Proteomic study of a model causative agent of harmful red tide, Prorocentrum triestinum I: Optimization of sample preparation methodologies for analyzing with two-dimensional electrophoresis

Upregulation of Peridinin-Chlorophyll A-Binding Protein in a Toxic Strain of Prorocentrum hoffmannianum under Normal and Phosphate-Depleted Conditions

Some strains of the dinoflagellate species Prorocentrum hoffmannianum show contrasting ability to produce diarrhetic shellfish poisoning (DSP) toxins. We previously compared the okadaic acid (OA) production level between a highly toxic strain (CCMP2804) and a non-toxic strain (CCMP683) of P. hoffmannianum and revealed that the cellular concentration of OA in CCMP2804 would increase significantly under the depletion of phosphate. To understand the molecular mechanisms, here, we compared and analyzed the proteome changes of both strains growing under normal condition and at phosphate depletion using two-dimensional gel electrophoresis (2-DE). There were 41 and 33 differential protein spots observed under normal condition and phosphate depletion, respectively, of which most were upregulated in CCMP2804 and 22 were common to both conditions. Due to the lack of matched peptide mass fingerprints in the database, de novo peptide sequencing was applied to identify the differentially expressed proteins. Of those upregulated spots in CCMP2804, nearly 60% were identified as peridinin-chlorophyll a-binding protein (PCP), an important light-harvesting protein for photosynthesis in dinoflagellates. We postulated that the high expression of PCP encourages the production of DSP toxins by enhancing the yields of raw materials such as acetate, glycolate and glycine. Other possible mechanisms of toxicity related to PCP might be through triggering the transcription of non-ribosomal peptide synthetase/polyketide synthase genes and the transportation of dinophysistoxin-4 from chloroplast to vacuoles.

Molecular taxonomical identification and phylogenetic relationships of some marine dominant algal species during red tide and harmful algal blooms along Egyptian coasts in the Alexandria region

Harmful algal blooms (HABs) threaten the aquatic ecosystems due to either poisonous effects on living organisms or oxygen-consuming. So HABs' accurate identification, including red tide, is crucial. This study aimed to molecular identification of dominant species during tide period in nine stations along Alexandria region at Egyptian costs during one year. Samples were collected weekly before water discoloration but daily during red tide intensive growth from both 50 cm below the surface and 3 m depth over the bottom from the water surface. The red tide detection was highly from early August to half of September, since its highest peak with a maximum frequency inside the Eastern Harbor. The examined cultures samples isolated during red tide had four dominant species. Peroxidase profile showed an expression pattern of three loci (Px1, Px2, and Px3) in most species. The Px2 was the only heterozygous locus among the three loci in all species. Protein profiling showed that 17 bands out of 65 were specific to the species. The phylogenetic relationships derived from profiles of protein and 18S rRNA gene operon sequences for the four isolated species were mostly similar. We identified the four dominant HABs species as Aplanochytrium sp., Chlamydomonas sp., Cryptophyceae sp., and Psammodictyon sp. based on their 18S rRNA sequences and deposited them at DDBJ/EMBL/GenBank database. Aplanochytrium sp. is recorded as a red tide causative species for the first time in the screened region despite belonging to the defunct fungi.

Omics study of harmful algal blooms in China: Current status, challenges, and future perspectives

In the past two decades, the frequency, scale, and scope of harmful algal blooms (HABs) have increased significantly in the coastal waters of China. HABs have become a major ecological and environmental problem in China that seriously threatens the structure and function of marine ecosystems, the sustainable development of mariculture, and the health of human beings. Much effort has been devoted to studying HABs in China, and great achievements have been made in understanding the oceanographic and ecological mechanisms of HABs as well as the biology and physiological ecology of HAB-causing species. Furthermore, state-of-the-art omics technologies, such as transcriptomics and proteomics, have been used to elucidate the physiological responses of HAB-causing species to environmental changes, the biosynthesis of paralytic shellfish toxin, and the mechanisms underlying the formation of HABs. This review summarizes omics studies of HABs in China over the past few years and discusses challenges and future perspectives of HAB research.

Assessing Protein Synthesis and Degradation Rates in Arabidopsis thaliana Using Amino Acid Analysis

Plants continually synthesize and degrade proteins, for example, to adjust protein content during development or during adaptation to new environments. In order to estimate global protein synthesis and degradation rates in plants, we developed a relatively simple and inexpensive method using a combination of ¹³ CO₂ labeling and mass spectrometry-based analyses. Arabidopsis thaliana plants are subjected to a 24-hr ¹³ CO₂ pulse followed by a 4-day ¹² CO₂ chase. Soluble alanine and serine from total protein and glucose from cell wall material are analyzed by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and their ¹³ C enrichment (%) is estimated. The rate of protein synthesis during the ¹³ CO₂ pulse experiment is defined as the rate of incorporation of labeled amino acids into proteins normalized by a correction factor for incomplete enrichment in free amino acid pools. The rate of protein degradation is estimated as the difference between the rate of protein synthesis and the relative growth rate calculated using the ¹³ C enrichment of glucose from cell wall material. Degradation rates are also estimated from the ¹² CO₂ pulse experiment. The following method description includes setting up and performing labeling experiments, preparation and measurement of samples, and calculation steps. In addition, an R script is provided for the calculations. 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Setting up the ¹³ CO₂ labeling system and stable isotope labeling of Arabidopsis thaliana rosette leaves Basic Protocol 2: Extraction of soluble amino acids for GC-TOF-MS analysis Basic Protocol 3: Preparation of amino acids from total protein for GC-TOF-MS analysis Basic Protocol 4: Preparation of sugars from cell wall material for GC-TOF-MS analysis Basis Protocol 5: GC-TOF-MS analysis of ¹³ C-labeled samples and estimation of ¹³ C enrichment (%) Basis Protocol 6: Estimation of protein synthesis and degradation rates.

Impact of Extraction Method on the Detection of Quality Biomarkers in Normal vs. DFD Meat

The objective of this work was to demonstrate how the extraction method affects the reliability of biomarker detection and how this detection depends on the biomarker location within the cell compartment. Different extraction methods were used to study the sarcoplasmic and myofibrillar fractions of the Longissimus thoracis et lumborum muscle of young bulls of the Asturiana de los Valles breed in two quality grades, standard (Control) or dark, firm, and dry (DFD) meat. Protein extractability and the expression of some of the main meat quality biomarkers—oxidative status (lipoperoxidation (LPO) and catalase activity (CAT)), proteome (SDS-PAGE electrophoretic pattern), and cell stress protein (Hsp70)—were analyzed. In the sarcoplasmic fraction, buffers containing Triton X-100 showed significantly higher protein extractability, LPO, and higher intensity of high-molecular-weight protein bands, whereas the TES buffer was more sensitive to distinguishing differences in the protein pattern between the Control and DFD meat. In the myofibrillar fraction, samples extracted with the lysis buffer showed significantly higher protein extractability, whereas samples extracted with the non-denaturing buffer showed higher results for LPO, CAT, and Hsp70, and higher-intensity bands in the electrophoretic pattern. These findings highlight the need for the careful selection of the extraction method used to analyze the different biomarkers considering their cellular location to adapt the extractive process.

Production of high-quality two-dimensional gel electrophoresis profile for marine medaka samples by using Trizol-based protein extraction approaches

Background

Marine medaka is among the most popular models of fish species for ecotoxicology and environmental research and proteomic studies are useful tools for understanding the molecular responses of medaka upon exposure to different environmental stressors. The preparation of high-quality protein samples is the key to producing high-quality two-dimensional gel electrophoresis (2-DE) results for proteomic analysis. In recent years, Trizol-based protein extraction has been gaining popularity because of its promising performance in producing high-quality 2-DE as well as the convenience of the method.

Methods

Three Trizol-based approaches (Trizol method, Aliquot Trizol method and Trizol method with a commercial clean-up kit) were used to extract proteins from a marine medaka sample and 2-DE profiles were produced. Quality of the 2-DE profiles and effectiveness of the extraction methods were evaluated. For comparison, two common protein extraction methods (lysis buffer method and trichloroacetic acid (TCA)/acetone precipitation extraction) were also applied in parallel to Trizol-based approaches.

Results

Any of the three Trizol-based approaches produced a high-quality 2-DE profile of marine medaka compared with both lysis buffer method and TCA/acetone precipitation extraction. In addition, Trizol method with a commercial clean-up kit produced the best 2-DE profile in terms of background clarity, number of spots and resolution of proteins.

Conclusions

Trizol-based approaches offered better choices than traditional protein extraction methods for 2-DE analysis of marine medaka. The modified version of Trizol method with a commercial clean-up kit was shown to produce the best 2-DE profile.

Interactome Analysis of the Differentially Expressed Proteins in Uterine Leiomyoma

BACKGROUND

Recent advances in proteomics present enormous opportunities to discover proteome related disparities and thus understanding the molecular mechanisms related to a disease. Uterine leiomyoma is a benign monoclonal tumor, located in the pelvic region, and affecting 40% of reproductive aged female.

OBJECTIVE

Identification and characterization of the differentially expressed proteins associated with leiomyogenesis by comparing uterine leiomyoma and normal myometrium.

METHODS

Paired samples of uterine leiomyoma and adjacent myometrium retrieved from twenty-five females suffering from uterine leiomyoma (n=50) were submitted to two-dimensional electrophoresis (2-DE), matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and to reverse transcription polymerase chain reaction (RT-PCR).

RESULTS

Comparison of protein patterns revealed seven proteins with concordantly increased spot intensities in leiomyoma samples. E3 ubiquitin-protein ligase MIB2 (MIB2), Mediator of RNA polymerase II transcription subunit 10 (MED10), HIRA-interacting protein (HIRP3) and Fatty acid binding protein brain (FABP7) were found to be upregulated. While, Biogenesis of lysosome-related organelles complex 1 subunit 2 (BL1S2), Shadow of prion protein (SPRN) and RNA binding motif protein X linked like 2 (RMXL2) were found to be exclusively present in leiomyoma sample. The expression modulations of the corresponding genes were further validated which corroborated with the 2-DE result showing significant upregulation in leiomyoma. We have generated a master network showing the interactions of the experimentally identified proteins with their close neighbors and further scrutinized the network to prioritize the routes leading to cell proliferation and tumorigenesis.

CONCLUSION

This study highlights the importance of identified proteins as potential targets for therapeutic purpose. This work provides an insight into the mechanism underlying the overexpression of the proteins but warrants further investigations.

Methods for Extraction of Muscle Proteins from Meat and Fish Using Denaturing and Nondenaturing Solutions

The objective of the present study was to test two extraction methods including solutions with different ionic strengths on the extraction and separation of the myofibrillar proteins from meat and fish muscles of different species. Meat samples from longissimus thoracis muscle of beef and lamb, pectoralis major muscle of chicken, and dorsal white muscle of fish from sole (Solea solea), European hake (Merluccius merluccius), and sea bass (Dicentrarchus labrax) were analyzed. The extraction method using nondenaturing solution led to a major extraction of high molecular-weight proteins as myosin heavy chain, α-actinin, and desmin; on the contrary, the denaturing method provided a good protein extractability of proteins and fragments with low molecular-weight as actin, troponin-T, tropomyosin, and myosin light chain 1 and 2 proteins for the most meat and fish samples. The nondenaturing extraction method showed several advantages resulting in time and labour saving and in minimizing the use of toxic and polluting agents.

Exploring dinoflagellate biology with high-throughput proteomics

Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation. Not only is the transcriptomic response of dinoflagellates to environmental change generally muted, but there is a markedly low degree of congruency between mRNA expression and protein expression in dinoflagellates. Herein we discuss the application of high-throughput proteomics to the study of dinoflagellate biology. By profiling the cellular protein complement (the proteome) instead of mRNA (the transcriptome), the biomolecular events that underlie the changes of phenotypes can be more readily evaluated, as proteins directly determine the structure and the function of the cell. Recent advances in proteomics have seen this technique become a high-throughput method that is now able to provide a perspective different from the more commonly employed nucleic acid sequencing. We suggest that the time is ripe to exploit these new technologies in addressing the many mysteries of dinoflagellate biology, such as how the symbiotic dinoflagellate inhabiting reef corals acclimate to increases in temperature, as well as how harmful algal blooms are initiated at the sub-cellular level. Furthermore, as dinoflagellates are not the only eukaryotes that demonstrate muted transcriptional responses, the techniques addressed within this review are amenable to a wide array of organisms.

Comparative proteomic studies of a Scrippsiella acuminata bloom with its laboratory-grown culture using a 15N-metabolic labeling approach

Comparative proteomic analysis was carried out using cells isolated from a natural bloom of Scrippsiella acuminata (formerly Scrippsiella trochoidea) in the early bloom (EB) and late bloom (LB) stages as well as with laboratory-grown cultures of cells isolated from the bloom in early growth (EG) and late growth (LG) stages. For quantitative proteomics, LG cells were grown for 20 generations in the presence of ¹⁵N as a reference (i.e. common denominator) for all comparison. In comparisons with early growth laboratory grown cells (EG/LG), nearly 64% of proteins identified had similar abundance levels, with the remaining 36% mostly more abundant in EG cells. Calvin cycle, amino acid metabolism, chlorophyll biosynthesis and transcription/translation were among the up-regulated processes. Cells from the early bloom (EB/LG) had a greater abundance of transporters and enzymes related to light harvesting and oxidative phosphorylation, while the abundance of these proteins decreased in late bloom cells (LB/LG). All natural bloom samples showed either constant or lower abundance levels of enzymes involved in sugar synthesis and glycolytic pathways compared to laboratory grown cells. Our results represent the first examination of the proteomic changes in the development of a natural dinoflagellate bloom. Importantly, our results demonstrate that the proteome of cells grown in the laboratory is distinctively different from cells in a natural bloom.

Isolation and Analysis of Keratins and Keratin-Associated Proteins from Hair and Wool

The presence of highly cross-linked protein networks in hair and wool makes them very difficult substrates for protein extraction, a prerequisite for further protein analysis and characterization. It is therefore imperative that these cross-links formed by disulfide bridges are first disrupted for the efficient extraction of proteins. Chaotropes such as urea are commonly used as efficient extractants. However, a combination of urea and thiourea not only improves recovery of proteins but also results in improved resolution of the keratins in 2DE gels. Reductants also play an important role in protein dissolution. Dithiothreitol effectively removes keratinous material from the cortex, whereas phosphines, like Tris(2-carboxyethyl)phosphine, remove material from the exocuticle. The relative extractability of the keratins and keratin-associated proteins is also dependent on the concentration of chaotropes, reductants, and pH, thus providing a means to preferentially extract these proteins. Ionic liquids such as 1-butyl-3-methylimidazolium chloride (BMIM(+)[Cl](-)) are known to solubilize wool by disrupting noncovalent interactions, specifically intermolecular hydrogen bonds. BMIM(+)[Cl](-) proved to be an effective extractant of wool proteins and complementary in nature to chaotropes such as urea and thiourea for identifying unique peptides of wool proteins using mass spectrometry (MS). Successful identification of proteins resolved by one- or two-dimensional electrophoresis and MS is highly dependent on the optimal recovery of its protease-digested peptides with an efficient removal of interfering substances. The detergent sodium deoxycholate used in conjunction with Empore™ disks improved identification of proteins by mass spectrometry leading to higher percentage sequence coverage, identification of unique peptides and higher score.

Selection of a protein solubilization method suitable for phytopathogenic bacteria: a proteomics approach

Background

Finding the best extraction method of proteins from lysed cells is the key step for detection and identification in all proteomics applications. These are important to complement the knowledge about the mechanisms of interaction between plants and phytopathogens causing major economic losses. To develop an optimized extraction protocol, strains of Acidovorax citrulli, Pectobacterium carotovorum subsp. carotovorum and Ralstonia solanacearum were used as representative cells in the study of phytopathogenic bacteria. This study aims to compare four different protein extraction methods, including: Trizol, Phenol, Centrifugation and Lysis in order to determine which are more suitable for proteomic studies using as parameters the quantity and quality of extracted proteins observed in two-dimensional gels.

Results

The bacteria studied showed different results among the tested methods. The Lysis method was more efficient for P. carotovorum subsp. carotovorum and R. solanacearum phytobacteria, as well as simple and fast, while for A. citrulli, the Centrifugation method was the best. This evaluation is based on results obtained in polyacrylamide gels that presented a greater abundance of spots and clearer and more consistent strips as detected by two-dimensional gels.

Conclusions

These results attest to the adequacy of these proteins extraction methods for proteomic studies.

Marine dinoflagellate proteomics: current status and future perspectives

Dinoflagellates are not only the important primary producers and an essential component of the food chain in the marine ecosystem, but also the major causative species resulting in harmful algal blooms (HABs) and various shellfish poisonings. Although much work has been devoted to the dinoflagellates, our understanding of them is still extremely limited owing to their unusual features. Proteomics, a large-scale study of the structure and function of proteins in complex biological samples, has been introduced to the study of marine dinoflagellates and has shown its powerful potential with regard to revealing their physiological and metabolic characteristics. However, the application of proteomic approaches to unsequenced dinoflagellates is still in its infancy and faces considerable challenges. This review summarizes recent progress in marine dinoflagellate proteomics and discusses the limitations and prospects for this approach to their study.

SCIENTIFIC QUESTION

The dinoflagellates are the major causative agent responsible for harmful algal blooms and paralytic shellfish poisoning around the world. However, our understanding of them is still extremely limited owing to their unusual features, such as large genome size and permanently condensed chromosomes, which impedes the monitoring, mitigation and prevention of HABs.

TECHNICAL SIGNIFICANCE

Proteomics, a large-scale study of the structure and function of proteins in complex biological samples, has been introduced to the study of marine dinoflagellates and has shown its powerful potential with regard to revealing their physiological and metabolic characteristics.

SCIENTIFIC SIGNIFICANCE

This review summarizes recent progress in marine dinoflagellate proteomics with regard to methodology, cell growth, toxin biosynthesis, environmental stress, cell wall and surface, and symbiosis, and discusses the limitations and prospects for this approach to dinoflagellate study. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Copper and cadmium effects on growth and extracellular exudation of the marine toxic dinoflagellate Alexandrium catenella: 3D-fluorescence spectroscopy approach

In this study, metal contamination experiments were conducted to investigate the effects of copper and cadmium on the growth of the marine toxic dinoflagellate Alexandrium catenella and on the production of dissolved organic matter (Dissolved Organic Carbon: DOC; Fluorescent Dissolved Organic Matter: FDOM). This species was exposed to increasing concentrations of Cu(2+) (9.93 × 10(-10)-1.00 × 10(-7)M) or Cd(2+) (1.30 × 10(-8)-4.38 × 10(-7)M), to simulate polluted environments. The drastic effects were observed at pCu(2+)=7.96 (Cu(2+): 1.08 × 10(-8)M) and pCd(2+)=7.28 (Cd(2+): 5.19 × 10(-8)M), where cyst formation occurred. Lower levels of Cu(2+) (pCu(2+)>9.00) and Cd(2+) (pCd(2+)>7.28) had no effect on growth. However, when levels of Cu(2+) and Cd(2+) were beyond 10(-7)M, the growth was totally inhibited. The DOC released per cell (DOC/Cell) was different depending on the exposure time and the metal contamination, with higher DOC/Cell values in response to Cu(2+) and Cd(2+), comparatively to the control. Samples were also analyzed by 3D-fluorescence spectroscopy, using the Parallel Factor Analysis (PARAFAC) algorithm to characterize the FDOM. The PARAFAC analytical treatment revealed four components (C1, C2, C3 and C4) that could be associated with two contributions: one, related to the biological activity; the other, linked to the decomposition of organic matter. The C1 component combined a tryptophan peak and a characteristic humic substances response, and the C2 component was considered as a tryptophan protein fluorophore. The C3 and C4 components were associated to marine organic matter production.

Comparative proteomic analysis reveals proteins putatively involved in toxin biosynthesis in the marine dinoflagellate Alexandrium catenella

Alexandrium is a neurotoxin-producing dinoflagellate genus resulting in paralytic shellfish poisonings around the world. However, little is known about the toxin biosynthesis mechanism in Alexandrium. This study compared protein profiles of A. catenella collected at different toxin biosynthesis stages (non-toxin synthesis, initial toxin synthesis and toxin synthesizing) coupled with the cell cycle, and identified differentially expressed proteins using 2-DE and MALDI-TOF-TOF mass spectrometry. The results showed that toxin biosynthesis of A. catenella occurred within a defined time frame in the G1 phase of the cell cycle. Proteomic analysis indicated that 102 protein spots altered significantly in abundance (P < 0.05), and 53 proteins were identified using database searching. These proteins were involved in a variety of biological processes, i.e., protein modification and biosynthesis, metabolism, cell division, oxidative stress, transport, signal transduction, and translation. Among them, nine proteins with known functions in paralytic shellfish toxin-producing cyanobacteria, i.e., methionine S-adenosyltransferase, chloroplast ferredoxin-NADP+ reductase, S-adenosylhomocysteinase, adenosylhomocysteinase, ornithine carbamoyltransferase, inorganic pyrophosphatase, sulfotransferase (similar to), alcohol dehydrogenase and arginine deiminase, varied significantly at different toxin biosynthesis stages and formed an interaction network, indicating that they might be involved in toxin biosynthesis in A. catenella. This study is the first step in the dissection of the behavior of the A. catenella proteome during different toxin biosynthesis stages and provides new insights into toxin biosynthesis in dinoflagellates.

Marine proteomics: a critical assessment of an emerging technology

The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

Protein expression from zooplankton communities in a metal contaminated NW mediterranean coastal ecosystem

Bidimensional and monodimensional polyacrylamide gel electrophoresis were used to study protein expression from zooplankton collected in thirteen stations of Toulon Bay (NW Mediterranean). In this ecosystem, Little Bay showed higher trace metal concentrations (13.5-23.8 nM for Cu, 0.73-1.24 nM for Pb, 27.8-58.7 nM for Zn) than Large Bay (Cu 2.2-15.6 nM; Pb 0.19-0.78 nM; Zn 9.0-38.8 nM). Trace metals positively correlated (p < 0.05) with expression of four zooplankton proteins (MW in kDa/pI: 25.0/5.6; 48.8/4.1; 38.2/4.4; 38.3/5.8) and with biomass of Oithona nana, predominant copepod in Little Bay. Sequencing by LC-MS/MS putatively provided zooplankton identity of these proteins: they were cytoskeleton actin, except one protein that was the chaperone calreticulin. We suggest that actin and calreticulin could be regarded as zooplankton markers of metal stress and be involved in a possible tolerance of O. nana to contamination, contributing to its development in a marine perturbed ecosystem.

Identification and Characterization of Cell Wall Proteins of a Toxic Dinoflagellate Alexandrium catenella Using 2-D DIGE and MALDI TOF-TOF Mass Spectrometry

The cell wall is an important subcellular component of dinoflagellate cells with regard to various aspects of cell surface-associated ecophysiology, but the full range of cell wall proteins (CWPs) and their functions remain to be elucidated. This study identified and characterized CWPs of a toxic dinoflagellate, Alexandrium catenella, using a combination of 2D fluorescence difference gel electrophoresis (DIGE) and MALDI TOF-TOF mass spectrometry approaches. Using sequential extraction and temperature shock methods, sequentially extracted CWPs and protoplast proteins, respectively, were separated from A. catenella. From the comparison between sequentially extracted CWPs labeled with Cy3 and protoplast proteins labeled with Cy5, 120 CWPs were confidently identified in the 2D DIGE gel. These proteins gave positive identification of protein orthologues in the protein database using de novo sequence analysis and homology-based search. The majority of the prominent CWPs identified were hypothetical or putative proteins with unknown function or no annotation, while cell wall modification enzymes, cell wall structural proteins, transporter/binding proteins, and signaling and defense proteins were tentatively identified in agreement with the expected role of the extracellular matrix in cell physiology. This work represents the first attempt to investigate dinoflagellate CWPs and provides a potential tool for future comprehensive characterization of dinoflagellate CWPs and elucidation of their physiological functions.

Extracellular proteomic analysis for degradation of PAHs in source of drinking water with fusant strains

Extracellular proteomic expressions of two fusant strains were analyzed to observe their abilities to degrade polycyclic aromatic hydrocarbons (PAHs) in the source of drinking water from Yangtze River. The extracellular proteomes for the hybrid strains, Fhhh and Xhhh, and one of their parental strain Phanerochaete chrysosporium were measured by the two-dimensional electrophoresis and MS/MS. The similarity of proteome expression was 34.7% between Fhhh and P. chrysosporium and that was 28.6% between Xhhh and P. chrysosporium. PAHs degeneration performance for Fhhh, Xhhh and the native bacterium NJ2007 was studied by biological activated carbon reactor. The specific degradation rate of Fhhh for PAHs was 3.05 x 10(-5) day(-1) which was significantly higher than that of the NJ2007 and Xhhh (P < 0.05). The results indicate that the fusant strain could not express the same proteome as that of its parental strain but could degrade PAHs in the source water with higher efficiency.

THE UTILITY OF PROTEOMICS IN ALGAL TAXONOMY: BOSTRYCHIA RADICANS/B. MORITZIANA (RHODOMELACEAE, RHODOPHYTA) AS A MODEL STUDY(1)

A comparison of the proteome of eight genetically well-characterized isolates of the Bostrychia radicans (Mont.) Mont./B. moritziana (Sond. ex Kütz.) J. Agardh species complex was undertaken to establish if genetic relationships among them can be determined using proteome data. Genetic distances were calculated on the basis of common and distinct spots in two-dimensional gel electrophoresis (2-DE). Proteomes of the male and female plants of each population were compared to analyze the range of genetic difference within an isolate. Haploid male and female plants of the same species had 3.7%-7.1% sex-specific proteins. The degree of similarity of the proteome was consistent with previous DNA sequence data and sexual compatibility studies between the isolates. Two sexually compatible isolates from Venezuela showed a pair-wise distance ranging from 0.14 to 0.21. The isolates from Mexico and Venezuela, which were partially compatible, showed a maximum pair-wise distance of 0.26. A high level of genetic difference was found among isolates that were sexually incompatible. The isolate from Brazil was reproductively isolated from the Mexico and Venezuela isolates and showed a maximum pair-wise distance of 0.65 and 0.58, respectively. Comparative proteomics may be helpful for studying genetic distances among algal samples, if intraisolate variation (gene expression) can be minimized or tested.

Characterization of cupric glutamate extinguishing mechanism of Alexandrium sp. LC3 with two-dimensional electrophoresis and MALDI-TOF MS

Mechanisms by which cupric glutamate, a novel algicide, extinguishes Alexandrium sp. LC3 are shown in this study. We show that cupric glutamate not only stimulated the production of malonaldehyde (MDA) and dramatically promoted cell plasma membrane permeability (p < 0.01) but also remarkably reduced sulfhydryl (SH) group content (p < 0.01). Analysis of protein expression profiles by two-dimensional electrophoresis (2-DE) indicated that only 47 protein spots were detected in both control and cupric glutamate treated cells. Three reliable spots were identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) as ribulose-bisphosphate carboxylase large subunit precursor, RNA polymerase beta chain, and hypothetical protein, which can be well correlated with cupric glutamate stress. Based on above results, we hypothesize that the extinguishing mechanisms include (1) the cell membrane being damaged by cupric glutamate; (2) cupric glutamate probably induced denaturation and disintegration of intracellular protein, which led to inhibition of cell growth.

Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples

Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.

Sample sonication after trichloroacetic acid precipitation increases protein recovery from cultured hippocampal neurons, and improves resolution and reproducibility in two-dimensional gel electrophoresis

Protein precipitation with TCA followed by acetone washing is frequently used to clean samples before 2-DE. However, the difficulty in solubilizing TCA-precipitated proteins causes some variability in 2-D gels and makes it difficult to detect some proteins. In this work we show that sonication of the samples, after TCA precipitation followed by elution in sample buffer, increases total protein recovery, and improves reproducibility and matching ratios between gels when analyzed by specialized software.

Identification and characterization of a “biomarker of toxicity” from the proteome of the paralytic shellfish toxin-producing dinoflagellateAlexandrium tamarense (Dinophyceae)

The objective of this study was to identify and characterize a "biomarker of toxicity" from the proteome of Alexandrium tamarense, a paralytic shellfish toxin (PST)-producing dinoflagellate. A combination of 2-DE and MS approaches was employed to identify proteins of interest in the vegetative cells of several strains of A. tamarense with different toxin compositions and from different geographical locations. The electrophoretic analysis of the total water-soluble proteins from these toxic strains by 2-DE showed that several abundant proteins, namely AT-T1, AT-T2 and AT-T3, differing slightly in apparent Mr and pIs, were consistently present in all toxic strains of A. tamarense. Further analysis by MALDI-TOF MS and N-terminal amino acid sequencing revealed that they are isoforms of the same protein. Even more intriguing is that these proteins in A. tamarense have similar amino acid sequences and are closely related to a "biomarker of toxicity" previously reported in A. minutum. Unambiguous and highly species-specific identification was later achieved by comparing the PMFs of proteins in these two species. An initial attempt to characterize these proteins by generation of murine polyclonal antibodies against the AT-T1 protein was successful. Western blot analysis using the murine AT-T1-polycolonal antibodies identified all the toxic strains of A. tamarense and A. minutum, but not the nontoxic strain of A. tamarense. These results indicate that these protein characteristics for toxic strains are species-specific and that they are stable properties of the tested algae which are clearly distinguishable irrespective of geographical location and toxin composition. To our knowledge, this is the first study to demonstrate the use of polyclonal antibodies against marker proteins purified from 2-DE gels to distinguish different strains and species of the PST-producing dinoflagellate Alexandrium. It provides the basis for the production of monoclonal antibody probes against the "biomarkers of toxicity" for those dinoflagellates whose genome is incompletely characterized. Potentially, immunoassays could be developed to detect the presence of toxic algae in routine monitoring programs as well as to predict bloom development and movement.

Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803

Proteome analysis by gel-free "shotgun" proteomics relies on the simplification of a peptide mixture before it is analyzed in a mass spectrometer. While separation on a reverse-phase (RP) liquid chromatographic column is widely employed, a variety of other methods have been used to fractionate both proteins and peptides before this step. We compared six different protein and peptide fractionation workflows, using Synechocystis sp. PCC 6803, a useful model cyanobacterium for potential exploitation to improve its production of hydrogen and other secondary metabolites. Pre-digestion protein separation was performed by strip-based isoelectric focusing, one-dimensional polyacrylamide gel electrophoresis, or weak anion exchange chromatography, while pre-RP peptide separation was accomplished by isoelectric focusing (IEF) or strong cation exchange chromatography. Peptides were identified using electrospray ionization quadrupole time of flight-tandem mass spectrometry. Mass spectrometry (MS) and tandem mass spectra were analyzed using ProID software employing both a single organism database and the entire NCBI non-redundant database, and a total of 776 proteins were identified using a stringent set of selection criteria. Method comparisons were made on the basis of the results obtained (number and types of proteins identified), as well as ease of use and other practical aspects. IEF-IEF protein and peptide fractionation prior to RP gave the best overall performance.

Two-dimensional gel electrophoresis characterization of the mouse leukocyte proteome, using a tri-reagent for protein extraction

The use of "tri-reagents" allows the concomitant isolation of DNA, RNA, and proteins for a complete molecular characterization of biological samples. The aim of the current study was to perform the comparative evaluation of two-dimensional gel proteomes isolated with or without a tri-reagent protein extraction step before dissolving the samples in the first-dimension electrophoresis buffer. We conclude that the use of tri-reagents increases the amount of protein extracted from the sample. Furthermore, an average of 301 +/- 3.6 spots were found in gels from both sample preparation methods, whereas 71.7 +/- 8.1 and 49.7 +/- 2.3 spots were uniquely seen in tri-reagent and non-tri-reagent samples, respectively.

Proteomics for protein expression profiling in neuroscience

As the technology of proteomics moves from a theoretical approach to a practical reality, neuroscientists will have to determine the most appropriate applications for this technology. Neuroscientists will have to surmount difficulties particular to their research, such as limited sample amounts, heterogeneous cellular compositions in samples, and the fact that many proteins of interest are rare, hydrophobic proteins. This review examines protein isolation and protein fractionation and separation using two-dimensional electrophoresis (2-DE) and mass spectrometry proteomic methods. Methods for quantifying relative protein expression between samples (e.g., 2-DIGE, and ICAT) are also described. The coverage of the proteome, ability to detect membrane proteins, resource requirements, and quantitative reliability of different approaches is also discussed. Although there are many challenges in proteomic neuroscience, this field promises many rewards in the future.

Use of two-dimensional gel electrophoresis proteome reference maps of dinoflagellates for species recognition of causative agents of harmful algal blooms

The sample preparation procedures established for Prorocentrum triestinum were adapted to cover both thecate and athecate dinoflagellates. Further, whether trichloroacetic acid (TCA) precipitation can be used to fix and preserve the harmful or nuisance species from local waters that they infest was tested. Optimized technical procedures developed were used to generate proteome reference maps for eight other local causative species of harmful algal blooms (HABs): Prorocentrum micans, Prorocentrum minimum, Prorocentrum sigmoides, Prorocentrum dentatum, Scrippsiella trochoidea, Karenia longicanalis, Karenia digitata and Karenia mikimotoi; together with one American species Karenia brevis (Florida, USA). These proteome maps were used to test their ability for species recognition in a mixed culture of dinoflagellates and whether such investigations will provide a comparative view at a global level. Comparisons of proteome profiles were made (i). between closely related species within the same family; (ii). between distantly related species belonging to different types, i.e., gymnodinioids, prorocentroids or peridinioids, or (iii). between different groups, i.e., thecate (armored) dinoflagellate cells against athecate (naked or unarmored) dinoflagellate cells. Species-specific two-dimensional electrophoresis (2-DE) protein profiles were observed in all ten species and it was possible to distinguish between even closely related species within the same family. To demonstrate the extent of reproducibility and usefulness of these 2-DE reference maps, 2-DE has been used to analyze three geographically distinct isolates of Prorocentrum dentatum, and to distinguish species composition in a mixed culture. Application of 2-D PAGE analysis to differentiate between taxonomically confused strains of a single species could be a powerful taxonomic tool.