Analysis of Root Plasma Membrane Aquaporins from Brassica oleracea: Post-Translational Modifications, de novo Sequencing and Detection of Isoforms by High Resolution Mass Spectrometry

Deciphering the effect of salinity and boron stress on broccoli plants reveals that membranes phytosterols and PIP aquaporins facilitate stress adaptation

Abiotic stresses, such as salinity and boron toxicity/deficiency, are prevalent in arid and semi-arid regions where broccoli is largely cultivated. This study aimed to investigate the physiological response of broccoli leaves to these stresses, focusing on parameters such as growth, relative water content, stomatal conductance, and mineral concentration after 15 days of treatment application. The effects of individual and combined stresses of salinity and boron (deficiency and toxicity) were examined. Additionally, the study explored the molecular aspects of PIP aquaporins in relation to their presence in the plasma membrane and their interaction with the lipid environment. The results showed that the combined stress of salinity and boron deficiency resulted in a significant reduction in plant biomass, suggesting a specific adaptation to this stress combination. Changes in stomatal conductance and mineral nutrient levels indicated that the adaptation mechanisms were associated with water and boron concentration in the leaves. The expression patterns of PIP aquaporins varied among the different stress treatments, either individually or in combination. Furthermore, the presence of aquaporins in the plasma membrane and microsomal fraction highlighted the potential regulatory roles of trafficking along with the membrane composition, particularly the concentration of phytosterols. The results underscore the importance of water transport by aquaporins and their interaction with the sterol composition in the membranes, in facilitating salinity-boron stress adaptation mechanisms.

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.

Plasma membrane vesicles from cauliflower meristematic tissue and their role in water passage

BACKGROUND

Cauliflower (Brassica oleracea L. var. botrytis) inflorescences are composed mainly of meristematic tissue, which has a high cellular proliferation. This considerable cellular density makes the inflorescence an organ with a large proportion of membranes. However, little is known about the specific role of the lipid and protein composition of the plasma membrane present in this organ.

RESULTS

In this work, we analyzed the lipids and proteins present in plasma membrane from two different stages of development of cauliflower inflorescence and compared them with leaf plasma membrane. For this purpose, plasma membrane vesicles were obtained by centrifugation for each sample and the vesicular diameter and osmotic permeability (Pf) were analyzed by dynamic light scattering and the stopped-flow technique, respectively. In addition, fatty acids and sterols were analyzed by gas chromatography and HPLC. The protein composition of the inflorescences and leaves was characterized by HPLC-ESI-QTOF-MS and the data obtained were compared with Brassicaceae proteins present in the UniProt database in relation to the presence of aquaporins determined by western blot analysis. The highest Pf value was found in 90 day inflorescences-derived plasma membrane vesicles (61.4 ± 4.14 μms- 1). For sterols and fatty acids, the concentrations varied according to the organ of origin. The protein profile revealed the presence of aquaporins from the PIP1 and PIP2 subfamilies in both inflorescences and leaves.

CONCLUSION

This study shows that the composition of the sterols, the degree of unsaturation of the fatty acids, and the proteins present in the membranes analyzed give them high functionality for water passage. This represents an important addition to the limited information available in this field.

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.

Phosphoproteomic and Metabolomic Analyses Reveal Sexually Differential Regulatory Mechanisms in Poplar to Nitrogen Deficiency

Nitrogen (N) is a key factor impacting physiological processes in plants. Many proteins have been investigated in male and female poplars under N limitation. However, little is known about sex differences in the protein modifications and metabolites that occur in poplar leaves in response to N deficiency. In this study, as compared to N-deficient males, N-deficient females suffered greater damage from N deficiency, including chloroplast disorganization and lipid peroxidation of cellular membranes. Male poplars had greater osmotic adjustment ability than did females, allowing greater accumulation of soluble metabolites. In addition, as compared to that in N-deficient males, glycolysis was less suppressed in N-deficient females for increased enzyme activities to consume excess energy. Moreover, we found that pronounced protein phosphorylation occurred during carbon metabolism and substance transport processes in both sexes of poplar under N-limiting conditions. Sex-specific metabolites mainly included intermediates in glycolysis, amino acids, and phenylpropanoid-derived metabolites. This study provides new molecular evidence that female poplars suffer greater negative effects from N deficiency than do male poplars.

Plant plasma membrane vesicles interaction with keratinocytes reveals their potential as carriers

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Broccoli root vesicles showed stability and high entrapment efficiency.

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Nanoencapsulation with membrane vesicles provide an efficient system for keratinocytes cell delivery.

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Effectivity is probed by penetrating in skin layers.

During the last few years, membrane vesicles (as exovesicles) have emerged as potential nanocarriers for therapeutic applications. They are receiving attention due to their proteo-lipid nature, size, biocompatibility and biodegradability. In this work, we investigated the potential use of isolated root plasma membrane vesicles from broccoli plants as nanocarriers. For that, the entrapment efficiency and integrity of the vesicles were determined. Also, the delivery of keratinocytes and penetrability through skin were studied. The results show that the broccoli vesicles had high stability, in relation to their proteins, and high entrapment efficiency. Also, the interaction between the vesicles and keratinocytes was proven by the delivery of an encapsulated fluorescent product into cells and by the detection of plant proteins in the keratinocyte plasma membrane, showing the interactions between the membranes of two species of distinct biological kingdoms. Therefore, these results, together with the capacity of brassica vesicles to cross the skin layers, detected by fluorescent penetration, enable us to propose a type of nanocarrier obtained from natural plant membranes for use in transdermal delivery.

An outlook on lysine methylation of non-histone proteins in plants

Protein methylation is a very diverse, widespread, and important post-translational modification affecting all aspects of cellular biology in eukaryotes. Methylation on the side-chain of lysine residues in histones has received considerable attention due to its major role in determining chromatin structure and the epigenetic regulation of gene expression. Over the last 20 years, lysine methylation of non-histone proteins has been recognized as a very common modification that contributes to the fine-tuned regulation of protein function. In plants, our knowledge in this field is much more fragmentary than in yeast and animal cells. In this review, we describe the plant enzymes involved in the methylation of non-histone substrates, and we consider historical and recent advances in the identification of non-histone lysine-methylated proteins in photosynthetic organisms. Finally, we discuss our current knowledge about the role of protein lysine methylation in regulating molecular and cellular functions in plants, and consider challenges for future research.

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.

Plant and animal aquaporins crosstalk: what can be revealed from distinct perspectives

Aquaporins (AQPs) can be revisited from a distinct and complementary perspective: the outcome from analyzing them from both plant and animal studies. (1) The approach in the study. Diversity found in both kingdoms contrasts with the limited number of crystal structures determined within each group. While the structure of almost half of mammal AQPs was resolved, only a few were resolved in plants. Strikingly, the animal structures resolved are mainly derived from the AQP2-lineage, due to their important roles in water homeostasis regulation in humans. The difference could be attributed to the approach: relevance in animal research is emphasized on pathology and in consequence drug screening that can lead to potential inhibitors, enhancers and/or regulators. By contrast, studies on plants have been mainly focused on the physiological role that AQPs play in growth, development and stress tolerance. (2) The transport capacity. Besides the well-described AQPs with high water transport capacity, large amount of evidence confirms that certain plant AQPs can carry a large list of small solutes. So far, animal AQP list is more restricted. In both kingdoms, there is a great amount of evidence on gas transport, although there is still an unsolved controversy around gas translocation as well as the role of the central pore of the tetramer. (3) More roles than expected. We found it remarkable that the view of AQPs as specific channels has evolved first toward simple transporters to molecules that can experience conformational changes triggered by biochemical and/or mechanical signals, turning them also into signaling components and/or behave as osmosensor molecules.

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.

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.

Involvement of a glucosinolate (sinigrin) in the regulation of water transport in Brassica oleracea grown under salt stress

Members of the Brassicaceae are known for their contents of nutrients and health-promoting phytochemicals, including glucosinolates. The concentrations of these chemopreventive compounds (glucosinolate-degradation products, the bioactive isothiocyanates) may be modified under salinity. In this work, the effect of the aliphatic glucosinolate sinigrin (2-propenyl-glucosinolate) on plant water balance, involving aquaporins, was explored under salt stress. For this purpose, water uptake and its transport through the plasma membrane were determined in plants after NaCl addition, when sinigrin was also supplied. We found higher hydraulic conductance (L0 ) and water permeability (Pf ) and increased abundance of PIP2 aquaporins after the direct administration of sinigrin, showing the ability of the roots to promote cellular water transport across the plasma membrane in spite of the stress conditions imposed. The higher content of the allyl-isothiocyanate and the absence of sinigrin in the plant tissues suggest that the isothiocyanate is related to water balance; in fact, a direct effect of this nitro-sulphate compound on water uptake is proposed. This work provides the first evidence that the addition of a glucosinolate can regulate aquaporins and water transport: this effect and the mechanism(s) involved merit further investigation.

Response of three broccoli cultivars to salt stress, in relation to water status and expression of two leaf aquaporins

The aim of this study was to compare differences in water relations in the leaves of three broccoli cultivars and differential induction of the expression of PIP2 aquaporin isoforms under salt stress. Although broccoli is known to be moderately tolerant to salinity, scarce information exists about the involvement of leaf aquaporins in its adaptation to salinity. Thus, leaf water relations, leaf cell hydraulic conductivity (Lpc), gas exchange parameters and the PIP2 expression pattern were determined for short- (15 h) and long- (15 days) term NaCl treatments. In the long term, the lower half-time of water exchange in the cells of cv. Naxos, compared with Parthenon and Chronos, and its increased PIP2 abundance may have contributed to its Lpc maintenance. This unmodified Lpc in cv. Naxos under prolonged salinity may have diluted NaCl in the leaves, as suggested by lower Na(+) concentrations in the leaf sap. By contrast, the increase in the half-time of water exchange and the lower PIP2 abundance in cvs. Chronos and Parthenon would have contributed to the reduced Lpc values. In cv. Parthenon, there were no differences between the ε values of control and salt-stressed plants; in consequence, cell turgor was enhanced. Also, the increases in BoPIP2;2 and BoPIP2;3 expression in cv. Chronos for the short-term NaCl treatment suggest that these isoforms are involved in osmotic regulation as downstream factors in this cultivar, in fact, in the short-term, Chronos had a significantly reduced osmotic potential and higher PIP2 isoforms expression.

Approaches for the study of cancer: towards the integration of genomics, proteomics and metabolomics

Recent technological advances, combined with the development of bioinformatic tools, allow us to better address biological questions combining -omic approaches (i.e., genomics, metabolomics and proteomics). This novel comprehensive perspective addresses the identification, characterisation and quantitation of the whole repertoire of genes, proteins and metabolites occurring in living organisms. Here we provide an overview of recent significant advances and technologies used in genomics, metabolomics and proteomics. We also underline the importance and limits of mass accuracy in mass spectrometry-based -omics and briefly describe emerging types of fragmentation used in mass spectrometry. The range of instruments and techniques used to address the study of each -omic approach, which provide vast amounts of information (usually termed "high-throughput" technologies in the literature) is briefly discussed, including names, links and descriptions of the main databases, data repositories and resources used. Integration of multiple -omic results and procedures seems necessary. Therefore, an emerging challenge is the integration of the huge amount of data generated and the standardisation of the procedures and methods used. Functional data integration will lead to answers to unsolved questions, hopefully, applicable to clinical practice and management of patients.

Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics

Recent innovations in liquid chromatography-mass spectrometry (LC-MS)-based methods have facilitated quantitative and functional proteomic analyses of large numbers of proteins derived from complex samples without any need for protein or peptide labelling. Regardless of its great potential, the application of these proteomics techniques to plant science started only recently. Here we present an overview of label-free quantitative proteomics features and their employment for analysing plants. Recent methods used for quantitative protein analyses by MS techniques are summarized and major challenges associated with label-free LC-MS-based approaches, including sample preparation, peptide separation, quantification and kinetic studies, are discussed. Database search algorithms and specific aspects regarding protein identification of non-sequenced organisms are also addressed. So far, label-free LC-MS in plant science has been used to establish cellular or subcellular proteome maps, characterize plant-pathogen interactions or stress defence reactions, and for profiling protein patterns during developmental processes. Improvements in both, analytical platforms (separation technology and bioinformatics/statistical analysis) and high throughput nucleotide sequencing technologies will enhance the power of this method.

Dual neofunctionalization of a rapidly evolving aquaporin-1 paralog resulted in constrained and relaxed traits controlling channel function during meiosis resumption in teleosts

The preovulatory hydration of teleost oocytes is a unique process among vertebrates. The hydration mechanism is most pronounced in marine acanthomorph teleosts that spawn pelagic (floating) eggs; however, the molecular pathway for water influx remains poorly understood. Recently, we revealed that whole-genome duplication (WGD) resulted in teleosts harboring the largest repertoire of molecular water channels in the vertebrate lineage and that a duplicated aquaporin-1 paralog is implicated in the oocyte hydration process. However, the origin and function of the aquaporin-1 paralogs remain equivocal. By integrating the molecular phylogeny with synteny and structural analyses, we show here that the teleost aqp1aa and -1ab paralogs (previously annotated as aqp1a and -1b, respectively) arose by tandem duplication rather than WGD and that the Aqp1ab C-terminus is the most rapidly evolving subdomain within the vertebrate aquaporin superfamily. The functional role of Aqp1ab was investigated in Atlantic halibut, a marine acanthomorph teleost that spawns one of the largest pelagic eggs known. We demonstrate that Aqp1ab is required for full hydration of oocytes undergoing meiotic maturation. We further show that the rapid structural divergence of the C-terminal regulatory domain causes ex vivo loss of function of halibut Aqp1ab when expressed in amphibian oocytes but not in zebrafish or native oocytes. However, by using chimeric constructs of halibut Aqp1aa and -1ab and antisera specifically raised against the C-terminus of Aqp1ab, we found that this cytoplasmic domain regulates in vivo trafficking to the microvillar portion of the oocyte plasma membrane when intraoocytic osmotic pressure is at a maximum. Interestingly, by coinjecting polyA(+) mRNA from postvitellogenic halibut follicles, ex vivo intracellular trafficking of Aqp1ab is rescued in amphibian oocytes. These data reveal that the physiological role of Aqp1ab during meiosis resumption is conserved in teleosts, but the remarkable degeneracy of the cytoplasmic domain has resulted in alternative regulation of the trafficking mechanism.

Identification and differential induction of the expression of aquaporins by salinity in broccoli plants

Plant aquaporins belong to a large superfamily of conserved proteins called the major intrinsic proteins (MIPs). There is limited information about the diversity of MIPs and their water transport capacity in broccoli (Brassica oleracea) plants. In this study, the cDNAs of isoforms of Plasma Membrane Intrinsic Proteins (PIPs), a class of aquaporins, from broccoli roots have been partially sequenced. Thus, sequencing experiments led to the identification of eight PIP1 and three PIP2 genes encoding PIPs in B. oleracea plants. The occurrence of different gene products encoding PIPs suggests that they may play different roles in plants. The screening of their expression as well as the expression of two specific PIP2 isoforms (BoPIP2;2 and BoPIP2;3), in different organs and under different salt-stress conditions in two varieties, has helped to unravel the function and the regulation of PIPs in plants. Thus, a high degree of BoPIP2;3 expression in mature leaves suggests that this BoPIP2;3 isoform plays important roles, not only in root water relations but also in the physiology and development of leaves. In addition, differences between gene and protein patterns led us to consider that mRNA synthesis is inhibited by the accumulation of the corresponding encoded protein. Therefore, transcript levels, protein abundance determination and the integrated hydraulic architecture of the roots must be considered in order to interpret the response of broccoli to salinity.