Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network

Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.

Cyanobacterial Proteomics: Diversity and Dynamics

Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.

Comparing and integrating TMT-SPS-MS3 and label-free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period

Despite substantial advances in the use of proteomic technologies, their widespread application in fruit tissues of non-model and recalcitrant species remains limited. This hampers the understanding of critical molecular events during the postharvest period of fleshy tropical fruits. Therefore, we evaluated label-free quantitation (LFQ) and TMT-SPS-MS3 (TMT) approaches to analyse changes in the protein profile of mango peels during postharvest period. We compared two extraction methods (phenol and chloroform/methanol) and two peptide fractionation schemes (SCX and HPRP). We accurately identified 3065 proteins, of which, 1492 were differentially accumulated over at 6 days after harvesting (DAH). Both LFQ and TMT approaches share 210 differential proteins including cell wall proteins associated with fruit softening, as well as aroma and flavour-related proteins, which were increased during postharvest period. The phenolic protein extraction and the high-pH reverse-phase peptide fractionation was the most effective pipeline for relative quantification. Nevertheless, the information provided by the other tested strategies was significantly complementary. Besides, LFQ spectra allowed us to track down intact N-glycopeptides corroborating N-glycosylations on the surface of a desiccation-related protein. This work represents the largest proteomic comparison of mango peels during postharvest period made so far, shedding light on the molecular foundation of edible fruit during ripening.

Extraction of Soluble Proteins from Leaves

Protein biochemistry can provide valuable answers to better understand plant performance and responses to the surrounding environment. In this chapter, we describe the process of extracting proteins from plant leaf samples. We highlight the key aspects to take into consideration to preserve protein integrity, from sample collection to extraction and preparation or storage for subsequent analysis of protein abundance and/or enzymatic activities.

Extraction of Proteins from Green Tissues of Plants and Phyllosphere

The proteomic approach plays a key role to characterize a biological system at any given time. In recent years, advances in proteomics have led to an increasing application in all biological fields, including plant matrices and associated microbiome studies. However, extracting adequate protein samples remains the most critical step for any plant proteomics study. The protein extraction protocols proposed for the phyllosphere involve an initial leaf washing step; however, this is an approach only applicable if interest is restricted to epiphytes. A metaproteomic approach is required to obtain an overall picture and consequently an extraction that considers proteins derived from the plant, epiphytic and endophytic microorganisms. The most commonly used extractions for plant tissue involve the use of phenol or TCA-acetone. However, for efficient protein recovery is essential to remove interfering components abundant in plant tissues, such as polysaccharides, lipids, and phenolic compounds. A well-proven protocol on the basis of a combination of TCA-acetone and phenol extraction is presented here, obtaining some cleaned protein pellets, suitable for electrophoresis and subsequent proteomics studies. Important points for the success of this protocol are (i) a proper sampling and sample preparation, (ii) maintaining samples at a low temperature during extraction and using protease inhibitors, (iii) an initial step in TCA-acetone to remove part of the interfering substances, and (iv) careful recovery of the phenolic phase. Furthermore, the protocol is timesaving and can be completed in one working day.

Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS

The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for 10-ng, 250-ng, and 10-µg peptide samples, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the most robust approach, even for the simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.

Suspension Trapping-Based Sample Preparation Workflow for In-Depth Plant Phosphoproteomics

Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Despite the widespread use of protein precipitation for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we developed an approach based on suspension trapping (S-Trap), termed tandem S-Trap-IMAC (immobilized metal ion affinity chromatography), by integrating an S-Trap micro-column with a Fe-IMAC tip. Compared with a precipitation-based workflow, the tandem S-Trap-IMAC method deepened the coverage of the Arabidopsis (Arabidopsis thaliana) phosphoproteome by more than 30%, with improved number of multiply phosphorylated peptides, quantification accuracy, and short sample processing time. We applied the tandem S-Trap-IMAC method for studying abscisic acid (ABA) signaling in Arabidopsis seedlings. We thus discovered that a significant proportion of the phosphopeptides induced by ABA are multiply phosphorylated peptides, indicating their importance in early ABA signaling and quantified several key phosphorylation sites on core ABA signaling components across four time points. Our results show that the optimized workflow aids high-throughput phosphoproteome profiling of low-input plant samples.

Proteomics-Guided Mining and Characterization of Epoxidase Involved in Camptothecin Biosynthesis from Camptotheca acuminata

The detailed metabolic map for camptothecin (CPT) biosynthesis in Camptotheca acuminata has been proposed according to our combined omics results. However, the CYP450-mediated epoxidation step in CPT biosynthesis remains unexplored. A proteomics-guided approach was used to identify and annotate the proteins enriched during the vigorous CPT metabolism period in mature C. acuminata and seedlings. Comparative analyses revealed that the CPT and flavonoid biosyntheses were vigorous in stems and all of the samples except the leaves, respectively. The CYP71BE genes were screened based on their enrichment patterns at the transcriptomic-proteomic level and biochemically characterized in Saccharomyces cerevisiae WAT11. Four CYP71BE proteins exhibited in vitro isoliquiritigenin epoxidase activity. Additionally, CYP71BE206 showed epoxidase activity toward strictosamide, the critical precursor for CPT biosynthesis, both in vitro and in Nicotiana benthamiana. In planta functional verification suggested that CYP71BE206 is involved in CPT biosynthesis. Their catalytic conditions were optimized, and the enzymatic parameters were determined. This study provides valuable insight into the CYP71BE-mediated epoxidation step for CPT biosynthesis and offers evidence to verify that the newly characterized epoxidase (CYP71BE206) is simultaneously responsible for the biosynthesis of CPT and the flavonoid in this plant. An evolution event probably happened on ancestral CYP71BE, resulting in the neofunctionalization of CYP71BE206.

Research Progress of Nucleic Acid Detection Technology for Genetically Modified Maize

Genetically modified (GM) maize is one of the earliest GM crops to have achieved large-scale commercial cultivation globally, and it is of great significance to excel in the development and implementation of safety policy regarding GM, and in its technical oversight. This article describes the general situation regarding genetically modified maize, including its varieties, applications, relevant laws and regulations, and so on. From a technical point of view, we summarize and critically analyze the existing methods for detecting nucleic acid levels in genetically modified maize. The nucleic acid extraction technology used for maize is explained, and the introduction of traditional detection techniques, which cover variable-temperature and isothermal amplification detection technology and gene chip technology, applications in maize are described. Moreover, new technologies are proposed, with special attention paid to nucleic acid detection methods using sensors. Finally, we review the current limitations and challenges of GM maize nucleic acid testing and share our vision for the future direction of this field.

Optimization of Targeted Plant Proteomics Using Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS)

This study was conducted to optimize a targeted plant proteomics approach from signature peptide selection and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analytical method development and optimization to sample preparation method optimization. Three typical protein extraction and precipitation methods, including trichloroacetic acid (TCA)/acetone method, phenol method, and TCA/acetone/phenol method, and two digestion methods, including trypsin digestion and LysC/trypsin digestion, were evaluated for selected proteins related to the impact of engineered nanomaterials (ENMs) on wheat (Triticum aestivum) plant growth. In addition, we compared two plant tissue homogenization methods: grinding freeze-dried tissue and fresh tissue into a fine powder using a mortar and pestle aided with liquid nitrogen. Wheat plants were grown under a 16 h photoperiod (light intensity 150 μmol·m^-2·s^-1) for 4 weeks at 22 °C with a relative humidity of 60% and were watered daily to maintain a 70-90% water content in the soil. Processed samples were analyzed with an optimized LC-MS/MS method. The concentration of selected signature peptides for the wheat proteins of interest indicated that the phenol extraction method using fresh plant tissue, coupled with trypsin digestion, was the best sample preparation method for the targeted proteomics study. Overall, the optimized approach yielded the highest total peptide concentration (68,831 ng/g, 2.4 times the lowest concentration) as well as higher signature peptide concentrations for most peptides (19 out of 28). In addition, three of the signature peptides could only be detected using the optimized approach. This study provides a workflow for optimizing targeted proteomics studies.

Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.

Getting Ready for Large-Scale Proteomics in Crop Plants

Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being up-regulated through a VviNAC60-VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologues to the NAC transcription factor AtNAP, VviNAC60 complemented the non-ripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase.

Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals

Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO₂ -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO₂ Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C₁₈ material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.

Plant Proteome Dynamics

Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions

The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.

Magnetic nanoparticles coated with carboxylate-terminated carbosilane dendrons as a reusable and green approach to extract/purify proteins

Extraction/purification of proteins, at both analytical and industrial levels, is a limiting step that usually requires the use of organic solvents and involves tedious work and a high cost. This work proposes a more sustainable alternative based on the use of magnetic nanoparticles (MNPs) coated with carboxylate-terminated carbosilane dendrons. MNPs coated with first- and second-generation carbosilane dendrons and bare MNPs were employed for the extraction of proteins with different molecular weights and charges. Interaction of proteins with MNPs significantly varied with the pH, the protein, and the dendron generation (different sizes and number of charges in the periphery). Optimal dendron:protein molar ratios and suitable conditions for disrupting interactions after protein extraction were also researched. Second-generation dendron-coated MNPs showed 100% retention capability for all proteins when using acidic conditions. They were reused without losing magnetism or interaction capacity after a disruption of protein-dendron interactions with 0.2% SDS at 100 °C for 10 min. The capacity of dendron-coated MNPs was successfully applied to the recovery/purification of proteins from two food by-products, olive seeds and cheese whey.

Plant and algal lysophosphatidic acid acyltransferases increase docosahexaenoic acid accumulation at the sn-2 position of triacylglycerol in transgenic Arabidopsis seed oil

Although docosahexaenoic acid (DHA), an important dietary omega-3 polyunsaturated fatty acid (PUFA), is at present primarily sourced from marine fish, bioengineered crops producing DHA may offer a more sustainable and cost-effective source. DHA has been produced in transgenic oilseed crops, however, DHA in seed oil primarily occupies the sn-1/3 positions of triacylglycerol (TAG) with relatively low amounts of DHA in the sn-2 position. To increase the amount of DHA in the sn-2 position of TAG and in seed oil, putative lysophosphatidic acid acyltransferases (LPAATs) were identified and characterized from the DHA-producing alga Schizochytrium sp. and from soybean (Glycine max). The affinity-purified proteins were confirmed to have LPAAT activity. Expression of the Schizochytrium or soybean LPAATs in DHA-producing Arabidopsis expressing the Schizochytrium PUFA synthase system significantly increased the total amount of DHA in seed oil. A novel sensitive band-selective heteronuclear single quantum coherence (HSQC) NMR method was developed to quantify DHA at the sn-2 position of glycerolipids. More than two-fold increases in sn-2 DHA were observed for Arabidopsis lines expressing Schizochytrium or soybean LPAATs, with one Schizochytrium LPAAT driving DHA accumulation in the sn-2 position to 61% of the total DHA. Furthermore, expression of a soybean LPAAT led to a redistribution of DHA-containing TAG species, with two new TAG species identified. Our results demonstrate that transgenic expression of Schizochytrium or soybean LPAATs can increase the proportion of DHA at the sn-2 position of TAG and the total amount of DHA in the seed oil of a DHA-accumulating oilseed plant. Additionally, the band-selective HSQC NMR method that we developed provides a sensitive and robust method for determining the regiochemistry of DHA in glycerolipids. These findings will benefit the advancement of sustainable sources of DHA via transgenic crops such as canola and soybean.

Optimization of Protein Isolation and Label-Free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng

Korean ginseng is one of the most valuable medicinal plants worldwide. However, our understanding of ginseng proteomics is largely limited due to difficulties in the extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone-MeOH/chloroform, phenol-TCA/acetone, and phenol-MeOH/chloroform methods. The TCA/acetone-MeOH/chloroform method displayed the highest extraction efficiency, and thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label-free quantitative proteomics approach. This approach led to the identification of 2604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis, including the methylerythritol 4-phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP-glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ-based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.

Extraction and identification of biologically important proteins from the medicinal plant God's crown (Phaleria macrocarpa)

The fruit and leaf of God's crown (Phaleria macrocarpa) have been traditionally used to treat a wide variety of diseases. However, the proteins of this tropical plant are still heavily understudied. Three protein extraction methods; phenol (Phe), trichloroacetic acid (TCA)-acetone-phenol (TCA-A-Phe), and ultrasonic (Ult) were compared on the fruit and leaf of P. macrocarpa. The Phe extraction method showed the highest percentage of recovered protein after the resolubilization process for both leaf (12.24%) and fruit (30.41%) based on protein yields of the leaf (6.15 mg/g) and fruit (36.98 mg/g). Phe and TCA-A-Phe extraction methods gave well-resolved bands over a wide range of molecular weights through sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Following liquid chromatography-tandem mass spectrometry analysis, proteins identified through the Phe extraction method were 30%-35% enzymatic proteins, including oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases that possess various biological functions. PRACTICAL APPLICATIONS: Every part of God's crown plant is traditionally consumed to treat various illnesses. While plant's benefits are well known and have led to a plethora of health products, the proteome remains mostly unknown. This study compares three protein extraction methods for the leaf and fruit of P. macrocarpa and identifies their proteins thru LC-MS/MS coupled with PEAKS. These method comparisons can be a guide for works on other plants as well. In addition, the proteomics data from this study may shed light on the functional properties of these plant parts and their products.

The toxicity of selenium and mercury in Suaeda salsa after 7-days exposure

Mercury is one of the major pollutants in the ocean, selenium causes toxicity beyond a certain limit, but there are few comparative toxic studies between them in halophytes. The study was to investigate the toxic effects of selenium (Se⁴⁺) and mercury (Hg²⁺) in halophyte Suaeda salsa at the level of genes, proteins and metabolites after exposure for 7 days. By integrating the results of proteomics and metabolomics, the pathway changed under different treatments were revealed. In Se⁴⁺-treated group, the changed 3 proteins and 10 metabolites participated in the process of substance metabolism (amino acid, pyrimidine), citrate cycle, pentose phosphate pathway, photosynthesis, energy, and protein biosynthesis. In Hg²⁺-treated group, the changed 10 proteins and 10 metabolites were related to photosynthesis, glycolysis, substance metabolism (cysteine and methionine, amino acid, pyrimidine), ATP synthesis and binding, tolerance, sugar-phosphatase activity, and citrate cycle. In Se⁴⁺+ Hg²⁺-treated group, the changed 5 proteins an 12 metabolites involved in stress defence, iron ion binding, mitochondrial respiratory chain, structural constituent of ribosome, citrate cycle, and amino acid metabolism. Furthermore, the separate and combined selenium and mercury both inhibited growth of S. salsa, enhanced activity of antioxidant enzymes (superoxide dismutase, peroxidase and catalase), and disturbed osmotic regulation through the genes of choline monoxygenase and betaine aldehyde dehydrogenase. Our experiments also showed selenium could induce synergistic effects in S. salsa. In all, we successfully characterized the effects of selenium and mercury in plant which was helpful to evaluate the toxicity and interaction of marine pollutants.

Exploitation of Novel Bt ICPs for the Management of Helicoverpa armigera (Hübner) in Cotton (Gossypium hirsutum L.): A Transgenic Approach

Cotton is a commercial crop of global importance. The major threat challenging the productivity in cotton has been the lepidopteron insect pest Helicoverpa armigera or cotton bollworm which voraciously feeds on various plant parts. Biotechnological interventions to manage this herbivore have been a universally inevitable option. The advent of plant genetic engineering and exploitation of Bacillus thuringiensis (Bt) insecticidal crystal proteins (ICPs) marked the beginning of plant protection in cotton through transgenic technology. Despite phenomenal success and widespread acceptance, the fear of resistance development in insects has been a perennial concern. To address this issue, alternate strategies like introgression of a combination of cry protein genes and protein-engineered chimeric toxin genes came into practice. The utility of chimeric toxins produced by domain swapping, rearrangement of domains, and other strategies aid in toxins emerging with broad spectrum efficacy that facilitate the avoidance of resistance in insects toward cry toxins. The present study demonstrates the utility of two Bt ICPs, cry1AcF (produced by domain swapping) and cry2Aa (produced by codon modification) in transgenic cotton for the mitigation of H. armigera. Transgenics were developed in cotton cv. Pusa 8–6 by the exploitation of an apical meristem-targeted in planta transformation protocol. Stringent trait efficacy-based selective screening of T₁ and T₂ generation transgenic plants enabled the identification of plants resistant to H. armigera upon deliberate challenging. Evaluation of shortlisted events in T₃ generation identified a total of nine superior transgenic events with both the genes (six with cry1AcF and three with cry2Aa). The transgenic plants depicted 80–100% larval mortality of H. armigera and 10–30% leaf damage. Molecular characterization of the shortlisted transgenics demonstrated stable integration, inheritance and expression of transgenes. The study is the first of its kind to utilise a non-tissue culture-based transformation strategy for the development of stable transgenics in cotton harbouring two novel genes, cry1AcF and cry2Aa for insect resistance. The identified transgenic events can be potential options toward the exploitation of unique cry genes for the management of the polyphagous insect pest H. armigera.

Evaluation of female Aedes aegypti proteome via LC-ESI-MS/MS using two protein extraction methods

Background

Proteomic analyses have broadened the horizons of vector control measures by identifying proteins associated with different biological and physiological processes and give further insight into the mosquitoes’ biology, mechanism of insecticide resistance and pathogens-mosquitoes interaction. Female Ae. aegypti ingests human blood to acquire the requisite nutrients to make eggs. During blood ingestion, female mosquitoes transmit different pathogens. Therefore, this study aimed to determine the best protein extraction method for mass spectrometry analysis which will allow a better proteome profiling for female mosquitoes.

Methods

In this present study, two protein extractions methods were performed to analyze female Ae. aegyti proteome, via TCA acetone precipitation extraction method and a commercial protein extraction reagent CytoBuster^TM. Then, protein identification was performed by LC-ESI-MS/MS and followed by functional protein annotation analysis.

Results

The CytoBuster^TM reagent gave the highest protein yield with a mean of 475.90 µg compared to TCA acetone precipitation extraction showed 283.15 µg mean of protein. LC-ESI-MS/MS identified 1,290 and 890 proteins from the CytoBuster^TM reagent and TCA acetone precipitation, respectively. When comparing the protein class categories in both methods, there were three additional categories for proteins identified using CytoBuster^TM reagent. The proteins were related to scaffold/adaptor protein (PC00226), protein binding activity modulator (PC00095) and intercellular signal molecule (PC00207). In conclusion, the CytoBuster^TM protein extraction reagent showed a better performance for the extraction of proteins in term of the protein yield, proteome coverage and extraction speed.

Pressurized water extraction - the fast and efficient method for isolation of bioactive proteins from Viscum album leaves

New strategies for the fast, efficient, and environmentally friendly extraction of proteins are required to isolate desired bioactive compounds from a technological point of view. In this study, utilization of the pressurized water extraction (PWE) at low temperature (40 °C) for isolation of mistletoe proteins was investigated. PWE effectiveness, based on protein fingerprints, were compared with those obtained by conventional extractions using 10 mmol L^-1 Tris-HCl buffer pH 8.3, 50 mmol L^-1 phosphate buffer pH 7, or deionized water. The extracts were precipitated using acetone, trichloroacetic acid (TCA), and 20% (w/v) TCA/acetone and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PWE was more or equally efficient for isolation of mistletoe proteins than evaluated conventional extraction methods. The proteomic analysis combining mass spectrometry and database searching confirmed the presence of 35 proteins in PWE extracts precipitated by acetone, which was the most compounds identified from all studied extracts. The PWE high extraction power was revealed for multiple viscotoxin isoforms and specific enzymes indispensable for the synthesis of terpenes.

Efficient protein extraction for shotgun proteomics from hydrated and desiccated leaves of resurrection Ramonda serbica plants

Resurrection plant Ramonda serbica is a suitable model to investigate vegetative desiccation tolerance. However, the detailed study of these mechanisms at the protein level is hampered by the severe tissue water loss, high amount of phenolics and polysaccharide, and possible protein modifications and aggregations during the extraction and purification steps. When applied to R. serbica leaves, widely used protein extraction protocols containing polyvinylpolypyrrolidone and ascorbate, as well as the phenol/SDS/buffer-based protocol recommended for recalcitrant plant tissues failed to eliminate persistent contamination and ensure high protein quality. Here we compared three protein extraction approaches aiming to establish the optimal one for both hydrated and desiccated R. serbica leaves. To evaluate the efficacy of these protocols by shotgun proteomics, we also created the first R. serbica annotated transcriptome database, available at http://www.biomed.unipd.it/filearrigoni/Trinity_Sample_RT2.fasta . The detergent-free phenol-based extraction combined with dodecyl-β-D-maltoside-assisted extraction enabled high-yield and high-purity protein extracts. The phenol-based protocol improved the protein-band resolution, band number, and intensity upon electrophoresis, and increased the protein yield and the number of identified peptides and protein groups by LC-MS/MS. Additionally, dodecyl-β-D-maltoside enabled solubilisation and identification of more membrane-associated proteins. The presented study paves the way for investigating the desiccation tolerance in R. serbica, and we recommend this protocol for similar recalcitrant plant material.

Transgenic Cotton (Gossypium hirsutum L.) to Combat Weed Vagaries: Utility of an Apical Meristem-Targeted in planta Transformation Strategy to Introgress a Modified CP4-EPSPS Gene for Glyphosate Tolerance

Weeds burden plant growth as they compete for space, sunlight, and soil nutrients leading to 25-80% yield losses. Glyphosate [N-(phosphonomethyl)glycine] is a widely used broad spectrum non-selective herbicide that controls weeds by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and interfering with the shikimate biosynthesis pathway. Cotton (Gossypium hirsutum L.) is one of the most important commercial crops grown worldwide for its fiber. We have developed herbicide tolerant transgenic cotton (cv. P8-6) by introgression of a codon-optimized and modified EPSPS gene (CP4-EPSPS) possessing an N-terminal chloroplast targeting peptide from Petunia hybrida. Because of the recalcitrant nature of cotton, a genotype-independent non-tissue culture-based apical meristem-targeted in planta transformation approach was used to develop transformants. Although in planta transformation methodologies are advantageous in developing a large number of transgenic plants, effective screening strategies are essential for initial identification of transformants. In the present study, the use of a two-level rigorous screening strategy identified 2.27% of T1 generation plants as tolerant to 800 and 1,500 mg/L of commercially available glyphosate (Roundup). Precise molecular characterization revealed stable integration, expression, and inheritance of CP4-EPSPS in advanced generations of the promising transgenic events. Further, superiority of selected transgenic plants in tolerating increasing levels of glyphosate (500-4,000 mg/L) was ascertained through reduced accumulation of shikimate. This report is the first of its kind where cotton transformants tolerating high levels of glyphosate (up to 4,000 mg/L) and accumulating low levels of shikimate have been identified. This study not only reiterated the genotype-independent nature of the transformation strategy but also reiterated the translational utility of the CP4-EPSPS gene in management of weeds.

Ionic liquid-assisted protein extraction method for plant phosphoproteome analysis

Protein phosphorylation is one of the most important post-translational modifications (PTM) and plays critical roles in maintaining many biological processes of plant species, such as being a significant signal related to resistance to tobacco mosaic virus (TMV) infection in tobacco. Compared to other organisms, in-depth profiling of plant phosphoproteome remains challenging due to the harsh extraction environment of plant proteins and low abundance of plant phosphorylation, generally requiring large amount of plant materials. Herein, we developed an integrated strategy for efficient sample preparation of amounts of plant tissues, by integrating ionic liquid (IL)-assisted protein extraction, in-solution digestion, precipitation-assisted IL removal, as well as immobilized metal ion affinity chromatography (IMAC) enrichment of phosphopeptides together. In this strategy, to improve the efficiency of protein extraction and enzymatic digestion, IL of 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was used as the solubilizer due to its excellent solubilizing ability and enzyme compatibility demonstrated in our previous work. Briefly, the extraction capability of C12Im-Cl for protein amount from tobacco leaves was improved 1.9-fold compared to the commonly used urea-assisted method. Notably, to avoid its interference with subsequent LC-MS analysis, the IL was easily removed from the peptide solution by our proposed ion substitution-mediated C12Im + precipitation strategy with high efficiency. By handling 10 mg of starting protein materials of tobacco leaves, 14,441 unique phosphopeptides, assigned to 5153 unique phosphoproteins were confidently identified. To the best of our knowledge, this was the most comprehensive phosphorylation dataset for tobacco so far. All the results demonstrated our strategy was of great potential to promote the large-scale analysis of plant phosphoproteome.

Comparison and optimization of protein extraction and two-dimensional gel electrophoresis protocols for liverworts

Objective

Liverworts possess historical adaptive strategies for abiotic stresses because they were the first plants that shifted from water to land. Proteomics is a state-of-the-art technique that can capture snapshots of events occurring at the protein level in many organisms. Herein, we highlight the comparison and optimization of an effective protein extraction and precipitation protocol for two-dimensional gel electrophoresis (2-DE) of liverworts.

Results

We compared three different protein extraction methods, i.e.,1.5 M Tris–HCl (pH 8.8), 50 mM Tris–HCl (pH 7.5), and polyvinylpolypyrrolidone (PVPP) extraction, followed by three precipitation methods, i.e., 80% ethanol, 80% acetone, and 20% tricholoroacetic acid (TCA)–acetone, in a liverwort Dumortiera hirsuta. Among these methods, 50 mM Tris–HCl (pH 7.5) extraction, followed by 20% TCA–acetone precipitation, appeared to be more suitable for 2-DE. Furthermore, we performed modifications during protein washing, re-solubilization in rehydration buffer and isoelectric focusing (IEF). The modifications provided us better results in terms of protein yield, resolution, spot numbers, and intensities for 2-DE gels of D. hirsuta and other two liverworts, i.e., Marchantia paleacea and Plagiochasma appendiculatum. Furthermore, we randomly selected spots from the 2-DE gel of D. hirsuta and identified using mass spectrometry, which confirms the applicability of this protocol for liverworts proteomics.

Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues Using Tandem Mass Tags

Proteins produce or regulate nearly every component of cells. Thus, the ability to quantitatively determine the protein abundance and posttranslational modification (PTM) state is a critical aspect toward our understanding of biological processes. In this chapter, we describe methods to globally quantify protein abundance and phosphorylation state using isobaric labeling with tandem mass tags followed by phosphopeptide enrichment.

Feasibility of cationic carbosilane dendrimers for sustainable protein sample preparation

Protein sample preparation is the bottleneck in the analysis of proteins. The aim of this work is to evaluate the feasibility of carbosilane dendrimers functionalized with cationic groups to make easier this step. Anionic carbosilane dendrimers (sulphonate- and carboxylate-terminated) have already demonstrated their interaction with proteins and their potential in protein sample preparation. In this work, interactions between positively charged carbosilane dendrimers and different model proteins were studied when working under different pH conditions, dendrimer concentrations, and dendrimer generations. Amino- and trimethylammonium-terminated carbosilane dendrimers presented, in some cases, weak interactions with proteins. Unlike them, carbosilane dendrimers with terminal dimethylamino groups could interact, in many cases, with proteins and these interactions were affected by the pH, the dendrimer concentration, and the dendrimer generation. Moreover, dendrimer precipitation was observed at all pHs, although just second and fourth generation (2 G and 4 G) dendrimers resulted in the formation of complexes with proteins. Under experimental conditions promoting dendrimer-protein interactions, 2 G dimethylamino-terminated dendrimers were proposed as an alternative to other methods used in analytical chemistry or analysis in which an organic solvent or a resin are required to enrich/purify proteins in a complex sample.

Condiciones para el análisis de proteínas del micelio de Lentinula edodes obtenido por fermentación en estado líquido

Lentinula edodes es una seta comestible con potencial para el desarrollo de nutraceúticos. Sin embargo, son incipientes los trabajos enfocados en su producción biotecnológica y el desarrollo de herramientas analíticas que permitan profundizar en su composición. En esta investigación se estudió la producción de biomasa del hongo en el tiempo mediante fermentación en estado líquido y se seleccionaron las condiciones que permiten la obtención de extractos para la aplicación de herramientas para análisis proteómicos. Los métodos de extracción de proteínas, ácido tricloroacético (TCA)-Acetona y TCA-Acetona-Fenol, fueron comparados en términos del rendimiento de extracción y los perfiles de separación usando electroforesis en 1D (SDS-PAGE) y 2D (IEF-SDS PAGE). Se determinó que a los 10 días de crecimiento se obtiene la mayor producción de biomasa y proteína total. La extracción con TCA-Acetona-Fenol presentó un mayor rendimiento, mayor resolución y número de bandas en la electroforesis 1D. En 2DE los dos métodos permitieron la extracción de proteínas con puntos isoeléctricos en el rango de pH 3-10, pero el método TCA-Acetona-Fenol conllevó a una extracción diferencial, favoreciendo el rango de 33 a 113 kDa. Estos resultados se constituyen en una primera aplicación de técnicas de separación electroforética para futuros estudios proteómicos

Comparative proteomic analysis of two sesame genotypes with contrasting salinity tolerance in response to salt stress

Sesame is one of the most important oilseed crops and has high nutritional value. The yield and quality of sesame are severely affected by high salinity in coastal and semi-arid/arid regions. In this study, the phenotypic, physiological, and proteomic changes induced by salt treatment were analyzed in salt-tolerant (G441) and salt-sensitive (G358) seedlings. Phenotypic and physiological results indicated that G441 had an enhanced capacity to withstand salinity stress compared to G358. Proteomic analysis revealed a strong induction of salt-responsive protein species in sesame, mainly related to catalytic, hydrolase, oxidoreductase, and binding activities. Pathway enrichment analysis showed that more salt-responsive proteins in G441 were involved in tyrosine metabolism, carbon fixation in photosynthetic organisms, carbon metabolism, alpha-linolenic acid metabolism, biosynthesis of amino acids, photosynthesis, and glutathione metabolism. Furthermore, G441 displayed unique differentially accumulated proteins in seedlings functioning as heat shock proteins, abscisic acid receptor PYL2-like, calcium-dependent protein kinases, serine/threonine-protein phosphatases, nucleoredoxin, and antioxidant enzymes. Quantitative real-time PCR analysis revealed that some of the proteins were also regulated by salinity stress at the transcript level. Our findings provide important information on salinity responses in plants and may constitute useful resources for enhancing salinity tolerance in sesame. SIGNIFICANCE: Our study identified potential biological pathways and salt-responsive protein species related to transducing stress signals and scavenging reactive oxygen species under salt stress. These findings will provide possible participants/pathways/proteins that contribute to salt tolerance and may serve as the basis for improving salinity tolerance in sesame and other plants.

A Brief Reminder of Systems of Production and Chromatography-Based Recovery of Recombinant Protein Biopharmaceuticals

Recombinant proteins are produced for various applications in laboratory and industrial settings. Among them, therapeutic applications have evolved into a mature field in recent years, affecting the face of contemporary medical treatment. This, in turn, has stimulated an ever-greater need for innovative technologies for the description, expression, and purification of recombinant protein biopharmaceuticals. Therefore, many biopharmaceuticals are synthesized in heterologous systems to obtain satisfactory yields that cannot be provided by natural sources. As more than 35 years has passed since the first recombinant biopharmaceutical (human insulin) successfully completed clinical trials in humans, we provide a brief review of the available prokaryotic and eukaryotic expression systems, listing the advantages and disadvantages of their use. Some examples of therapeutic proteins expressed in heterologous hosts are also provided. Moreover, technologies for the universal extraction of protein molecules are mentioned here, as is the methodology of their purification.

Modified TCA/acetone precipitation of plant proteins for proteomic analysis

Protein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.

Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling

A major challenge in the field of proteomics is obtaining high-quality peptides for comprehensive proteome profiling by LC-MS. Here, evaluation and modification of a range of sample preparation methods using photosynthetically active Arabidopsis leaf tissue are done. It was found that inclusion of filter-aided sample preparation (FASP) based on filter digestion improves all protein extraction methods tested. Ultimately, a detergent-free urea-FASP approach that enables deep and robust quantification of leaf and root proteomes is shown. For example, from 4-day-old leaf tissue, up to 11 690 proteins were profiled from a single sample replicate. This method should be broadly applicable to researchers working with difficult to process plant samples.

Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria

The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis

The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). This optimized protein extraction method will be a significant stride toward seagrass proteome mining and identifying the protein biomarkers to stress response of seagrasses under the scenario of global climate change and anthropogenic perturbations.

Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue

Often plant tissues are recalcitrant and, due to that, methods relying on protein precipitation, such as TCA/acetone precipitation and phenol extraction, are usually the methods of choice for protein extraction in plant proteomic studies. However, the addition of precipitation steps to protein extraction methods may negatively impact protein recovery, due to problems associated with protein re-solubilization. Moreover, we show that when working with non-recalcitrant plant tissues, such as young maize leaves, protein extraction methods with precipitation steps compromise the maintenance of some labile post-translational modifications (PTMs), such as phosphorylation. Therefore, a critical issue when studying PTMs in plant proteins is to ensure that the protein extraction method is the most appropriate, both at qualitative and quantitative levels. In this work, we compared five methods for protein extraction of the C4-photosynthesis related proteins, in the tip of fully expanded third-leaves. These included: TCA/Acetone Precipitation; Phenol Extraction; TCA/Acetone Precipitation followed by Phenol Extraction; direct extraction in Lysis Buffer (a urea-based buffer); and direct extraction in Lysis Buffer followed by Cleanup with a commercial kit. Protein extraction in Lysis Buffer performed better in comparison to the other methods. It gave one of the highest protein yields, good coverage of the extracted proteome and phosphoproteome, high reproducibility, and little protein degradation. This was also the easiest and fastest method, warranting minimal sample handling. We also show that this method is adequate for the successful extraction of key enzymes of the C4-photosynthetic metabolism, such as PEPC, PPDK, PEPCK, and NADP-ME. This was confirmed by MALDI-TOF/TOF MS analysis of excised spots of 2DE analyses of the extracted protein pools. Staining for phosphorylated proteins in 2DE revealed the presence of several phosphorylated isoforms of PEPC, PPDK, and PEPCK.