Proteomic analysis of cadmium-induced protein profile alterations from marine alga Nannochloropsis oculata

Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity

Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.

Salinization and heavy metal cadmium impair growth but have contrasting effects on defensive colony formation of Scenedesmus obliquus

Driven by anthropogenic activities, freshwater salinization has become an emerging global environmental issue. Recent studies indicate that salinization increases the mobility of heavy metals in soil and causes higher flux into surface waterbodies. The present study assessed the combined effects of salinization (0, 3, 6 PSU) and the heavy metal Cd²⁺ (0, 0.2, 0.4 mg L^-1) on the anti-grazing colony formation and population growth of Scenedesmus obliquus, a common freshwater alga. The results showed that the increase in salinity promoted colony formation of S. obliquus with or without the presence of grazing cues and, in contrast, Cd²⁺ contamination depressed the defensive colony formation of S. obliquus to Daphnia filtrate. The increase in both salinity and Cd²⁺ concentration depressed the population growth of S. obliquus, including impaired photosynthesis and a decreased population growth rate. Salinization moderated the negative effects of Cd²⁺ on defensive colony formation of S. obliquus, suggesting increased absorption of Cd²⁺ ions by a thicker outer layer of the algal cell wall under saltier conditions. As a result, larger defensive colonies of S. obliquus under freshwater salinization may cause higher bioaccumulation of heavy metals by algal cells and heavier influence on zooplankton. This study provides evidence that freshwater salinization could interfere with plankton interactions by affecting algal defense and growth, which may lead to bottom-up cascading effects on freshwater food webs.

Recent advancements in cadmium-microbe interactive relations and their application for environmental remediation: a mechanistic overview

The toxic and persistent nature of cadmium (Cd) in the environment has become a matter of concern with its drastic increase in the concentrations over past few decades. Among the various techniques, the microbial remediation has been accepted as an effective decontamination tool for environmental applications, which is sustainable over a period of time. The Cd decontamination potential of the microbes depends on various internal and external factors that play a crucial role in selection of the microbes for application in a particular environment. Thus, it is important to understand the role of these factors for optimal application of the microbes. This study provides an insight into the mechanisms involved between the microbes and the environmental Cd. The study also briefly reviews the mathematical models that have been used to predict the remediation potential of the microbes and the kinetics involved during the process. A critical analysis of the recent advancements in the techniques for use of bacteria, fungi, and algal cells to remove Cd has been also presented in the manuscript.

Metal stresses modify soluble proteomes and toxin profiles in two Mediterranean strains of the distributed dinoflagellate Alexandrium pacificum

HABs involving Alexandrium pacificum have been reported in metal-contaminated ecosystems, suggesting that this distributed species adapts to and/or can tolerate the effects of metals. Modifications in soluble proteomes and PST contents were characterized in two Mediterranean A. pacificum strains exposed to mono- or polymetallic stresses (zinc, lead, copper, cadmium). These strains were isolated from two anthropized locations: Santa Giusta Lagoon (Italy, SG C10-3) and the Tarragona seaport (Spain, TAR C5-4F). In both strains, metals primarily downregulated key photosynthesis proteins. Metals also upregulated other proteins involved in photosynthesis (PCP in both strains), the oxidative stress response (HSP 60, proteasome and SOD in SG C10-3; HSP 70 in TAR C5-4F), energy metabolism (AdK in TAR C5-4F), neoglucogenesis/glycolysis (GAPDH and PEP synthase in SG C10-3) and protein modification (PP in TAR C5-4F). These proteins, possibly involved in adaptive proteomic responses, may explain the development of these A. pacificum strains in metal-contaminated ecosystems. The two strains showed different proteomic responses to metals, with SG C10-3 upregulating more proteins, particularly PCP. Among the PSTs, regardless of the metal and the strain studied, C2 and GTX4 predominated, followed by GTX5. Under the polymetallic cocktail, (i) total PSTs, C2 and GTX4 reached the highest levels in SG C10-3 only, and (ii) total PSTs, C2, GTX5 and neoSTX were higher in SG C10-3 than in TAR C5-4F, whereas in SG C10-3 under copper stress, total PSTs, GTX5, GTX1 and C1 were higher than in the controls, revealing variability in PST biosynthesis between the two strains. Total PSTs, C2, GTX4 and GTX1 showed significant positive correlations with PCP, indicating that PST production may be positively related to photosynthesis. Our results showed that the A. pacificum strains adapt their proteomic and physiological responses to metals, which may contribute to their ecological success in highly anthropized areas.

Physiological and metabolic responses of Microcystis aeruginosa to a salinity gradient

Microcystis is a well-known toxic cyanobacterium in eutrophic environments, and an increasing number of Microcystis blooms have emerged in salty reservoirs and coastal rivers. This study observed that many Microcystis were identified in a coastal river in June 2020. The relative abundance of Microcystis decreased from 81.2 to 10.2% in the sampling sites from a salinity of 0 (Sal. 0) to a salinity of 12 (Sal. 12). Hepatotoxic microcystins (MCs) were identified in the coastal river and its estuary. Of the samples, those with a salinity of 5 (Sal. 5) had the highest concentration of MCs at 7.81 ± 0.67 μg L^-1. In a saline water simulation experiment, the results showed that salt inhibited Microcystis (M.) aeruginosa growth, enhanced the activity levels of superoxide dismutase (SOD) and catalase (CAT) and stimulated microcystin production. Transcription analysis showed that the expression levels of the psaB and rbcL genes controlling photosymbiotic processes were downregulated, and capD and csaBgene-related polysaccharide productions were upregulated by salt incubation. Notably, metabolism analysis showed that the total polysaccharides, proteins and small molecular matter, such as sucrose, methionine and N-acetyl-D-glucosamine, in the Microcystis cells increased substantially to resist the extracellular hyperosmotic pressure caused by the high salinity levels in culture. These findings indicate that increased salt in a natural aquatic body shifts the phytoplankton community by influencing the physiological metabolism of cyanobacteria and poses a high risk of microcystin exposure during cyanobacterial blooms in coastal rivers.

Development of the "Applied Proteomics" Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana

Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the "omics" approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.

The efficient biomineralization and adsorption of cadmium (Cd2+) using secretory organo-biominerals (SOBs) produced by screened Alcaligenes faecalis K2

Cadmium-contaminated wastewater has attracted increasing concerns due to its non-biodegradable properties and high toxicity. To explore eco-friendly and economically feasible strategies, the screened Alcaligenes faecalis K2 were employed for the biomineralization and recovery of Cd²⁺ from wastewater while producing considerable secretory organo-biominerals (SOBs) as bioadsorbents. At 75 mg/L Cd²⁺ exposure, 85.5% of Cd²⁺ was removed by K2, 43.0% of which was fixed in the granular SOBs. SOBs were convenient for separating from the solution. The adsorption capacity of granular sorbent made from SOBs was verified to be greater than 77.1 mg/g. Practically, 89.5% of 75 mg/L of Cd²⁺ could be stably removed while ereK2 continuously generated SOBs in a moving-bed biofilm reactor (MBBR). To sum up, the production of bioadsorbents can be achieved by K2, while removing Cd with live microorganisms, which was conducive to making full use of materials and improving Cd removal efficiency.

Accumulation and cellular toxicity of engineered metallic nanoparticle in freshwater microalgae: Current status and future challenges

Metal nanoparticles (MNPs) are employed in a variety of medical and non-medical applications. Over the past two decades, there has been substantial research on the impact of metallic nanoparticles on algae and cyanobacteria, which are at the base of aquatic food webs. In this review, the current status of our understanding of mechanisms of uptake and toxicity of MNPs and metal ions released from MNPs after dissolution in the surrounding environment were discussed. Also, the trophic transfer of MNPs in aquatic food webs was analyzed in this review. Approximately all metallic nanoparticles cause toxicity in algae. Predominantly, MNPs are less toxic compared to their corresponding metal ions. There is a sufficient evidence for the trophic transfer of MNPs in aquatic food webs. Internalization of MNPs is indisputable in algae, however, mechanisms of their transmembrane transport are inadequately known. Most of the toxicity studies are carried out with solitary species of MNPs under laboratory conditions rarely found in natural ecosystems. Oxidative stress is the primary toxicity mechanism of MNPs, however, oxidative stress seems a general response predictable to other abiotic stresses. MNP-specific toxicity in an algal cell is yet unknown. Lastly, the mechanism of MNP internalization, toxicity, and excretion in algae needs to be understood carefully for the risk assessment of MNPs to aquatic biota.

Using multiple endpoints to assess the toxicity of cadmium and cobalt for chlorophycean Raphidocelis subcapitata

Metals may cause damage to the biota of contaminated environments. Moreover, using multiple endpoints in ecotoxicological studies is useful to better elucidate the mechanisms of toxicity of these compounds. Therefore, this study aimed to evaluate the effects of cadmium (Cd) and cobalt (Co) on growth, biochemical and photosynthetic parameters of the microalgae Raphidocelis subcapitata, through quantification of lipid classes composition, chlorophyll a (Chl a) content, maximum (Φ_M) and effective (Φ'_M) quantum yields and efficiency of the oxygen-evolving complex (OEC). Both metals affected the algal population growth, with an IC_50-96h of 0.67 and 1.53 μM of Cd and Co, respectively. Moreover, the metals led to an increase in the total lipid content and reduced efficiency of OEC and Φ_M. Cell density was the most sensitive endpoint to detect Cd toxicity after 96 h of treatment. Regarding Co, the photosynthetic parameters were the most affected and the total lipid content was the most sensitive endpoint as it was altered by the exposure to this metal in all concentrations. Cd led to increased contents of the lipid class wax esters (0.89 μM) and phospholipids (PL - at 0.89 and 1.11 μM) and decreased values of triglycerides (at 0.22 μM) and acetone-mobile polar lipids (AMPL - at 0.44 and 1.11 μM). The percentage of free fatty acids (FFA) and PL of microalgae exposed to Co increased, whereas AMPL decreased in all concentrations tested. We were able to detect differences between the toxicity mechanisms of each metal, especially how Co interferes in the microalgae at a biochemical level. Furthermore, to the best of our knowledge, this is the first study reporting Co effects in lipid classes of a freshwater Chlorophyceae. The damage caused by Cd and Co may reach higher trophic levels, causing potential damage to the aquatic communities as microalgae are primary producers and the base of the food chain.

Development of New Antiproliferative Compound against Human Tumor Cells from the Marine Microalgae Nannochloropsis gaditana by Applied Proteomics

Proteomics is a crucial tool for unravelling the molecular dynamics of essential biological processes, becoming a pivotal technique for basic and applied research. Diverse bioinformatic tools are required to manage and explore the huge amount of information obtained from a single proteomics experiment. Thus, functional annotation and protein-protein interactions are evaluated in depth leading to the biological conclusions that best fit the proteomic response in the system under study. To gain insight into potential applications of the identified proteins, a novel approach named "Applied Proteomics" has been developed by comparing the obtained protein information with the existing patents database. The development of massive sequencing technology and mass spectrometry (MS/MS) improvements has allowed the application of proteomics nonmodel microorganisms, which have been deeply described as a novel source of metabolites. Between them, Nannochloropsis gaditana has been pointed out as an alternative source of biomolecules. Recently, our research group has reported the first complete proteome analysis of this microalga, which was analysed using the applied proteomics concept with the identification of 488 proteins with potential industrial applications. To validate our approach, we selected the UCA01 protein from the prohibitin family. The recombinant version of this protein showed antiproliferative activity against two tumor cell lines, Caco2 (colon adenocarcinoma) and HepG-2 (hepatocellular carcinoma), proving that proteome data have been transformed into relevant biotechnological information. From Nannochloropsis gaditana has been developed a new tool against cancer-the protein named UCA01. This protein has selective effects inhibiting the growth of tumor cells, but does not show any effect on control cells. This approach describes the first practical approach to transform proteome information in a potential industrial application, named "applied proteomics". It is based on a novel bioalgorithm, which is able to identify proteins with potential industrial applications. From hundreds of proteins described in the proteome of N. gaditana, the bioalgorithm identified over 400 proteins with potential uses; one of them was selected as UCA01, "in vitro" and its potential was demonstrated against cancer. This approach has great potential, but the applications are potentially numerous and undefined.

Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application

Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.

Can Omics Approaches Improve Microalgal Biofuels under Abiotic Stress?

Microalgae hold the promise of an inexpensive and sustainable source of biofuels. The existing microalgal cultivation technologies need significant improvement to outcompete other biofuel sources such as terrestrial plants. Application of 'algomics' approaches under different abiotic stress conditions could be an effective strategy for optimization of microalgal growth and production of high-quality biofuels. In this review, we discuss the roles of omics in understanding genome structure and biocomponents metabolism in various microalgal species to optimize sustainable biofuel production. Application of individual and integrated omics revealed that genes and metabolic pathways of microalgae have been altered under multiple stress conditions, resulting in an increase in biocomponents, providing a research platform for expansion of genetic engineering studies in microalgal strains.

Lipid extraction from wet Nannochloropsis biomass via enzyme-assisted three phase partitioning

A green and efficient enzyme assisted three phase partitioning (EA-TPP) process was firstly developed to extract microalgal lipids using wet Nannochloropsis sp. biomass. In the pretreatment of microalgal biomass by four hydrolytic enzymes, TPP obtained a higher TFAs lipid extraction efficiency by cellulase compared with the resting enzymes. After optimization by EA-TPP of the wet disrupted Nannochloropsis biomass (3 g), the maximum TFAs extraction yield (90.40%) was attained at 20% ammonium sulphate, 6-7 pH, 1:2 slurry/tert-butanol ratio and 70 °C for 2 h incubation time and two extraction cycles. Moreover, results also revealed that the lipidic species compositions of Nannochloropsis sp. biomass were greatly related with the EA-TPP parameters. In the laboratory scale for wet disrupted microalgae biomass, EA-TPP process achieved 88.70% TFAs extraction yield under the optimized conditions. In all, EA-TPP process could be a promising approach to extract microalgae lipids for food application using wet microalgae biomass.

Improved Algal Toxicity Test System for Robust Omics-Driven Mode-of-Action Discovery in Chlamydomonas reinhardtii

Algae are key components of aquatic food chains. Consequently, they are internationally recognised test species for the environmental safety assessment of chemicals. However, existing algal toxicity test guidelines are not yet optimized to discover molecular modes of action, which require highly-replicated and carefully controlled experiments. Here, we set out to develop a robust, miniaturised and scalable Chlamydomonas reinhardtii toxicity testing approach tailored to meet these demands. We primarily investigated the benefits of synchronised cultures for molecular studies, and of exposure designs that restrict chemical volatilisation yet yield sufficient algal biomass for omics analyses. Flow cytometry and direct-infusion mass spectrometry metabolomics revealed significant and time-resolved changes in sample composition of synchronised cultures. Synchronised cultures in sealed glass vials achieved adequate growth rates at previously unachievably-high inoculation cell densities, with minimal pH drift and negligible chemical loss over 24-h exposures. Algal exposures to a volatile test compound (chlorobenzene) yielded relatively high reproducibility of metabolic phenotypes over experimental repeats. This experimental test system extends existing toxicity testing formats to allow highly-replicated, omics-driven, mode-of-action discovery.

Algal cell response to laboratory-induced cadmium stress: a multimethod approach

We examined the response of algal cells to laboratory-induced cadmium stress in terms of physiological activity, autonomous features (motility and fluorescence), adhesion dynamics, nanomechanical properties, and protein expression by employing a multimethod approach. We develop a methodology based on the generalized mathematical model to predict free cadmium concentrations in culture. We used algal cells of Dunaliella tertiolecta, which are widespread in marine and freshwater systems, as a model organism. Cell adaptation to cadmium stress is manifested through cell shape deterioration, slower motility, and an increase of physiological activity. No significant change in growth dynamics showed how cells adapt to stress by increasing active surface area against toxic cadmium in the culture. It was accompanied by an increase in green fluorescence (most likely associated with cadmium vesicular transport and/or beta-carotene production), while no change was observed in the red endogenous fluorescence (associated with chlorophyll). To maintain the same rate of chlorophyll emission, the cell adaptation response was manifested through increased expression of the identified chlorophyll-binding protein(s) that are important for photosynthesis. Since production of these proteins represents cell defence mechanisms, they may also signal the presence of toxic metal in seawater. Protein expression affects the cell surface properties and, therefore, the dynamics of the adhesion process. Cells behave stiffer under stress with cadmium, and thus, the initial attachment and deformation are slower. Physicochemical and structural characterizations of algal cell surfaces are of key importance to interpret, rationalize, and predict the behaviour and fate of the cell under stress in vivo.

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.

Distinctive protein expression patterns of the strain Brevundimonas sp. ZF12 isolated from the aqueous zone containing high levels of radiation to cadmium-induced stress

In the current study, different protein expression profiles in a strain Brevundimonas sp. ZF12, isolated from the aqueous zone containing high levels of radiation, were characterized following exposure to cadmium (II) using a proteomic strategy. In order to gain a deeper understanding of the cellular events that allow this strain to survive and undergo cadmium adaptation and sorption, the strain was tested under three experimental conditions of 5, 10 and 30 ppm cadmium (II) ions stress. Two-dimensional polyacrylamide gel electrophoresis and mass spectrometry were used to identify the differentially expressed proteins under cadmium (II) stress. 20 differentially expressed spots were successfully identified by MS/MS analysis. These proteins are involved in DNA repair and protection, amino acid metabolism, nucleotide metabolism, energy homeostasis, oxidative stress response, redox homeostasis, protein folding and heat-shock response. The results obviously indicate that the ZF12 strain tends to endure the cadmium (II) stress conditions by modification in many aspects of its cellular physiology and metabolism.

Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions

This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed.

BIOLOGICAL SIGNIFICANCE

This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.

Differential protein profile in zebrafish (Danio rerio) brain under the joint exposure of methyl parathion and cadmium

As different chemicals, methyl parathion (MP) and cadmium (Cd) can induce neurotoxicity on the brain of aquatic ecosystems. This study aims to explore the differential expression proteins in the brain induced by their joint stress and their joint effects, which are poorly reported, and devotes finding novel biomarkers for monitoring their contamination in water and assessing their neurological effects. The bioaccumulation of MP and Cd in tissues after 96 h of exposure was first analyzed by GC and inductively coupled plasma-MS to provide insights into the interaction. Protein profile changes in the brains of the zebrafish (Danio rerio) exposed to MP and Cd were further investigated using the proteomic approach. The correlation of gene expression on the transcription level of mRNA and the translation level of protein was examined by real-time quantitative PCR and Western blotting analysis. It showed that Cd and MP have an interaction on their bioaccumulation, which suggests that their joint effect over 96 h might be antagonistic. Proteomics revealed that 22 protein spots changed their expression levels under stress, of which 16 proteins were identified using MS. These proteins were involved in oxidation/reduction, metabolism, energy production, receptor activity, and cytoskeleton assembly. Among them, five proteins with a remarkable abundance change are significantly suggested to play important roles in the joint effect. This work demonstrates that there exists an interaction between MP and Cd toxicities, which may aid in our understanding of the mechanism of neurotoxicity induced by joint stress. The results may also provide the possibility of the establishment of candidate biomarkers for monitoring MP and Cd contamination in water.

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.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

NUCLEAR MONOPLOIDY AND ASEXUAL PROPAGATION OF NANNOCHLOROPSIS OCEANICA (EUSTIGMATOPHYCEAE) AS REVEALED BY ITS GENOME SEQUENCE(1)

Species in genus Nannochloropsis are promising candidates for both biofuel and biomass production due to their ability to accumulate rich fatty acids and grow fast; however, their sexual reproduction has not been studied. It is clear that the construction of their metabolic pathways, such as that of polyunsaturated fatty acid (PUFA) biosynthesis, and understanding of their biological characteristics, such as nuclear ploidy and reproductive strategy, will certainly facilitate their genetic improvement through gene engineering and mutation and clonal expansion. In this study, the genome of N. oceanica S. Suda et Miyashita was sequenced with the next-generation Illumina GA sequencing technologies. The genome was ∼30 Mb in size, which contained 11,129 protein-encoding genes. Of them, 59.65% were annotated by aligning with those in diverse protein databases, and 29.68% were assigned at least one function described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Less frequent polymorphic nucleotides (one in 22.06 kb) and the obvious deviation from 1:1 (major:minor, minor ≥10) expectation indicated the nuclear monoploidy of N. oceanica. The lack of the majority of meiosis-specific proteins implied the asexual reproduction of this alga. In combination, the nuclear monoploidy and asexual propagation led us to favor the hypothesis that N. oceanica was a premeiotic or ameiotic alga. In addition, sequence similarity-based searching identified the elongase- and desaturase-encoding genes involved in the biosynthesis of long-chain PUFAs, which provided the genetic basis of its rich content of eicosapentaenoic acid (EPA). The functional genes and their metabolic pathways profiled against its genome sequence will facilitate its integrative investigations.

Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga

Biofuels derived from algal lipids represent an opportunity to dramatically impact the global energy demand for transportation fuels. Systems biology analyses of oleaginous algae could greatly accelerate the commercialization of algal-derived biofuels by elucidating the key components involved in lipid productivity and leading to the initiation of hypothesis-driven strain-improvement strategies. However, higher-level systems biology analyses, such as transcriptomics and proteomics, are highly dependent upon available genomic sequence data, and the lack of these data has hindered the pursuit of such analyses for many oleaginous microalgae. In order to examine the triacylglycerol biosynthetic pathway in the unsequenced oleaginous microalga, Chlorella vulgaris, we have established a strategy with which to bypass the necessity for genomic sequence information by using the transcriptome as a guide. Our results indicate an upregulation of both fatty acid and triacylglycerol biosynthetic machinery under oil-accumulating conditions, and demonstrate the utility of a de novo assembled transcriptome as a search model for proteomic analysis of an unsequenced microalga.

Proteomic identification of the differentially expressed proteins in human lung epithelial cells by airborne particulate matter

Exposure to airborne PM₁₀, particulate matter with a median aerodynamic diameter of less than 10 µm, is known to be associated with a number of adverse health effects. To gain a better understanding of the cytotoxic mechanism and to develop protein biomarker candidates for PM₁₀-induced toxicity, proteomic analyses were performed in human lung epithelial cells. Two-dimensional gel electrophoresis (2-DE) was followed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze the proteins differentially expressed by exposure to PM₁₀. Analysis of 2-DE gels revealed more than 1270 protein spots in the cells, of which 36 showed changes of more than 2-fold on exposure to PM₁₀ (up-regulation, n = 6; down-regulation, n = 30). The glycolytic enzyme pyruvate kinase, which also plays a role in tumor metabolism, showed a marked increase in expression, whereas the cytoskeleton-related vinculin and anti-inflammatory annexin 1 showed marked decreases in expression.

Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure

BACKGROUND

Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS.

RESULTS

Dose-dependent molecular response to Pb (II) involved a total of 14 up-regulated and 21 down-regulated proteins. The induction of an isoform of glyceraldehyde 3-phosphate dehydrogenase, alcohol dehydrogenase class V, mRNA splicing factor, ATP-dependent RNA helicase, thioredoxin reductase and actin required a Pb (II) dose of at least 50 μM. Analysis of the proteome dynamics of mid-exponential phase cells of P. chrysosporium subjected to 50 μM lead at exposure time intervals of 1, 2, 4 and 8 h, identified a total of 23 proteins in increased and 67 proteins in decreased amount. Overall, the newly induced/strongly up-regulated proteins involved in (i) amelioration of lipid peroxidation products, (ii) defense against oxidative damage and redox metabolism, (iii) transcription, recombination and DNA repair (iv) a yet unknown function represented by a putative protein.

CONCLUSION

The present study implicated the particular role of the elements of DNA repair, post-tanscriptional regulation and heterotrimeric G protein signaling in response to Pb (II) stress as shown for the first time for a basidiomycete.

Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology

In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.

TWO-DIMENSIONAL GEL ELECTROPHORESIS ANALYSIS OF BROWN ALGAL PROTEIN EXTRACTS(1)

High-quality protein extracts are required for proteomic studies, a field that is poorly developed for marine macroalgae. A reliable phenol extraction protocol using Scytosiphon gracilis Kogame and Ectocarpus siliculosus (Dillwyn) Lyngb. (Phaeophyceae) as algal models resulted in high-quality protein extracts. The performance of the new protocol was tested against four methods available for vascular plants and a seaweed. The protocol, which includes an initial step to remove salts from the algal tissues, allowed the use of highly resolving two-dimensional gel electrophoresis (2-DE) protein analyses, providing the opportunity to unravel potentially novel physiological processes unique to this group of marine organisms.

Proteomic applications in ecotoxicology

Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.

Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity

Seed germination is a complex physiological process in plants that can be affected severely by heavy metals. The interference of germination by cadmium stress has not been well documented at the proteomic level. In the present study, in order to investigate the protein profile alternations during the germination stage following exposure to cadmium, a proteomic approach has been adopted in combination with morphological and physiological parameters. Seeds were exposed with a wide range of cadmium between 0.2 and 1.0 mM. Increases of cadmium concentration in the medium resulted in increased cadmium accumulation in seeds and TBARS content, whereas germination rate, shoot elongation, biomass, and water content were decreased significantly. Temporal changes of the total proteins were investigated by two-dimensional electrophoresis (2-DE). Twenty-one proteins were identified using MALDI-TOF mass spectrometry, which were upregulated at least 1.5-fold in response to cadmium stress. The identified proteins are involved in several processes, including defense and detoxification, antioxidant, protein biosynthesis, and germination processes. The identification of these proteins in the cadmium stress response provides new insight that can lead to a better understanding of the molecular basis of heavy metal responses of seeds at the germination stage.

Data processing and classification analysis of proteomic changes: a case study of oil pollution in the mussel, Mytilus edulis

BACKGROUND

Proteomics may help to detect subtle pollution-related changes, such as responses to mixture pollution at low concentrations, where clear signs of toxicity are absent. The challenges associated with the analysis of large-scale multivariate proteomic datasets have been widely discussed in medical research and biomarker discovery. This concept has been introduced to ecotoxicology only recently, so data processing and classification analysis need to be refined before they can be readily applied in biomarker discovery and monitoring studies.

RESULTS

Data sets obtained from a case study of oil pollution in the Blue mussel were investigated for differential protein expression by retentate chromatography-mass spectrometry and decision tree classification. Different tissues and different settings were used to evaluate classifiers towards their discriminatory power. It was found that, due the intrinsic variability of the data sets, reliable classification of unknown samples could only be achieved on a broad statistical basis (n > 60) with the observed expression changes comprising high statistical significance and sufficient amplitude. The application of stringent criteria to guard against overfitting of the models eventually allowed satisfactory classification for only one of the investigated data sets and settings.

CONCLUSION

Machine learning techniques provide a promising approach to process and extract informative expression signatures from high-dimensional mass-spectrometry data. Even though characterisation of the proteins forming the expression signatures would be ideal, knowledge of the specific proteins is not mandatory for effective class discrimination. This may constitute a new biomarker approach in ecotoxicology, where working with organisms, which do not have sequenced genomes render protein identification by database searching problematic. However, data processing has to be critically evaluated and statistical constraints have to be considered before supervised classification algorithms are employed.

Nuclear translocation and overexpression of GAPDH by the hyper-pressure in retinal ganglion cell

To investigate the effect of hyper-pressure on retinal ganglion cells (RGC-5), RGC-5 cells were exposed to an ambient hydrostatic pressure of 100 mmHg. Upon treatment, the proliferation of RGC-5 cells was inhibited and neuronal apoptosis was detected by specific apoptosis marker TUNEL (terminal deoxynucleotidyl transferase dUTP nick-end labeling). To probe into the mechanism mediating the apoptosis of RGC-5 cells in 100 mmHg, protein profile alterations following hyper-pressure treatment were examined using two-dimensional gel electrophoresis (2-DE) followed by MALDI-TOF. Out of the 400 protein spots of RGC-5 cells detected on 2-DE gels, 37 differentially expressed protein spots were further identified using in gel tryptic digestion and mass spectrometry. Among these proteins, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) was significantly expressed 10 times more in 100 mmHg than in normal pressure. The accumulation of GAPDH in the nucleus and its translocation from the cytosol to the nucleus in 100 mmHg were observed using a microscope. These results suggest that the hyper-pressure-induced apoptosis in RGC-5 cells may be involved with not only the increase of GAPDH expression, but also the accumulation and the translocalization of GAPDH to the nucleus.