking, signal transduction, cell wall metabolism or endocytosis. Proteins imbibed in these domains play important roles in these cellular functions, but there are few studies concerning DRMs under abiotic stress. In this work, we determine DRMs from the PM of broccoli roots, the lipid and protein content, the vesicles structure, their water osmotic permeability and a proteomic characterization focused mainly in aquaporin isoforms under salinity (80 mM NaCl). Based on biochemical lipid composition, higher fatty acid saturation and enriched sterol content under stress resulted in membranes, which decreased osmotic water permeability with regard to other PM vesicles, but this permeability was maintained under control and saline conditions; this maintenance may be related to a lower amount of total PIP1 and PIP2. Selective aquaporin isoforms related to the stress response such as PIP1;2 and PIP2;7 were found in DRMs and this protein partitioning may act as a mechanism to regulate aquaporins involved in the response to salt stress. Other proteins related to protein synthesis, metabolism and energy were identified in DRMs independently of the treatment, indicating their preference to organize in DMRs.

Phosphorylation of plasma membrane aquaporin PIP2;1 in C-terminal affects light-induced stomatal opening in Arabidopsis

Guard cells undergo quick volume changes during stomatal movements. However, the contribution of aquaporins to stomatal movements has not been well understood. The plasma membrane aquaporin PIP2;1in Arabidopsis has been found to mediate abscisic acid-induced or flag22-induced stomatal closure. In this research, we investigated the role of PIP2;1 in light-induced stomatal opening by measuring the stomatal apertures of the pip2;1 mutant and PIP2;1 overexpression lines after light treatment. pip2;1 mutant exhibited a larger stomatal aperture, and the overexpression lines displayed a smaller stomatal aperture. It has been reported that the phosphorylation at Ser-280 and Ser-283 of PIP2;1 in rosette tissue increased in response to darkness, whereas osmotic water permeability (P_f) in mesophyll protoplasts in darkness was lower than that under light, suggesting that phosphorylation at Ser-280 and Ser-283 of PIP2;1 affected P_f in mesophyll protoplasts. Therefore, we obtained the pip2;1 mutant expressing phosphorylation-deficient (PIP2;1 AA) or phosphomimetic (PIP2;1 DD) forms of PIP2;1. The PIP2;1 AA lines exhibited a larger stomatal aperture as pip2;1 mutant, whereas PIP2;1 DD lines exhibited a smaller stomatal aperture as PIP2;1 overexpression lines under light. These results suggest that PIP2;1 plays a negative role in light-induced stomatal opening, and phosphorylation of PIP2;1 at Ser-280 and Ser-283 causes reduced water absorption in guard cells and decreased stomatal opening.

Evolutionary Understanding of Aquaporin Transport System in the Basal Eudicot Model Species Aquilegia coerulea

Aquaporins (AQPs) play a pivotal role in the cellular transport of water and many other small solutes, influencing many physiological and developmental processes in plants. In the present study, extensive bioinformatics analysis of AQPs was performed in Aquilegia coerulea L., a model species belonging to basal eudicots, with a particular focus on understanding the AQPs role in the developing petal nectar spur. A total of 29 AQPs were identified in Aquilegia, and their phylogenetic analysis performed with previously reported AQPs from rice, poplar and Arabidopsis depicted five distinct subfamilies of AQPs. Interestingly, comparative analysis revealed the loss of an uncharacterized intrinsic protein II (XIP-II) group in Aquilegia. The absence of the entire XIP subfamily has been reported in several previous studies, however, the loss of a single clade within the XIP family has not been characterized. Furthermore, protein structure analysis of AQPs was performed to understand pore diversity, which is helpful for the prediction of solute specificity. Similarly, an AQP AqcNIP2-1 was identified in Aquilegia, predicted as a silicon influx transporter based on the presence of features such as the G-S-G-R aromatic arginine selectivity filter, the spacing between asparagine-proline-alanine (NPA) motifs and pore morphology. RNA-seq analysis showed a high expression of tonoplast intrinsic proteins (TIPs) and plasma membrane intrinsic proteins (PIPs) in the developing petal spur. The results presented here will be helpful in understanding the AQP evolution in Aquilegia and their expression regulation, particularly during floral development.

Aquaporins and their function in root water transport under salt stress conditions in Eutrema salsugineum

Eutrema salsugineum is considered as extremophile model species. To gain insights into the root hydraulic conductivity and the role played by aquaporins in E. salsugineum, we investigated the aquaporin family profiles, plant water status and root hydraulic conductivity under standard (salt-free) and salt stress conditions. We found that there was no variation in the relative electric conductivity of the leaves when the salt concentration was less than 200 mM NaCl, and the transpiration rate dropped to 60.6% at 100 mM NaCl for 14 days compared to that at standard conditions. The pressure chamber techniques indicated that the root hydraulic conductivity of E. salsugineum was repressed by salt stress. However, propionic acid, usually used as an aquaporin inhibitor, unexpectedly enhanced the root hydraulic conductivity of E. salsugineum. The aquaporin family in E. salsugineum was profiled and the PIP aquaporin expression was investigated at the transcriptional and translational levels. Finally, two EsPIPs were identified to play a role in salt stress. The overall study provides evidence on how halophytes maintain their water status and aquaporin regulation pattern under salt stress conditions.

Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus

Environmental salinity is an important abiotic factor influencing normal physiological functions and productive performance in the sea cucumber Apostichopus japonicus. It is therefore important to understand how changes in salinity affect sea cucumbers in the face of global climate change. In this study, we investigated the responses to salinity stress in sea cucumbers using mRNA and miRNA sequencing. The regulatory network of mRNAs and miRNAs involved in salinity stress was examined, and the metabolic pathways enriched for differentially expressed miRNAs and target mRNAs were identified. The top 20 pathways were involved in carbohydrate metabolism, fatty acid metabolism, degradation, and elongation, amino acid metabolism, genetic information processing, metabolism of cofactors and vitamins, transport and catabolism, and environmental information processing. A total of 22 miRNAs showed differential expression during salinity acclimation. The predicted 134 target genes were enriched in functions consistent with the results of gene enrichment based on transcriptome analysis. These results suggested that sea cucumbers deal with salinity stress via changes in amino acid metabolism, ion channels, transporters, and aquaporins, under stimulation by environmental signals, and that this process requires energy from carbohydrate and fatty acid metabolism. Salinity challenge also induced miRNA expression. These results provide a valuable genomic resource that extends our understanding of the unique biological characteristics of this economically important species under conditions of salinity stress.

Oscillating Aquaporin Phosphorylation and 14-3-3 Proteins Mediate the Circadian Regulation of Leaf Hydraulics

The circadian clock regulates plant tissue hydraulics to synchronize water supply with environmental cycles and thereby optimize growth. The circadian fluctuations in aquaporin transcript abundance suggest that aquaporin water channels play a role in these processes. Here, we show that hydraulic conductivity (K _ros) of Arabidopsis (Arabidopsis thaliana) rosettes displays a genuine circadian rhythmicity with a peak around midday. Combined immunological and proteomic approaches revealed that phosphorylation at two C-terminal sites (Ser280, Ser283) of PLASMA MEMBRANE INTRINSIC PROTEIN 2;1 (AtPIP2;1), a major plasma membrane aquaporin in rosettes, shows circadian oscillations and is correlated with K _ros Transgenic expression of phosphodeficient and phosphomimetic forms of this aquaporin indicated that AtPIP2;1 phosphorylation is necessary but not sufficient for K _ros regulation. We investigated the supporting role of 14-3-3 proteins, which are known to interact with and regulate phosphorylated proteins. Individual knockout plants for five 14-3-3 protein isoforms expressed in rosettes lacked circadian activation of K _ros Two of these [GRF4 (14-3-3Phi); GRF10 (14-3-3Epsilon)] showed direct interactions with AtPIP2;1 in the plant and upon coexpression in Xenopus laevis oocytes and activated AtPIP2;1, preferentially when the latter was phosphorylated at its two C-terminal sites. We propose that this regulatory mechanism assists in the activation of phosphorylated AtPIP2;1 during circadian regulation of K _ros.

Plasma membrane aquaporins mediates vesicle stability in broccoli

The use of in vitro membrane vesicles is attractive because of possible applications in therapies. Here we aimed to compare the stability and functionality of plasma membrane vesicles extracted from control and salt-treated broccoli. The impact of the amount of aquaporins was related to plasma membrane osmotic water permeability and the stability of protein secondary structure. Here, we describe for first time an increase in plant aquaporins acetylation under high salinity. Higher osmotic water permeability in NaCl vesicles has been related to higher acetylation, upregulation of aquaporins, and a more stable environment to thermal denaturation. Based on our findings, we propose that aquaporins play an important role in vesicle stability.

Isolation of Plasmodesmata

Plasmodesmata (PD) are plasma membrane lined pores that cross the plant cell wall and connect adjacent cells. Plasmodesmata are composed of elements of the endoplasmic reticulum, plasma membrane, cytosol, and cell wall and thus, as multicomposite structures that are embedded in the cell wall, they are notoriously difficult to isolate from whole plant tissue. However, understanding PD structure, function, and regulation necessitates identification of their molecular components and therefore proteomic and lipidomic analyses of PD fractions are an essential strategy for plasmodesmal biology. Here we outline a simple two-step purification procedure that allows isolation of PD-derived membranes from Arabidopsis suspension cells. The method involves isolation of purified cell wall fragments containing intact PD which is followed by enzymatic degradation of the cell wall to release the PD. This membrane-rich fraction can be subjected to protein and lipid extraction for molecular characterization of PD components. The first step of this procedure involves the isolation of cell wall fragments containing intact PD, free from contamination from other cellular compartments. Purified PD membranes are then released from the cell wall matrix by enzymatic degradation. Isolated PD membranes provide a suitable starting material for the analysis of PD-associated proteins and lipids.

Multiwalled carbon nanotubes enter broccoli cells enhancing growth and water uptake of plants exposed to salinity

BACKGROUND

Carbon nanotubes have been shown to improve the germination and growth of some plant species, extending the applicability of the emerging nano-biotechnology field to crop science.

RESULTS

In this work, exploitation of commercial multiwalled carbon nanotubes (MWCNTs) in control and 100 mM NaCl-treated broccoli was performed. Transmission electron microscopy demonstrated that MWCNTs can enter the cells in adult plants with higher accumulation under salt stress. Positive effect of MWCNTs on growth in NaCl-treated plants was consequence of increased water uptake, promoted by more-favourable energetic forces driving this process, and enhanced net assimilation of CO2. MWCNTs induced changes in the lipid composition, rigidity and permeability of the root plasma membranes relative to salt-stressed plants. Also, enhanced aquaporin transduction occurred, which improved water uptake and transport, alleviating the negative effects of salt stress.

CONCLUSION

Our work provides new evidences about the effect of MWCNTs on plasma membrane properties of the plant cell. The positive response to MWCNTs in broccoli plants opens novel perspectives for their technological uses in new agricultural practices, especially when 1plants are exposed to saline environments.

Dual regulation of root hydraulic conductivity and plasma membrane aquaporins by plant nitrate accumulation and high-affinity nitrate transporter NRT2.1

The water status and mineral nutrition of plants critically determine their growth and development. Nitrate (NO3(-)), the primary nitrogen source of higher plants, is known to impact the water transport capacity of roots (root hydraulic conductivity, Lpr). To explore the effects and mode of action of NO3(-) on Lpr, we used an extended set of NO3(-) transport (nrt1.1, nrt1.2, nrt1.5 and nrt2.1), signaling (nrt1.1 and nrt2.1) and metabolism (nia) mutants in Arabidopsis, grown under various NO3(-) conditions. First, a strong positive relationship between Lpr and NO3(-) accumulation, in shoots rather than in roots, was revealed. Secondly, a specific 30% reduction of Lpr in nrt2.1 plants unraveled a major role for the high-affinity NO3(-) transporter NRT2.1 in increasing Lpr These results indicate that NO3(-)signaling rather than nitrogen assimilation products governs Lpr in Arabidopsis. Quantitative real-time reverse transcription-PCR and enzyme-linked immunosorbent assays (ELISAs) were used to investigate the effects of NO3(-) availability on plasma membrane aquaporin (plasma membrane intrinsic protein; PIP) expression. Whereas PIP regulation mostly occurs at the post-translational level in wild-type plants, a regulation of PIPs at both the transcriptional and translational levels was uncovered in nrt2.1 plants. In conclusion, this work reveals that control of Arabidopsis Lpr and PIP functions by NO3(-) involves novel shoot to root signaling and NRT2.1-dependent functions.

The Arabidopsis tonoplast is almost devoid of glycoproteins with complex N-glycans, unlike the rat lysosomal membrane

The distribution of the N-glycoproteome in integral membrane proteins of the vacuolar membrane (tonoplast) or the plasma membrane of Arabidopsis thaliana and, for further comparison, of the Rattus norvegicus lysosomal and plasma membranes, was analyzed. In silico analysis showed that potential N-glycosylation sites are much less frequent in tonoplast proteins. Biochemical analysis of Arabidopsis subcellular fractions with the lectin concanavalin A, which recognizes mainly unmodified N-glycans, or with antiserum against Golgi-modified N-glycans confirmed the in silico results and showed that, unlike the plant plasma membrane, the tonoplast is almost or totally devoid of N-glycoproteins with Golgi-modified glycans. Lysosomes share with vacuoles the hydrolytic functions and the position along the secretory pathway; however, our results indicate that their membranes had a divergent evolution. We propose that protection against the luminal hydrolases that are abundant in inner hydrolytic compartments, which seems to have been achieved in many lysosomal membrane proteins by extensive N-glycosylation of the luminal domains, has instead been obtained in the vast majority of tonoplast proteins by limiting the length of such domains.

Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings

The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were subsequently characterized by tandem mass spectroscopy. This combined high-quality plasma membrane isolation technique produced a reproducible proteomic library of over 1000 proteins with an extended dynamic range including plasma membrane-associated proteins. The approach enabled the detection of a number of putative plasma membrane proteins not previously identified by other studies, including peripheral membrane proteins. Utilizing multiple data sources, we developed a PM-confidence score to provide a value indicating association to the plasma membrane. This study highlights over 700 proteins that, while seemingly abundant at the plasma membrane, are mostly unstudied. To validate this data set, we selected 14 candidates and transiently localized 13 to the plasma membrane using a fluorescent tag. Given the importance of the plasma membrane, this data set provides a valuable tool to further investigate important proteins. The mass spectrometry data are available via ProteomeXchange, identifier PXD001795.

Overexpression of a Barley Aquaporin Gene, HvPIP2;5 Confers Salt and Osmotic Stress Tolerance in Yeast and Plants

We characterized an aquaporin gene HvPIP2;5 from Hordeum vulgare and investigated its physiological roles in heterologous expression systems, yeast and Arabidopsis, under high salt and high osmotic stress conditions. In yeast, the expression of HvPIP2;5 enhanced abiotic stress tolerance under high salt and high osmotic conditions. Arabidopsis plants overexpressing HvPIP2;5 also showed better stress tolerance in germination and root growth under high salt and high osmotic stresses than the wild type (WT). HvPIP2;5 overexpressing plants were able to survive and recover after a 3-week drought period unlike the control plants which wilted and died during stress treatment. Indeed, overexpression of HvPIP2;5 caused higher retention of chlorophylls and water under salt and osmotic stresses than did control. We also observed lower accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), an end-product of lipid peroxidation in HvPIP2;5 overexpressing plants than in WT. These results suggest that HvPIP2;5 overexpression brought about stress tolerance, at least in part, by reducing the secondary oxidative stress caused by salt and osmotic stresses. Consistent with these stress tolerant phenotypes, HvPIP2;5 overexpressing Arabidopsis lines showed higher expression and activities of ROS scavenging enzymes such as catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) under salt and osmotic stresses than did WT. In addition, the proline biosynthesis genes, Δ ¹-Pyrroline-5-Carboxylate Synthase 1 and 2 (P5CS1 and P5CS2) were up-regulated in HvPIP2;5 overexpressing plants under salt and osmotic stresses, which coincided with increased levels of the osmoprotectant proline. Together, these results suggested that HvPIP2;5 overexpression enhanced stress tolerance to high salt and high osmotic stresses by increasing activities and/or expression of ROS scavenging enzymes and osmoprotectant biosynthetic genes.

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research.

Aquaporins in Plants

Aquaporins are membrane channels that facilitate the transport of water and small neutral molecules across biological membranes of most living organisms. In plants, aquaporins occur as multiple isoforms reflecting a high diversity of cellular localizations, transport selectivity, and regulation properties. Plant aquaporins are localized in the plasma membrane, endoplasmic reticulum, vacuoles, plastids and, in some species, in membrane compartments interacting with symbiotic organisms. Plant aquaporins can transport various physiological substrates in addition to water. Of particular relevance for plants is the transport of dissolved gases such as carbon dioxide and ammonia or metalloids such as boron and silicon. Structure-function studies are developed to address the molecular and cellular mechanisms of plant aquaporin gating and subcellular trafficking. Phosphorylation plays a central role in these two processes. These mechanisms allow aquaporin regulation in response to signaling intermediates such as cytosolic pH and calcium, and reactive oxygen species. Combined genetic and physiological approaches are now integrating this knowledge, showing that aquaporins play key roles in hydraulic regulation in roots and leaves, during drought but also in response to stimuli as diverse as flooding, nutrient availability, temperature, or light. A general hydraulic control of plant tissue expansion by aquaporins is emerging, and their role in key developmental processes (seed germination, emergence of lateral roots) has been established. Plants with genetically altered aquaporin functions are now tested for their ability to improve plant tolerance to stresses. In conclusion, research on aquaporins delineates ever expanding fields in plant integrative biology thereby establishing their crucial role in plants.

The calcium-dependent protein kinase CPK7 acts on root hydraulic conductivity

The hydraulic conductivity of plant roots (Lp(r)) is determined in large part by the activity of aquaporins. Mechanisms occurring at the post-translational level, in particular phosphorylation of aquaporins of the plasma membrane intrinsic protein 2 (PIP2) subfamily, are thought to be of critical importance for regulating root water transport. However, knowledge of protein kinases and phosphatases acting on aquaporin function is still scarce. In the present work, we investigated the Lp(r) of knockout Arabidopsis plants for four Ca(2+)-dependent protein kinases. cpk7 plants showed a 30% increase in Lp(r) because of a higher aquaporin activity. A quantitative proteomic analysis of wild-type and cpk7 plants revealed that PIP gene expression and PIP protein quantity were not correlated and that CPK7 has no effect on PIP2 phosphorylation. In contrast, CPK7 exerts a negative control on the cellular abundance of PIP1s, which likely accounts for the higher Lp(r) of cpk7. In addition, this study revealed that the cellular amount of a few additional proteins including membrane transporters is controlled by CPK7. The overall work provides evidence for CPK7-dependent stability of specific membrane proteins.

Subcellular Redistribution of Root Aquaporins Induced by Hydrogen Peroxide

Aquaporins are water channel proteins that mediate the fine-tuning of cell membrane water permeability during development or in response to environmental stresses. The present work focuses on the oxidative stress-induced redistribution of plasma membrane intrinsic protein (PIP) aquaporins from the plasma membrane (PM) to intracellular membranes. This process was investigated in the Arabidopsis root. Sucrose density gradient centrifugation showed that exposure of roots to 0.5 mM H2O2 induces significant depletion in PM fractions of several abundant PIP homologs after 15 min. Analyses by single-particle tracking and fluorescence correlative spectroscopy showed that, in the PM of epidermal cells, H2O2 treatment induces an increase in lateral motion and a reduction in the density of a fluorescently tagged form of the prototypal AtPIP2;1 isoform, respectively. Co-expression analyses of AtPIP2;1 with endomembrane markers revealed that H2O2 triggers AtPIP2;1 accumulation in the late endosomal compartments. Life-time analyses established that the high stability of PIPs was maintained under oxidative stress conditions, suggesting that H2O2 triggers a mechanism for intracellular sequestration of PM aquaporins without further degradation. In addition to information on cellular regulation of aquaporins, this study provides novel and complementary insights into the dynamic remodeling of plant internal membranes during oxidative stress responses.

Aquaporins Contribute to ABA-Triggered Stomatal Closure through OST1-Mediated Phosphorylation

Stomatal movements in response to environmental stimuli critically control the plant water status. Although these movements are governed by osmotically driven changes in guard cell volume, the role of membrane water channels (aquaporins) has remained hypothetical. Assays in epidermal peels showed that knockout Arabidopsis thaliana plants lacking the Plasma membrane Intrinsic Protein 2;1 (PIP2;1) aquaporin have a defect in stomatal closure, specifically in response to abscisic acid (ABA). ABA induced a 2-fold increase in osmotic water permeability (Pf) of guard cell protoplasts and an accumulation of reactive oxygen species in guard cells, which were both abrogated in pip2;1 plants. Open stomata 1 (OST1)/Snf1-related protein kinase 2.6 (SnRK2.6), a protein kinase involved in guard cell ABA signaling, was able to phosphorylate a cytosolic PIP2;1 peptide at Ser-121. OST1 enhanced PIP2;1 water transport activity when coexpressed in Xenopus laevis oocytes. Upon expression in pip2;1 plants, a phosphomimetic form (Ser121Asp) but not a phosphodeficient form (Ser121Ala) of PIP2;1 constitutively enhanced the Pf of guard cell protoplasts while suppressing its ABA-dependent activation and was able to restore ABA-dependent stomatal closure in pip2;1. This work supports a model whereby ABA-triggered stomatal closure requires an increase in guard cell permeability to water and possibly hydrogen peroxide, through OST1-dependent phosphorylation of PIP2;1 at Ser-121.

Specific membrane lipid composition is important for plasmodesmata function in Arabidopsis

Plasmodesmata (PD) are nano-sized membrane-lined channels controlling intercellular communication in plants. Although progress has been made in identifying PD proteins, the role played by major membrane constituents, such as the lipids, in defining specialized membrane domains in PD remains unknown. Through a rigorous isolation of "native" PD membrane fractions and comparative mass spectrometry-based analysis, we demonstrate that lipids are laterally segregated along the plasma membrane (PM) at the PD cell-to-cell junction in Arabidopsis thaliana. Remarkably, our results show that PD membranes display enrichment in sterols and sphingolipids with very long chain saturated fatty acids when compared with the bulk of the PM. Intriguingly, this lipid profile is reminiscent of detergent-insoluble membrane microdomains, although our approach is valuably detergent-free. Modulation of the overall sterol composition of young dividing cells reversibly impaired the PD localization of the glycosylphosphatidylinositol-anchored proteins Plasmodesmata Callose Binding 1 and the β-1,3-glucanase PdBG2 and altered callose-mediated PD permeability. Altogether, this study not only provides a comprehensive analysis of the lipid constituents of PD but also identifies a role for sterols in modulating cell-to-cell connectivity, possibly by establishing and maintaining the positional specificity of callose-modifying glycosylphosphatidylinositol proteins at PD. Our work emphasizes the importance of lipids in defining PD membranes.

Intrinsic stability of Brassicaceae plasma membrane in relation to changes in proteins and lipids as a response to salinity

Changes in plasma membrane lipids, such as sterols and fatty acids, have been observed as a result of salt stress. These alterations, together with modification of the plasma membrane protein profile, confer changes in the physical properties of the membrane to be taken into account for biotechnological uses. In our experiments, the relationship between lipids and proteins in three different Brassicaceae species differing in salinity tolerance (Brassica oleracea, B. napus and Cakile maritima) and the final plasma membrane stability were studied. The observed changes in the sterol (mainly an increase in sitosterol) and fatty acid composition (increase in RUFA) in each species led to physical adaptation of the plasma membrane to salt stress. The in vitro vesicles stability was higher in the less tolerant (B. oleracea) plants together with low lipoxygenase activity. These results indicate that the proteins/lipids ratio and lipid composition is an important aspect to take into account for the use of natural vesicles in plant biotechnology.

Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway?

MAIN CONCLUSION

Enhancing the membrane content of PtdInsP 2 , the already-recognized protein-regulating lipid, increased the osmotic water permeability of tobacco protoplasts, apparently by increasing the abundance of active aquaporins in their membranes. While phosphoinositides are implicated in cell volume changes and are known to regulate some ion channels, their modulation of aquaporins activity has not yet been reported for any organism. To examine this, we compared the osmotic water permeability (P f) of protoplasts isolated from tobacco (Nicotiana tabacum) cultured cells (NT1) with different (genetically lowered or elevated relative to controls) levels of inositol trisphosphate (InsP3) and phosphatidyl inositol [4,5] bisphosphate (PtdInsP2). To achieve this, the cells were transformed with, respectively, the human InsP3 5-phosphatase ('Ptase cells') or human phosphatidylinositol (4) phosphate 5-kinase ('PIPK cells'). The mean P f of the PIPK cells was several-fold higher relative to that of controls and Ptase cells. Three results favor aquaporins over the membrane matrix as underlying this excessive P f: (1) transient expression of the maize aquaporin ZmPIP2;4 in the PIPK cells increased P f by 12-30 μm s(-1), while in the controls only by 3-4 μm s(-1). (2) Cytosol acidification-known to inhibit aquaporins-lowered the P f in the PIPK cells down to control levels. (3) The transcript of at least one aquaporin was elevated in the PIPK cells. Together, the three results demonstrate the differences between the PIPK cells and their controls, and suggest a hitherto unobserved regulation of aquaporins by phosphoinositides, which could occur through direct interaction or indirect phosphoinositides-dependent cellular effects.

Membrane nanodomains in plants: capturing form, function, and movement

The plasma membrane is the interface between the cell and the external environment. Plasma membrane lipids provide scaffolds for proteins and protein complexes that are involved in cell to cell communication, signal transduction, immune responses, and transport of small molecules. In animals, fungi, and plants, a substantial subset of these plasma membrane proteins function within ordered sterol- and sphingolipid-rich nanodomains. High-resolution microscopy, lipid dyes, pharmacological inhibitors of lipid biosynthesis, and lipid biosynthetic mutants have been employed to examine the relationship between the lipid environment and protein activity in plants. They have also been used to identify proteins associated with nanodomains and the pathways by which nanodomain-associated proteins are trafficked to their plasma membrane destinations. These studies suggest that plant membrane nanodomains function in a context-specific manner, analogous to similar structures in animals and fungi. In addition to the highly conserved flotillin and remorin markers, some members of the B and G subclasses of ATP binding cassette transporters have emerged as functional markers for plant nanodomains. Further, the glycophosphatidylinositol-anchored fasciclin-like arabinogalactan proteins, that are often associated with detergent-resistant membranes, appear also to have a functional role in membrane nanodomains.

AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip

Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3(-)) and phosphate (PO4(3-)) are also signalling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signalling pathways are integrated. Here we report the identification of a highly NO3(-)-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory elements. We demonstrate that this transcription factor and a close homologue repress the primary root growth in response to P deficiency conditions, but only when NO3(-) is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3(-) and P signalling converge via double transcriptional and post-transcriptional control of the same protein, HRS1.

AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip

Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO₃⁻) and phosphate (PO₄³⁻) are also signaling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signaling pathways are integrated. Here we report the identification of a highly NO₃⁻-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory-elements. We demonstrate that this transcription factor and a close homolog repress primary root growth in response to P deficiency conditions, but only when NO₃⁻ is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO₃⁻ and P signaling converge via double transcriptional and post-transcriptional control of the same protein, HRS1

The role of plasma membrane aquaporins in regulating the bundle sheath-mesophyll continuum and leaf hydraulics

Our understanding of the cellular role of aquaporins (AQPs) in the regulation of whole-plant hydraulics, in general, and extravascular, radial hydraulic conductance in leaves (K(leaf)), in particular, is still fairly limited. We hypothesized that the AQPs of the vascular bundle sheath (BS) cells regulate K(leaf). To examine this hypothesis, AQP genes were silenced using artificial microRNAs that were expressed constitutively or specifically targeted to the BS. MicroRNA sequences were designed to target all five AQP genes from the PLASMA MEMBRANE-INTRINSIC PROTEIN1 (PIP1) subfamily. Our results show that the constitutively silenced PIP1 (35S promoter) plants had decreased PIP1 transcript and protein levels and decreased mesophyll and BS osmotic water permeability (P(f)), mesophyll conductance of CO2, photosynthesis, K(leaf), transpiration, and shoot biomass. Plants in which the PIP1 subfamily was silenced only in the BS (SCARECROW:microRNA plants) exhibited decreased mesophyll and BS Pf and decreased K(leaf) but no decreases in the rest of the parameters listed above, with the net result of increased shoot biomass. We excluded the possibility of SCARECROW promoter activity in the mesophyll. Hence, the fact that SCARECROW:microRNA mesophyll exhibited reduced P(f), but not reduced mesophyll conductance of CO2, suggests that the BS-mesophyll hydraulic continuum acts as a feed-forward control signal. The role of AQPs in the hierarchy of the hydraulic signal pathway controlling leaf water status under normal and limited-water conditions is discussed.

Aquaporins: highly regulated channels controlling plant water relations

Plant growth and development are dependent on tight regulation of water movement. Water diffusion across cell membranes is facilitated by aquaporins that provide plants with the means to rapidly and reversibly modify water permeability. This is done by changing aquaporin density and activity in the membrane, including posttranslational modifications and protein interaction that act on their trafficking and gating. At the whole organ level aquaporins modify water conductance and gradients at key "gatekeeper" cell layers that impact on whole plant water flow and plant water potential. In this way they may act in concert with stomatal regulation to determine the degree of isohydry/anisohydry. Molecular, physiological, and biophysical approaches have demonstrated that variations in root and leaf hydraulic conductivity can be accounted for by aquaporins but this must be integrated with anatomical considerations. This Update integrates these data and emphasizes the central role played by aquaporins in regulating plant water relations.

Expression of AQP3 and 8 in loperamide induced constipation in rats

AIM: To observe the differential expression of AQP3 and 8 in loperamide induced constipation in rats, and to explore the role of these two proteins in constipation.

METHODS: Thirty male SD rats were randomly divided into five groups. One group was killed at the beginning to measure intestinal transit function and the expression of AQP3 and 8 in human colonic epithelial cells as basic references. Loperamide [1.5 mg/(kg•d)] was given by intragastric administration in the remaining four groups of rats to induce constipation. Two groups of rats were killed on days 3 and 7 after initial loperamide administration, respectively, while the other two groups were killed 3 and 7 d after last loperamide administration, respectively. Intestinal transmission function was determined, and the expression of AQP3 and 8 was detected.

RESULTS: Intestinal transit function kept stable (67.72% vs 58.64%, P > 0.05) throughout the experimental process, while fecal water content decreased. The fecal water content could not return to normal 7 d after stopping loperamide (2.29 g ± 1.17 g vs 0.80 g ± 0.27 g, P = 0.01). AQP8 expression in the proximal colon had an upward trend 3 to 7 d after the initial loperamide administration, greatly higher than that in the normal control group (P = 0.00). Seven days after stopping loperamide, AQP8 had a rising trend in both the proximal and distal colons (0.43 ± 0.31 vs 2.66 ± 0.87, P = 0.008), while AQP3 expression declined (6.37 ± 0.23 vs 0.79 ± 0.13, P = 0.015).

CONCLUSION: Loperamide enhances the expression of AQP8 in the intestine of rats, which facilitates water movement across the membrane. Deficient water absorption may play a role in the pathogenesis of loperamide induced constipation.

Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation

Background

The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology.

Results

We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process.

Conclusion

This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab.

Plant aquaporins: roles in plant physiology

BACKGROUND

Aquaporins are membrane channels that facilitate the transport of water and small neutral molecules across biological membranes of most living organisms.

SCOPE OF REVIEW

Here, we present comprehensive insights made on plant aquaporins in recent years, pointing to their molecular and physiological specificities with respect to animal or microbial counterparts.

MAJOR CONCLUSIONS

In plants, aquaporins occur as multiple isoforms reflecting a high diversity of cellular localizations and various physiological substrates in addition to water. Of particular relevance for plants is the transport by aquaporins of dissolved gases such as carbon dioxide or metalloids such as boric or silicic acid. The mechanisms that determine the gating and subcellular localization of plant aquaporins are extensively studied. They allow aquaporin regulation in response to multiple environmental and hormonal stimuli. Thus, aquaporins play key roles in hydraulic regulation and nutrient transport in roots and leaves. They contribute to several plant growth and developmental processes such as seed germination or emergence of lateral roots.

GENERAL SIGNIFICANCE

Plants with genetically altered aquaporin functions are now tested for their ability to improve plant resistance to stresses. This article is part of a Special Issue entitled Aquaporins.

Proteomics in deciphering the auxin commitment in the Arabidopsis thaliana root growth

The development of plant root systems is characterized by a high plasticity, made possible by the continual propagation of new meristems. Root architecture is fundamental for overall plant growth, abiotic stress resistance, nutrient uptake, and response to environmental changes. Understanding the function of genes and proteins that control root architecture and stress resistance will contribute to the development of more sustainable systems of intensified crop production. To meet these challenges, proteomics provide the genome-wide scale characterization of protein expression pattern, subcellular localization, post-translational modifications, activity regulation, and molecular interactions. In this review, we describe a variety of proteomic strategies that have been applied to study the proteome of the whole organ and of specific cell types during root development. Each has advantages and limitations, but collectively they are providing important insights into the mechanisms by which auxin structures and patterns the root system and into the interplay between signaling networks, auxin transport and growth. The acquisition of proteomic, transcriptomic, and metabolomic data sets of the root apex on the cell scale has revealed the high spatial complexity of regulatory networks and fosters the use of new powerful proteomic tools for a full understanding of the control of root developmental processes and environmental responses.

Coordinated post-translational responses of aquaporins to abiotic and nutritional stimuli in Arabidopsis roots

In plants, aquaporins play a crucial role in regulating root water transport in response to environmental and physiological cues. Controls achieved at the post-translational level are thought to be of critical importance for regulating aquaporin function. To investigate the general molecular mechanisms involved, we performed, using the model species Arabidopsis, a comprehensive proteomic analysis of root aquaporins in a large set of physiological contexts. We identified nine physiological treatments that modulate root hydraulics in time frames of minutes (NO and H2O2 treatments), hours (mannitol and NaCl treatments, exposure to darkness and reversal with sucrose, phosphate supply to phosphate-starved roots), or days (phosphate or nitrogen starvation). All treatments induced inhibition of root water transport except for sucrose supply to dark-grown plants and phosphate resupply to phosphate-starved plants, which had opposing effects. Using a robust label-free quantitative proteomic methodology, we identified 12 of 13 plasma membrane intrinsic protein (PIP) aquaporin isoforms, 4 of the 10 tonoplast intrinsic protein isoforms, and a diversity of post-translational modifications including phosphorylation, methylation, deamidation, and acetylation. A total of 55 aquaporin peptides displayed significant changes after treatments and enabled the identification of specific and as yet unknown patterns of response to stimuli. The data show that the regulation of PIP and tonoplast intrinsic protein abundance was involved in response to a few treatments (i.e. NaCl, NO, and nitrate starvation), whereas changes in the phosphorylation status of PIP aquaporins were positively correlated to changes in root hydraulic conductivity in the whole set of treatments. The identification of in vivo deamidated forms of aquaporins and their stimulus-induced changes in abundance may reflect a new mechanism of aquaporin regulation. The overall work provides deep insights into the in vivo post-translational events triggered by environmental constraints and their possible role in regulating plant water status.

Relative abundance of integral plasma membrane proteins in Arabidopsis leaf and root tissue determined by metabolic labeling and mass spectrometry

Metabolic labeling of proteins with a stable isotope (¹⁵N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome.

Two aquaporins of Jatropha are regulated differentially during drought stress and subsequent recovery

Jatropha has potential to be an important bio-fuel crop due to such advantages as high seed oil content and the ability to grow well on marginal lands less suited for food crops. Despite its ability to grow on marginal land, Jatropha is still susceptible to high salt and drought stresses, which can significantly reduce plant growth, stomatal conductance, sap-flow rate, and plant sap volume. This study was undertaken to collect basic knowledge of the physiological and molecular aspects of Jatropha response to salt and drought stresses, and to elucidate how Jatropha recovers from stress. From these studies we identified candidate genes that may be useful for the development of Jatropha cultivars that will grow efficiently in arid and barren lands. Of particular interest, two plasma membrane intrinsic proteins were identified: Jatropha plasma membrane intrinsic protein 1 (JcPIP1) and Jatropha plasma membrane intrinsic protein 2 (JcPIP2). The expression levels of JcPIP1 were dramatically increased in roots, stems, and leaves during the recovery from stress, whereas the JcPIP2 gene transcripts levels were induced in roots and stems during the water deficit stress. The protein levels of JcPIP1 and JcPIP2 were consistent with the gene expression patterns. Based on these results, we hypothesized that JcPIP1 plays a role in the recovery events from water stresses, while JcPIP2 is important in early responses to water stress. Virus induced gene silencing technology revealed that both JcPIP1 and JcPIP2 have positive roles in response to water deficit stresses, but have antagonistic functions at the recovery stage. We suggest that both JcPIP1 and JcPIP2 may play important roles in responses to water deficit conditions and both have potential as targets for genetic engineering.

Bimolecular fluorescence complementation and interaction of various Arabidopsis major intrinsic proteins expressed in yeast

Tonoplast intrinsic proteins (TIPs) and plasma membrane intrinsic proteins (PIPs) form subgroups of plant major intrinsic proteins (MIPs) that channel water as well as various small neutral molecules across the tonoplast and plasma membrane. Most MIPs are believed to form homotetramers, while some plant PIPs have been shown to form heterotetramers composed of different isoforms. This study investigated in vivo molecular interactions between different Arabidopsis TIP isoforms and between TIPs and a PIP member. The interactions were assayed by bimolecular fluorescence complementation optimized for use in Saccharomyces cerevisiae as a heterologous expression system. Fluorescence of re-assembled Venus yellow fluorescent protein was monitored by fluorescence microscopy and flow cytometry. The results showed strong interactions between TIP1;2, TIP2;1 and TIP3;1. Surprisingly, the three TIP isoforms also interacted with PIP2;1. The potassium channel AKT1 was used as a negative control and exhibited no interaction with any of the MIPs. The observed interactions may play a role in targeting and regulation of MIPs in plants.

Advancements in the analysis of the Arabidopsis plasma membrane proteome

The plasma membrane (PM) regulates diverse processes essential to plant growth, development, and survival in an ever-changing environment. In addition to maintaining normal cellular homeostasis and plant nutrient status, PM proteins perceive and respond to a myriad of environmental cues. Here we review recent advances in the analysis of the plant PM proteome with a focus on the model plant Arabidopsis thaliana. Due to membrane heterogeneity, hydrophobicity, and low relative abundance, analysis of the PM proteome has been a special challenge. Various experimental techniques to enrich PM proteins and different protein and peptide separation strategies have facilitated the identification of thousands of integral and membrane-associated proteins. Numerous classes of proteins are present at the PM with diverse biological functions. PM microdomains have attracted much attention. However, it still remains a challenge to characterize these cell membrane compartments. Dynamic changes in the PM proteome in response to different biotic and abiotic stimuli are highlighted. Future prospects for PM proteomics research are also discussed.

Genome and transcriptome analyses provide insight into the euryhaline adaptation mechanism of Crassostrea gigas

Background

The Pacific oyster, Crassostrea gigas, has developed special mechanisms to regulate its osmotic balance to adapt to fluctuations of salinities in coastal zones. To understand the oyster’s euryhaline adaptation, we analyzed salt stress effectors metabolism pathways under different salinities (salt 5, 10, 15, 20, 25, 30 and 40 for 7 days) using transcriptome data, physiology experiment and quantitative real-time PCR.

Results

Transcriptome data uncovered 189, 480, 207 and 80 marker genes for monitoring physiology status of oysters and the environment conditions. Three known salt stress effectors (involving ion channels, aquaporins and free amino acids) were examined. The analysis of ion channels and aquaporins indicated that 7 days long-term salt stress inhibited voltage-gated Na⁺/K⁺ channel and aquaporin but increased calcium-activated K⁺ channel and Ca²⁺ channel. As the most important category of osmotic stress effector, we analyzed the oyster FAAs metabolism pathways (including taurine, glycine, alanine, beta-alanine, proline and arginine) and explained FAAs functional mechanism for oyster low salinity adaptation. FAAs metabolism key enzyme genes displayed expression differentiation in low salinity adapted individuals comparing with control which further indicated that FAAs played important roles for oyster salinity adaptation. A global metabolic pathway analysis (iPath) of oyster expanded genes displayed a co-expansion of FAAs metabolism in C. gigas compared with seven other species, suggesting oyster’s powerful ability regarding FAAs metabolism, allowing it to adapt to fluctuating salinities, which may be one important mechanism underlying euryhaline adaption in oyster. Additionally, using transcriptome data analysis, we uncovered salt stress transduction networks in C. gigas.

Conclusions

Our results represented oyster salt stress effectors functional mechanisms under salt stress conditions and explained the expansion of FAAs metabolism pathways as the most important effectors for oyster euryhaline adaptation. This study was the first to explain oyster euryhaline adaptation at a genome-wide scale in C. gigas.

Regulation of Arabidopsis leaf hydraulics involves light-dependent phosphorylation of aquaporins in veins

The water status of plant leaves depends on the efficiency of the water supply, from the vasculature to inner tissues. This process is under hormonal and environmental regulation and involves aquaporin water channels. In Arabidopsis thaliana, the rosette hydraulic conductivity (Kros) is higher in darkness than it is during the day. Knockout plants showed that three plasma membrane intrinsic proteins (PIPs) sharing expression in veins (PIP1;2, PIP2;1, and PIP2;6) contribute to rosette water transport, and PIP2;1 can fully account for Kros responsiveness to darkness. Directed expression of PIP2;1 in veins of a pip2;1 mutant was sufficient to restore Kros. In addition, a positive correlation, in both wild-type and PIP2;1-overexpressing plants, was found between Kros and the osmotic water permeability of protoplasts from the veins but not from the mesophyll. Thus, living cells in veins form a major hydraulic resistance in leaves. Quantitative proteomic analyses showed that light-dependent regulation of Kros is linked to diphosphorylation of PIP2;1 at Ser-280 and Ser-283. Expression in pip2;1 of phosphomimetic and phosphorylation-deficient forms of PIP2;1 demonstrated that phosphorylation at these two sites is necessary for Kros enhancement under darkness. These findings establish how regulation of a single aquaporin isoform in leaf veins critically determines leaf hydraulics.