Proteomic analysis of Pteris vittata fronds: two arbuscular mycorrhizal fungi differentially modulate protein expression under arsenic contamination

Proteomics as a tool to decipher plant responses in arbuscular mycorrhizal interactions: a meta-analysis

The beneficial symbiosis between plants and arbuscular mycorrhizal (AM) fungi leads to a deep reprogramming of plant metabolism, involving the regulation of several molecular mechanisms, many of which are poorly characterized. In this regard, proteomics is a powerful tool to explore changes related to plant-microbe interactions. This study provides a comprehensive proteomic meta-analysis conducted on AM-modulated proteins at local (roots) and systemic (shoots/leaves) level. The analysis was implemented by an in-depth study of root membrane-associated proteins and by a comparison with a transcriptome meta-analysis. A total of 4262 differentially abundant proteins were retrieved and, to identify the most relevant AM-regulated processes, a range of bioinformatic studies were conducted, including functional enrichment and protein-protein interaction network analysis. In addition to several protein transporters which are present in higher amounts in AM plants, and which are expected due to the well-known enhancement of AM-induced mineral uptake, our analysis revealed some novel traits. We detected a massive systemic reprogramming of translation with a central role played by the ribosomal translational apparatus. On one hand, these new protein-synthesis efforts well support the root cellular re-organization required by the fungal penetration, and on the other they have a systemic impact on primary metabolism.

The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades

Ferns are a diverse evolutionary lineage, sister to the seed plants, which is of great ecological importance and has a high biotechnological potential. Fern gametophytes represent one of the simplest autotrophic, multicellular plant forms and show several experimental advantages, including a simple and space-efficient in vitro culture system. However, the molecular basis of fern growth and development has hardly been studied. Here, we report on a proteomic study that identified 417 proteins shared by gametophytes of the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. Most proteins are predicted to localize to the cytoplasm, the chloroplast, or the nucleus, and are linked to enzymatic, binding, and structural activities. A subset of 145 proteins are involved in growth, reproduction, phytohormone signaling and biosynthesis, and gene expression, including homologs of SHEPHERD (SHD), HEAT SHOCK PROTEIN 90-5 (CR88), TRP4, BOBBER 1 (BOB1), FLAVONE 3'-O-METHYLTRANSFERASE 1 (OMT1), ZEAXANTHIN EPOXIDASE (ABA1), GLUTAMATE DESCARBOXYLASE 1 (GAD), and dsRNA-BINDING DOMAIN-LIKE SUPERFAMILY PROTEIN (HLY1). Nearly 25% of the annotated proteins are associated with responses to biotic and abiotic stimuli. As for biotic stress, the proteins PROTEIN SGT1 HOMOLOG B (SGT1B), SUPPRESSOR OF SA INSENSITIVE2 (SSI2), PHOSPHOLIPASE D ALPHA 1 (PLDALPHA1), SERINE/THREONINE-PROTEIN KINASE SRK2E (OST1), ACYL CARRIER PROTEIN 4 (ACP4), and NONHOST RESISTANCE TO P. S. PHASEOLICOLA1 (GLPK) are worth mentioning. Regarding abiotic stimuli, we found proteins associated with oxidative stress: SUPEROXIDE DISMUTASE[CU-ZN] 1 (CSD1), and GLUTATHIONE S-TRANSFERASE U19 (GSTU19), light intensity SERINE HYDROXYMETHYLTRANSFERASE 1 (SHM1) and UBIQUITIN-CONJUGATING ENZYME E2 35 (UBC35), salt and heavy metal stress included MITOCHONDRIAL PHOSPHATE CARRIER PROTEIN 3 (PHT3;1), as well as drought and thermotolerance: LEA7, DEAD-BOX ATP-DEPENDENT RNA HELICASE 38 (LOS4), and abundant heat-shock proteins and other chaperones. In addition, we identified interactomes using the STRING platform, revealing protein-protein associations obtained from co-expression, co-occurrence, text mining, homology, databases, and experimental datasets. By focusing on ferns, this proteomic study increases our knowledge on plant development and evolution, and may inspire future applications in crop species.

Arsenic uptake and toxicity in wheat (Triticum aestivum L.): A review of multi-omics approaches to identify tolerance mechanisms

Arsenic (As) due to its widespread has become a primary concern for sustainable food production, especially in Southeast Asian countries. In that context, the present review presented a comprehensive detail of the available literature marking an assortment of As-induced impacts on wheat. The conclusive findings of past research suggest that As tends to grossly affect the germination, elongation, biomass, grain yield, and induce oxidative stress. Several human studies are suggestive of higher cancer risks (>1 × 10^-6) due to the ingestion of wheat grains. However, the body of proof is limited and the scarcity of information limited understanding about tolerance mechanism in wheat against As. Therefore, the paper provided a reference from tolerance mechanism based studies in other crops like rice and maize. The generated knowledge of arsenomics would pave the way for plant breeders to develop resistant varieties for As to ensure sustainable food production.

Phytoremediation of a Highly Arsenic Polluted Site, Using Pteris vittata L. and Arbuscular Mycorrhizal Fungi

Phytoremediation is a promising green technique for the restoration of a polluted environment, but there is often a gap between lab and field experiments. The fern, Pteris vittata L., can tolerate a high soil arsenic concentration and rapidly accumulate the metalloid in its fronds. Arbuscular mycorrhizal fungi (AMF) are mutualistic fungi that form a symbiosis with most land plants' roots, improve their growth, and induce stress tolerance. This paper reports the results obtained using P. vittata inoculated with AMF, to extract Arsenic (As) from an industrial site highly contaminated also by other pollutants. Two experiments have been performed. In the first one, AMF colonized ferns were grown for two years under controlled conditions in soil coming from the metallurgic site. Positive effects on plant health and As phytoextraction and accumulation were detected. Then, considering these results, we performed a three year in situ experiment in the industrial site, to assess the remediation of As at two different depths. Our results show that the colonization of P. vittata with AMF improved the remediation process of As with a significant impact on the depth 0-0.2 m.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.

Effect of arsenic stress on 5-methylcytosine, photosynthetic parameters and nutrient content in arsenic hyperaccumulator Pteris cretica (L.) var. Albo-lineata

BACKGROUND

Arsenic toxicity induces a range of metabolic responses in plants, including DNA methylation. The focus of this paper was on the relationship between As-induced stress and plant senescence in the hyperaccumulator Pteris cretica var. Albo-lineata (Pc-Al). We assume difference in physiological parameters and level of DNA methylation in young and old fronds as symptoms of As toxicity.

RESULTS

The As accumulation of Pc-Al fronds, grown in pots of haplic chernozem contaminated with 100 mg As kg- 1 for 122 days, decreased with age. Content of As was higher in young than old fronds for variants with 100 mg As kg- 1 (2800 and 2000 mg As kg- 1 dry matter, respectively). The highest As content was determined in old fronds of Pc-Al grown in pots with 250 mg As kg- 1. The increase with age was confirmed for determined nutrients - Cu, Mg, Mn, S and Zn. A significant elevation of all analysed nutrients was showed in old fronds. Arsenic accumulation affected DNA methylation status in fronds, but content of 5-methylcytosine (5mC) decreased only in old fronds of Pc-Al (from 25 to 12%). Determined photosynthetic processes showed a decrease of fluorescence, photosynthetic rate and chlorophylls of As treatments in young and old fronds. Water potential was decreased by As in both fronds. Thinning of the sclerenchymatous inner cortex and a reduction in average tracheid metaxylem in the vascular cylinder was showed in roots of As treatment. Irrespective to fronds age, physiological parameters positively correlated with a 5mC while negatively with direct As toxicity. Opposite results were found for contents of Cu, Mg, Mn, S and Zn.

CONCLUSIONS

The results of this paper point to changes in the metabolism of the hyperaccumulator plant Pc-Al, upon low and high exposure to As contamination. The significant impact of As on DNA methylation was found in old fronds. Irrespective to fronds age, significant correlations were confirmed for 5mC and As toxicity. Our analysis of the very low water potential values and lignification of cell walls in roots showed that transports of assimilated metabolites and water between roots and fronds were reduced. As was showed by our results, epigenetic changes could affect studied parameters of the As hyperaccumulator plant Pc-Al, especially in old fronds.

Mycorrhizal frequency, physiological parameters, and yield of strawberry plants inoculated with endomycorrhizal fungi and rhizosphere bacteria

Due to the impoverishment of agricultural and horticultural soils and replant diseases, there is a need to use bioproducts and beneficial microorganisms in order to improve the quality of soils and growth substrates. For this reason, research was undertaken to assess the impact of arbuscular mycorrhizal fungi and rhizosphere bacteria on changes in soil microbiology, the degree of colonization of plant roots by mycorrhizal fungi, selected physiological parameters, and fruit quality and yield of the strawberry cultivar "Rumba." The plants were inoculated with the mycorrhizal preparation Mykoflor (Rhizophagus irregularis, Funneliformis mosseae, Claroideoglomus etunicatum), MYC 800 (Rhizophagus intraradices), and the bacterial preparation Rhizocell C (Bacillus amyloliquefaciens IT45). The applied preparations increased the total number of bacteria and fungi in the soil and mycorrhizal frequency in the roots of the strawberry plants. They increased the chlorophyll "a" and total chlorophyll concentrations in the leaves as well as the rate of transpiration and CO₂ concentration in the intercellular spaces in the leaves. The plants treated with Rhizocell C and MYC 800 exhibited a higher CO₂ assimilation rate than control plants. The biopreparations increased chlorophyll fluorescence parameters such as maximum fluorescence (F_M) and the maximum potential photochemical reaction efficiency in PS II (F_V/F_M). The influence of the species of rhizosphere bacteria and mycorrhizal fungi used in the experiment on the physiological traits of strawberry plants contributed, especially in the second year of the study, to increase the yield and mean weight of strawberry fruit.

Potential use of the Pteris vittata arsenic hyperaccumulation-regulation network for phytoremediation

Arsenic accumulation in soil is a global problem typically addressed using phytoremediation methods. Pteris vittata, a model arsenic hyperaccumulator, has great potential as a genetically engineered plant for phytoremediation. However, the lack of omic information on this species has severely limited the identification and application of its arsenic hyperaccumulation and regulation components. In this study, we used an optimized single-molecular real-time (SMRT) strategy to create a de novo full-length transcriptomic-tonoplast proteomic database for this unsequenced fern and to determine the genetic components underlying its arsenic hyperaccumulation-regulation mechanisms. We established a comprehensive network consisting of six major transporter families, two novel resistance pathways, and a regulatory system by examining alternative splicing (AS) and long non-coding RNA (lncRNA) in different tissues following As(III) and As(V) treatment. The database and network established in this study will deepen our understanding of the unique hyperaccumulation and regulation mechanisms of P. vittata, ultimately providing a valuable resource for futher research on phytoremediation of arsenic-contaminated soil.

Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity

The contamination of soil with toxic metals is a worldwide problem, resulting in the disruption of plant vegetation and subsequent crop production. Thus, remediation techniques for contaminated soil and water remain a constant interest of researchers. Phytoremediation, which utilizes plants to remove or stabilize contaminants, is perceived to be a promising strategy. However, phytoremediation's use to date is limited because of constraints associated with such factors as slow plant growth rates or metal toxicity. Microbial-assisted phytoremediation serves as an alternative solution, since the impact of the microbial symbionts on plant growth and stress tolerance has frequently been described. Endophytic fungi occur in almost every plant in the natural environment and contribute to plant growth and tolerance to environmental stress conditions. Although this group of symbiotic fungi was found to form association with a wide range of hosts, including the non-mycorrhizal Brassicaceae metallophytes, their role in the response of plants to metal toxicity has not been thoroughly elucidated to date. This review summarizes the current knowledge regarding the role of endophytic fungi in the tolerance of plants to toxic metals and highlights the similarities and differences between this group of symbiotic fungi and mycorrhizal associations in terms of the survival of the plant during heavy metal stress.

Mechanisms of efficient As solubilization in soils and As accumulation by As-hyperaccumulator Pteris vittata

Arsenic (As) in soils is of major environmental concern due to its ubiquity and carcinogenicity. Pteris vittata (Chinese brake fern) is the first known As-hyperaccumulator, which is highly efficient in extracting As from soils and translocating it to the fronds, making it possible to be used for phytoremediation of As-contaminated soils. In addition, P. vittata has served as a model plant to study As metabolisms in plants. Based on the recent advances, we reviewed the mechanisms of efficient As solubilization and transformation in rhizosphere soils of P. vittata and effective As uptake, translocation and detoxification in P. vittata. We also provided future research perspectives to further improve As phytoremediation by P. vittata.

Modifications of the soluble proteome of a mediterranean strain of the invasive neurotoxic dinoflagellate Alexandrium catenella under metal stress conditions

The soluble proteome of the mediterranean strain ACT03 of the invasive neurotoxic dinoflagellate Alexandrium catenella exposed to lead or zinc at 6, 12 or 18μM (total concentrations), or under control conditions, was characterized by two-dimensional gel electrophoresis (2-DE). Zinc reduced (P<0.05) the total number of protein spots (-41%, -52% and -60%, at 6, 12 or 18μM, respectively). Besides, most of the proteins constituting the soluble proteome were down-regulated in response to lead or zinc stresses. These proteins were involved mainly in photosynthesis (20-37% for lead; 36-50% for zinc) (ribulose-1,5-bisphosphate carboxylase/oxygenase: RUBISCO; ferredoxin-NADP⁺ reductase: FNR; peridinin-chlorophyll a-protein: PCP), and in the oxidative stress response (29-34% for lead; 17-36% for zinc) (superoxide dismutase: SOD; proteasome α/β subunits). These negative effects could be partly compensated by the up-regulation of specific proteins such as ATP-synthase β subunit (+16.3 fold after exposure to lead at 12μM). Indeed, an increase in the abundance of ATP-synthase could enrich the ATP pool and provide more energy available for the cells to survive under metal stress, and make the ATP-synthase transport of metal cations out of the cells more efficient. Finally, this study shows that exposure to lead or zinc have a harmful effect on the soluble proteome of A. catenella ACT03, but also suggests the existence of an adaptative proteomic response to metal stresses, which could contribute to maintaining the development of this dinoflagellate in trace metal-contaminated ecosystems.

Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp. affinis

Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a "species-specific transcriptome database" (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non-model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.

Arsenic hyperaccumulation induces metabolic reprogramming in Pityrogramma calomelanos to reduce oxidative stress

Arsenic (As) pollution is a major environmental concern due to its worldwide distribution and high toxicity to organisms. The fern Pityrogramma calomelanos is one of the few plant species known to be able to hyperaccumulate As, although the mechanisms involved are largely unknown. This study aimed to investigate the metabolic adjustments involved in the As-tolerance of P. calomelanos. For this purpose, ferns with five to seven fronds were exposed to a series of As concentrations. Young fronds were used for biochemical analysis and metabolite profiling using gas chromatography-mass spectrometry. As treatment increased the total concentration of proteins and soluble phenols, enhanced peroxidase activities, and promoted disturbances in nitrogen and carbon metabolism. The reduction of the glucose pool was one of the striking responses to As. Remarkable changes in amino acids levels were observed in As-treated plants, including those related to biosynthesis of glutathione and phenols, osmoregulation and two photorespiratory intermediates. In addition, increases in polyamines levels and antioxidant enzyme activities were observed. In summary, this study indicates that P. calomelanos tolerates high concentration of As due to its capacity to upregulate biosynthesis of amino acids and antioxidants, without greatly disturbing central carbon metabolism. At extremely high As concentrations, however, this protective mechanism fails to block reactive oxygen species production, leading to lipid peroxidation and leaf necrosis.

Arbuscular mycorrhizal symbiosis affects the grain proteome of Zea mays: a field study

Maize is one of the most important crops worldwide and is strongly dependent on arbuscular mycorrhiza (AM) fungi, organisms that form a mutualistic association with land plants. In maize, AM symbiosis enhances spike dry weight, spike length, spike circumference, and the dry weight and dimensions of the grain. Notwithstanding its ubiquitous nature, the detailed relationship between AM fungal colonization and plant development is not completely understood. To facilitate a better understanding of the effects of AM fungi on plants, the work reported here assessed the effects of a consortium of AM fungi on the kernel proteome of maize, cultivated in open-field conditions. To our knowledge, this is the first report of the modulation of a plant seed proteome following AM fungal inoculation in the field. Here, it was found that AM fungi modify the maize seed proteome by up-regulating enzymes involved in energetic metabolism, embryo development, nucleotide metabolism, seed storage and stress responses.

Toxicity of heavy metals and metal-containing nanoparticles on plants

Plants are under the continual threat of changing climatic conditions that are associated with various types of abiotic stresses. In particular, heavy metal contamination is a major environmental concern that restricts plant growth. Plants absorb heavy metals along with essential elements from the soil and have evolved different strategies to cope with the accumulation of heavy metals. The use of proteomic techniques is an effective approach to investigate and identify the biological mechanisms and pathways affected by heavy metals and metal-containing nanoparticles. The present review focuses on recent advances and summarizes the results from proteomic studies aimed at understanding the response mechanisms of plants under heavy metal and metal-containing nanoparticle stress. Transport of heavy metal ions is regulated through the cell wall and plasma membrane and then sequestered in the vacuole. In addition, the role of different metal chelators involved in the detoxification and sequestration of heavy metals is critically reviewed, and changes in protein profiles of plants exposed to metal-containing nanoparticles are discussed in detail. Finally, strategies for gaining new insights into plant tolerance mechanisms to heavy metal and metal-containing nanoparticle stress are presented. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

The arsenic hyperaccumulating Pteris vittata expresses two arsenate reductases

Enzymatic reduction of arsenate to arsenite is the first known step in arsenate metabolism in all organisms. Although the presence of one mRNA arsenate reductase (PvACR2) has been characterized in gametophytes of P. vittata, no arsenate reductase protein has been directly observed in this arsenic hyperaccumulating fern, yet. In order to assess the possible presence of arsenate reductase in P. vittata, two recombinant proteins, ACR2-His6 and Trx-His6-S-Pv2.5-8 were prepared in Escherichia coli, purified and used to produce polyclonal antibodies. The presence of these two enzymes was evaluated by qRT-PCR, immunoblotting and direct MS analysis. Enzymatic activity was detected in crude extracts. For the first time we detected and identified two arsenate reductase proteins (PvACR2 and Pv2.5-8) in sporophytes and gametophytes of P. vittata. Despite an increase of the mRNA levels for both proteins in roots, no difference was observed at the protein level after arsenic treatment. Overall, our data demonstrate the constitutive protein expression of PvACR2 and Pv2.5-8 in P. vittata tissues and propose their specific role in the complex metabolic network of arsenic reduction.

AM fungi and PGP pseudomonads increase flowering, fruit production, and vitamin content in strawberry grown at low nitrogen and phosphorus levels

There is increasing interest in the quality of crops because of the implications concerning health, economic revenue, and food quality. Here we tested if inoculation with a mixture of arbuscular mycorrhizal fungi (AMF) and/or two strains of plant growth-promoting bacteria (PGPB), in conditions of reduced chemical inputs, affects the quality and yield of strawberry fruits. Fruit quality was measured by concentrations of soluble sugars, various organic acids, and two vitamins (ascorbic and folic acid). Co-inoculation with the AMF and each of the two PGPB resulted in increased flower and fruit production, larger fruit size, and higher concentrations of sugars and ascorbic and folic acid in comparison with fruits of uninoculated plants. These results provide further evidence that rhizospheric microorganisms affect fruit crop quality and show that they do so even under conditions of reduced chemical fertilization and can thus be exploited for sustainable agriculture.

Omics and biotechnology of arsenic stress and detoxification in plants: current updates and prospective

Arsenic (As), a naturally occurring metallic element, is a dreadful health hazard to millions of people across the globe. Arsenic is present in low amount in the environment and originates from anthropogenic impact and geogenic sources. The presence of As in groundwater used for irrigation is a worldwide problem as it affects crop productivity, accumulates to different tissues and contaminates food chain. The consumption of As contaminated water or food products leads to several diseases and even death. Recently, studies have been carried out to explore the biochemical and molecular mechanisms which contribute to As toxicity, accumulation, detoxification and tolerance acquisition in plants. This information has led to the development of the biotechnological tools for developing plants with modulated As tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. This review aims to provide current updates about the biochemical and molecular networks involved in As uptake by plants and the recent developments in the area of functional genomics in terms of developing As tolerant and low As accumulating plants.

Enhanced Photosynthesis and Carbon Metabolism Favor Arsenic Tolerance in Artemisia annua, a Medicinal Plant as Revealed by Homology-Based Proteomics

This paper provides the first proteomic evidence of arsenic (As) tolerance and interactive regulatory network between primary and secondary metabolism in the medicinal plant, Artemisia annua. While chlorophyll fluorescence and photosynthetic rate depicted mild inhibition, there was a significant enhancement in PSI activity, whole chain, ATP, and NADPH contents in 100 μM As treatments compared to the control plants. However, a decrease in the above variables was recorded under 150 μM treatments. Proteomic decoding of the survival strategy of A. annua under As stress using 2-DE followed by MALDI-MS/MS revealed a total of 46 differentially expressed protein spots. In contrast to other plants where As inhibits photosynthesis, A. annua showed appreciable photosynthetic CO₂ assimilation and allocation of carbon resources at 100 μM As concentration. While an increased accumulation of ATP synthase, ferredoxin-NADP(H) oxidoreductase, and FeS-rieske proteins supported the operation of cyclic electron transport, mdr ABC transporter protein and pcs gene might be involved in As detoxification. The most interesting observation was an increased accumulation of LEAFY like novel protein conceivably responsible for an early onset of flowering in A. annua under As stress. This study not only affirmed the role of energy metabolism proteins but also identified potential candidates responsible for As tolerance in plants.

Maize development and grain quality are differentially affected by mycorrhizal fungi and a growth-promoting pseudomonad in the field

Arbuscular mycorrhizal (AM) fungi and plant growth-promoting bacteria (PGPB) can increase the growth and yield of major crops, and improve the quality of fruits and leaves. However, little is known about their impact on seed composition. Plants were inoculated with AM fungi and/or the bacterial strain Pseudomonas fluorescens Pf4 and harvested after 7 months of growth in open-field conditions. Plant growth parameters were measured (biomass, length and circumference of spikes, number of grains per cob, grain yield, and grain size) and protein, lipid, and starch content in grains were determined. Plant growth and yield were increased by inoculation with the microorganisms. Moreover, spikes and grains of inoculated plants were bigger than those produced by uninoculated plants. Regarding grain composition, the bacterial strain increased grain starch content, especially the digestible components, whereas AM fungi-enhanced protein, especially zein, content. Plant inoculation with the fluorescent pseudomonad and mycorrhizal fungi resulted in additive effects on grain composition. Overall, results showed that the bacterial strain and the AM fungi promoted maize growth cultivated in field conditions and differentially affected the grain nutritional content. Consequently, targeted plant inoculation with beneficial microorganisms can lead to commodities fulfilling consumer and industrial requirements.

The fronds tonoplast quantitative proteomic analysis in arsenic hyperaccumulator Pteris vittata L

Pteris vittata, the first known arsenic hyperaccumulating plant, can accumulate very high concentration arsenic in its aboveground tissues, while low in roots. Previous studies have suggested that arsenic vacuole compartmentalization may play an important role in the arsenic-hyperaccumulation in P. vittata, but the mechanism(s) of arsenic transport to vacuole are largely unknown. We obtained tonoplast isolated from fronds of P. vittata sporophyte grown under minus and 1mM arsenate for 3weeks by iodixanol step gradient centrifugation method, and then used TMPP protein labeling technology followed by liquid chromatography-a linear ion trap-Orbitrap hybrid mass spectrometer analysis for the quantitative detection of proteins. And we designed and used an "artificial" database for database searching. In total, 56 tonoplast proteins were identified; more than 70% of them were transport proteins. Under arsenate treatment, one TDT transporter protein, a member of the TerC family and a PDR-like protein were upregulated differentially. While V-ATPase subunits c, E, and G, and V-PPase, were downregulated. Additionally, the identified tonoplast proteins in our present study provide an informative basis for arsenic carriers or channels and help to clarify the regulation of tonoplast arsenic transport processes in P. vittata.

BIOLOGICAL SIGNIFICANCE

Vacuole compartmentalization is crucial to As hyperaccumulator P. vittata, while there is limited known arsenic transport proteins involved in vacuole compartmentalization. In this paper, we obtained tonoplast of P. vittata fronds by iodixanol step gradient centrifugation method and then used TMPP protein labeling proteome technology for the quantitative detection of fronds tonoplast proteins. Our findings are the first challenge to the tonoplast proteins data mining of P. vittata which provide an informative basis for As carriers or channels. The proteomic approach in our study is suited for detecting alterations tonoplast protein and help to clarify the regulation of tonoplast transport processes. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Recent advances in the analysis of metal hyperaccumulation and hypertolerance in plants using proteomics

Hyperaccumulator/hypertolerant plant species have evolved strategies allowing them to grow in metal-contaminated soils, where they accumulate high concentrations of heavy metals in their shoots without signs of toxicity. The mechanisms that allow enhanced metal uptake, root-to-shoot translocation and detoxification in these species are not fully understood. Complementary approaches such as transcriptomic-based DNA microarrays and proteomics have recently been used to gain insight into the molecular pathways evolved by metal hyperaccumulator/hypertolerant species. Proteomics has the advantage of focusing on the translated portion of the genome and it allows to analyze complex networks of proteins. This review discusses the recent analysis of metal hyperaccumulator/hypertolerant plant species using proteomics. Changes in photosynthetic proteins, sulfur, and glutathione metabolism, transport, biotic and xenobiotic defenses as well as the differential regulation of proteins involved in signaling and secondary metabolism are discussed in relation to metal hyperaccumulation. We also consider the potential contribution of several proteins to the hyperaccumulation phenotype.

The proteomics of heavy metal hyperaccumulation by plants

Hyperaccumulators are distinguished from non-hyperaccumulators on the basis of their capacity to extract heavy metal ions from the soil, their more efficient root-to-shoot translocation of these ions and their greater ability to detoxify and sequester heavy metals in the shoot. The understanding of the mechanisms underlying metal ion accumulation has progressed beyond the relevant biochemistry and physiology to encompass the genetic and molecular regulatory systems which differentiate hyperaccumulators from non-hyperaccumulators. This paper reviews the literature surrounding the application of proteomics technology to plant metal hyperaccumulation, in particular involving the elements As, Cd, Cu, Ni, Pb and Zn. The hyperaccumulation process across a number of unrelated plant species appears to be associated with proteins involved in energy metabolism, the oxidative stress response and abiotic and biotic stress. The relevance of transducers of the metal stress response to the phenomenon of hyperaccumulation is summarized. Proteomic data complement the more voluminous genomic and transcriptomic data sets in providing a more nuanced picture of the process, and should therefore help in the identification of the major genetic determinants of the hyperaccumulation phenomenon.

Identification of a 2-cys peroxiredoxin as a tetramethyl benzidine-hydrogen peroxide stained protein from the thylakoids of the extreme halophyte Arthrocnemum macrostachyum L

Tetramethylbenzidine-H(2)O(2) staining of SDS-polyacrylamide gel is a widely used method for the specific detection of proteins with heme-dependent peroxidase activity. When this method was used with thylakoids from the halophytic plant Arthrocnemum macrostachyum, besides the cytochrome f and cytochrome b6 proteins usually found in higher plants and cyanobacteria, at least four additional bands were detected. One of them, a 46-kDa protein, was shown to be an extrinsic protein, and identified by mass spectrometry and immunoblotting as a 2-cys peroxiredoxin. Peroxidase activity was insensitive to oxidizing agents such as trans-4,4-diydroxy-1,2-dithiane or hydrogen peroxide, but was inhibited by treatment of thylakoids with reducing agents such as dithiothreitol or mercaptoethanol. By immunoblotting, it was shown that loss of peroxidase activity was paralleled by disappearance of the 46-kDa band, which was converted to a 23-kDa immunoreactive form. A dimer/monomer relationship between the two proteins is suggested, with the dimeric form likely being a heme-binding protein. This possibility was further supported by anionic exchange chromatography and de novo sequencing of tryptic fragments of the protein and sequence comparison, as most of the residues previously implicated in heme binding in 2-cys peroxiredoxin from Rattus norvegicus were conserved in A. macrostachyum. The amount of this protein was modulated by environmental conditions, and increased when salt concentration in the growth medium was higher or lower than the optimal one.

Arsenomics: omics of arsenic metabolism in plants

Arsenic (As) contamination of drinking water and groundwater used for irrigation can lead to contamination of the food chain and poses serious health risk to people worldwide. To reduce As intake through the consumption of contaminated food, identification of the mechanisms for As accumulation and detoxification in plant is a prerequisite to develop efficient phytoremediation methods and safer crops with reduced As levels. Transcriptome, proteome, and metabolome analysis of any organism reflects the total biological activities at any given time which are responsible for the adaptation of the organism to the surrounding environmental conditions. As these approaches are very important in analyzing plant As transport and accumulation, we termed "Arsenomics" as approach which deals transcriptome, proteome, and metabolome alterations during As exposure. Although, various studies have been performed to understand modulation in transcriptome in response to As, many important questions need to be addressed regarding the translated proteins of plants at proteomic and metabolomic level, resulting in various ecophysiological responses. In this review, the comprehensive knowledge generated in this area has been compiled and analyzed. There is a need to strengthen Arsenomics which will lead to build up tools to develop As-free plants for safe consumption.

Effects of heavy metals and arbuscular mycorrhiza on the leaf proteome of a selected poplar clone: a time course analysis

Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with the roots of most plant species. While receiving photosynthates, they improve the mineral nutrition of the plant and can also increase its tolerance towards some pollutants, like heavy metals. Although the fungal symbionts exclusively colonize the plant roots, some plant responses can be systemic. Therefore, in this work a clone of Populus alba L., previously selected for its tolerance to copper and zinc, was used to investigate the effects of the symbiosis with the AM fungus Glomus intraradices on the leaf protein expression. Poplar leaf samples were collected from plants maintained in a glasshouse on polluted (copper and zinc contaminated) or unpolluted soil, after four, six and sixteen months of growth. For each harvest, about 450 proteins were reproducibly separated on 2DE maps. At the first harvest the most relevant effect on protein modulation was exerted by the AM fungi, at the second one by the metals, and at the last one by both treatments. This work demonstrates how importantly the time of sampling affects the proteome responses in perennial plants. In addition, it underlines the ability of a proteomic approach, targeted on protein identification, to depict changes in a specific pattern of protein expression, while being still far from elucidating the biological function of each protein.

Arsenic toxicity: the effects on plant metabolism

The two forms of inorganic arsenic, arsenate (AsV) and arsenite (AsIII), are easily taken up by the cells of the plant root. Once in the cell, AsV can be readily converted to AsIII, the more toxic of the two forms. AsV and AsIII both disrupt plant metabolism, but through distinct mechanisms. AsV is a chemical analog of phosphate that can disrupt at least some phosphate-dependent aspects of metabolism. AsV can be translocated across cellular membranes by phosphate transport proteins, leading to imbalances in phosphate supply. It can compete with phosphate during phosphorylation reactions, leading to the formation of AsV adducts that are often unstable and short-lived. As an example, the formation and rapid autohydrolysis of AsV-ADP sets in place a futile cycle that uncouples photophosphorylation and oxidative phosphorylation, decreasing the ability of cells to produce ATP and carry out normal metabolism. AsIII is a dithiol reactive compound that binds to and potentially inactivates enzymes containing closely spaced cysteine residues or dithiol co-factors. Arsenic exposure generally induces the production of reactive oxygen species that can lead to the production of antioxidant metabolites and numerous enzymes involved in antioxidant defense. Oxidative carbon metabolism, amino acid and protein relationships, and nitrogen and sulfur assimilation pathways are also impacted by As exposure. Readjustment of several metabolic pathways, such as glutathione production, has been shown to lead to increased arsenic tolerance in plants. Species- and cultivar-dependent variation in arsenic sensitivity and the remodeling of metabolite pools that occurs in response to As exposure gives hope that additional metabolic pathways associated with As tolerance will be identified.

Arsenate toxicity and stress responses in the freshwater ciliate Tetrahymena pyriformis

The arsenic metabolism in different biological organisms has been studied extensively. However, little is known about protozoa. Herein, we investigated the cell stress responses of the freshwater ciliate Tetrahymena pyriformis to arsenate toxicity. An acute toxicity assay revealed an 18-h EC(50) arsenate concentration of ca. 40 μM, which caused significant changes in the cell shape, growth and organism mobility. Whereas, under exposure to 30 μM arsenate, T. pyriformis could grow reasonably well, indicating a certain resistance of this organism. Arsenic speciation analysis revealed that 94-98% of the total arsenate in cells of T. pyriformis could be transformed to monomethylarsonic acid, dimethylarsinic acid and a small proportion of arsenite after 18 h of arsenate exposure, thus indicating the major detoxification pathway by arsenic oxidation/reduction and biomethylation. Finally, comparative proteomic analysis unveiled significant changes in the expression of multiple proteins involved in anti-oxidation, sugar and energy metabolism, proteolysis, and signal transduction. Our results revealed multiple pathways of arsenate detoxification in T. pyriformis, and indicated that protozoa may play important roles in the biogeochemical cycles of arsenic.

Proteomic analysis as a tool for investigating arsenic stress in Pteris vittata roots colonized or not by arbuscular mycorrhizal symbiosis

Pteris vittata can tolerate very high soil arsenic concentration and rapidly accumulates the metalloid in its fronds. However, its tolerance to arsenic has not been completely explored. Arbuscular mycorrhizal (AM) fungi colonize the root of most terrestrial plants, including ferns. Mycorrhizae are known to affect plant responses in many ways: improving plant nutrition, promoting plant tolerance or resistance to pathogens, drought, salinity and heavy metal stresses. It has been observed that plants growing on arsenic polluted soils are usually mycorrhizal and that AM fungi enhance arsenic tolerance in a number of plant species. The aim of the present work was to study the effects of the AM fungus Glomus mosseae on P. vittata plants treated with arsenic using a proteomic approach. Image analysis showed that 37 spots were differently affected (21 identified). Arsenic treatment affected the expression of 14 spots (12 up-regulated and 2 down-regulated), while in presence of G. mosseae modulated 3 spots (1 up-regulated and 2 down-regulated). G. mosseae, in absence of arsenic, modulated 17 spots (13 up-regulated and 4 down-regulated). Arsenic stress was observed even in an arsenic tolerant plant as P. vittata and a protective effect of AM symbiosis toward arsenic stress was observed.