Linking proteome responses with physiological and biochemical effects in herbicide-exposed Chlamydomonas reinhardtii

Multi-proteomic analyses of 5xFAD mice reveal new molecular signatures of early-stage Alzheimer's disease

An early diagnosis of Alzheimer's disease is crucial as treatment efficacy is limited to the early stages. However, the current diagnostic methods are limited to mid or later stages of disease development owing to the limitations of clinical examinations and amyloid plaque imaging. Therefore, this study aimed to identify molecular signatures including blood plasma extracellular vesicle biomarker proteins associated with Alzheimer's disease to aid early-stage diagnosis. The hippocampus, cortex, and blood plasma extracellular vesicles of 3- and 6-month-old 5xFAD mice were analyzed using quantitative proteomics. Subsequent bioinformatics and biochemical analyses were performed to compare the molecular signatures between wild type and 5xFAD mice across different brain regions and age groups to elucidate disease pathology. There was a unique signature of significantly altered proteins in the hippocampal and cortical proteomes of 3- and 6-month-old mice. The plasma extracellular vesicle proteomes exhibited distinct informatic features compared with the other proteomes. Furthermore, the regulation of several canonical pathways (including phosphatidylinositol 3-kinase/protein kinase B signaling) differed between the hippocampus and cortex. Twelve potential biomarkers for the detection of early-stage Alzheimer's disease were identified and validated using plasma extracellular vesicles from stage-divided patients. Finally, integrin α-IIb, creatine kinase M-type, filamin C, glutamine γ-glutamyltransferase 2, and lysosomal α-mannosidase were selected as distinguishing biomarkers for healthy individuals and early-stage Alzheimer's disease patients using machine learning modeling with approximately 79% accuracy. Our study identified novel early-stage molecular signatures associated with the progression of Alzheimer's disease, thereby providing novel insights into its pathogenesis.

Weed biology and management in the multi-omics era: Progress and perspectives

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

Methyl viologen-induced changes in the Arabidopsis proteome implicate PATELLIN 4 in oxidative stress responses

The photosynthesis-induced accumulation of reactive oxygen species in chloroplasts can lead to oxidative stress, triggering changes in protein synthesis, degradation, and the assembly/disassembly of protein complexes. Using shot-gun proteomics, we identified methyl viologen-induced changes in protein abundance in wild-type Arabidopsis and oxidative stress-hypersensitive fsd1-1 and fsd1-2 knockout mutants, which are deficient in IRON SUPEROXIDE DISMUTASE 1 (FSD1). The levels of proteins that are localized in chloroplasts and the cytoplasm were modified in all lines treated with methyl viologen. Compared with the wild-type, fsd1 mutants showed significant changes in metabolic protein and chloroplast chaperone levels, together with increased ratio of cytoplasmic, peroxisomal, and mitochondrial proteins. Different responses in proteins involved in the disassembly of photosystem II-light harvesting chlorophyll a/b binding proteins were observed. Moreover, the abundance of PATELLIN 4, a phospholipid-binding protein enriched in stomatal lineage, was decreased in response to methyl viologen. Reverse genetic studies using patl4 knockout mutants and a PATELLIN 4 complemented line indicate that PATELLIN 4 affects plant responses to oxidative stress by effects on stomatal closure.

Microalgae-Based Fluorimetric Bioassays for Studying Interferences on Photosynthesis Induced by Environmentally Relevant Concentrations of the Herbicide Diuron

The widespread agricultural use of the phenylurea herbicide Diuron (DCMU) requires the investigation of ecotoxicological risk in freshwater and soil ecosystems in light of potential effects on non-target primary producers and a heavier effect on higher trophic levels. We used microalgae-based fluorimetric bioassays for studying the interferences on the photosynthesis of a freshwater and soil model green microalga (Chlamydomonas reinhardtii) induced by environmentally relevant concentrations of the herbicide DCMU. Measurements of steady-state chlorophyll a (Chl-a) fluorescence emission spectra were performed; as well, the kinetics of the Chl-a fluorescence transient were recorded. Percentage indexes of interference on photosynthesis were calculated after comparison of steady-state and kinetic Chl-a fluorescence measurements of DCMU-exposed and control C. reinhardtii cell suspensions. The results obtained after 30 min exposure to the herbicide DCMU confirmed a significant inhibitory effect of DCMU 2 μg/L, and no significant differences between %ι values for DCMU 0.2 μg/L and 0.02 μg/L exposures. Positive %ε values from kinetic measurements of the Chl-a fluorescence transient confirmed the same interfering effect of 2 μg/L DCMU on PSII photochemistry in the exposed C. reinhardtii cell suspensions. Negative values of %ε observed for 0.2 and 0.02 μg/L DCMU exposures could be attributable to a presumptive ‘stimulatory-like’ effect in the photochemistry of photosynthesis. Short-term exposure to sub-μg/L DCMU concentration (≤0.2 μg/L) affects the photosynthetic process of the model microalga C. reinhardtii. Similar environmental exposures could affect natural communities of unicellular autotrophs, with hardly predictable cascading secondary effects on higher trophic levels.

Proton Leakage Is Sensed by IM30 and Activates IM30-Triggered Membrane Fusion

The inner membrane-associated protein of 30 kDa (IM30) is crucial for the development and maintenance of the thylakoid membrane system in chloroplasts and cyanobacteria. While its exact physiological function still is under debate, it has recently been suggested that IM30 has (at least) a dual function, and the protein is involved in stabilization of the thylakoid membrane as well as in Mg2+-dependent membrane fusion. IM30 binds to negatively charged membrane lipids, preferentially at stressed membrane regions where protons potentially leak out from the thylakoid lumen into the chloroplast stroma or the cyanobacterial cytoplasm, respectively. Here we show in vitro that IM30 membrane binding, as well as membrane fusion, is strongly increased in acidic environments. This enhanced activity involves a rearrangement of the protein structure. We suggest that this acid-induced transition is part of a mechanism that allows IM30 to (i) sense sites of proton leakage at the thylakoid membrane, to (ii) preferentially bind there, and to (iii) seal leaky membrane regions via membrane fusion processes.

Differential toxicity of the UV-filters BP-3 and BP-4 in Chlamydomonas reinhardtii: A flow cytometric approach

Due to the concern about the negative effects of exposure to sunlight, UV-filters are being introduced in all kind of cosmetic formulas. Wastewater treatment plants are not able to remove and/or degrade them; consequently they find their way into rivers, lakes and oceans. These chemicals are acquiring a concerning status due to their increasingly common use and the potential risk for the environment. Benzophenone-3 (BP-3) and Benzophenone-4 (BP-4) are broad-spectrum UV-filters used for the same purpose in personal care products, insecticides and plastic bags; however, after 96 h of exposure to several concentrations of these UV-filters, the growth of C. reinhardtii was more affected by BP-3 than by BP-4, being the 96 h-EC₅₀ for growth 5 mg L^-1 and 38 mg L^-1, respectively. Based on these values Chlamydomonas reinhardtii cultures were exposed during 24 h to 2.5, 5 and 10 mg L^-1 of BP-3 and 19, 38 and 76 mg L^-1 of BP-4. A cytometric panel was carried out to evaluate the effect of sublethal concentrations of these UV-filters, thus several cytotoxicity biomarkers were analysed, including chlorophyll a fluorescence, viability, metabolic activity, oxidative stress, cytoplasmic and mitochondrial membrane potentials, and intracellular pH. BP-3 and BP-4 affect C.reinhardtii cells in a different way, showing differences for three of the examined parameters. Chlorophyll a fluorescence and mitochondrial membrane potential showed a significant increase (p < 0.05) in BP-3 and a significant decrease in BP-4, whereas viability only decreased significantly in the highest concentrations of BP-3. Regarding to the other parameters analysed, a similar pattern of cytotoxicity was observed. Growth rate, vital population and metabolic activity (esterase activity) and intracellular pH decreased significantly and cytoplasmic membrane potential and ROS levels increased significantly in cultures exposed to both pollutants.

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.

Oxidative stress potential of the herbicides bifenox and metribuzin in the microalgae Chlamydomonas reinhardtii

The widespread presence of herbicides in the aquatic environment has raised awareness about the need to develop further in depth ecotoxicological risk assessments, more specifically on potential effects on photosynthetic organisms as microalgae. The majority of the information available regarding the toxicity of herbicides towards microalgae is related to traditional toxicological and regulatory-relevant endpoints such as growth inhibition, leaving a significant gap on knowledge regarding underlying interactions and damage to biological targets. In this context, this study aimed to supplement the general toxicity information of bifenox and metribuzin in the microalgae Chlamydomonas reinhardtii using a battery of selected high-throughput methods. This multiple-endpoint approach included the measurement of formation of reactive oxygen species (ROS), alterations in reduced glutathione (GSH) content, formation of lipid peroxidation (LPO), photosystem II (PSII) performance and loss of photosynthetic pigments after 24 h exposure. Results obtained showed that both herbicides caused a concentration-dependent increase in ROS formation, with bifenox showing higher but less reactive ROS. This increase in ROS production by bifenox and metribuzin was followed by alterations in the antioxidant capacity of algae, oxidative damage in the form of LPO and alterations in pigment content. Furthermore, both herbicides impacted the photosynthetic activity of algae, as seen by alterations in the maximum and effective quantum efficiency of PSII, PSII photochemistry and energy dissipation pathways, impact in the water-splitting apparatus and reduction in the electron transport rate. The inhibitory effect of metribuzin on photosynthetic processes/components was larger than that seen for bifenox. The impact of bifenox and metribuzin in the photosynthetic processes of C. reinhardtii seems to be in close association with the formation of ROS and consequent oxidative stress and damage in algal cells. Overall, this study showed that the high-throughput methods developed could successfully characterise both potential Modes of Action and adverse effects of bifenox and metribuzin in C. reinhardtii.

Discovery of Pyruvate Kinase as a Novel Target of New Fungicide Candidate 3-(4-Methyl-1,2,3-thiadiazolyl)-6-trichloromethyl-[1,2,4]-triazolo-[3,4- b][1,3,4]-thiadizole

Target identification is an essential basis for novel-pesticide development in new molecular design and lead optimization. 3-(4-Methyl-1,2,3-thiadiazolyl)-6-trichloromethyl[1,2,4]triazolo[3,4- b][1,3,4]thiadizole (YZK-C22) is a novel fungicide candidate with specific antifungal activity. We investigated its mode of action, and our studies indicated that YZK-C22 showed no cross resistance against Saccharomyces cerevisiae mutants with classic fungicide targets. Mec1 and Rad53 are two kinases that respond to DNA-replication damage, and the efficacy test showed that YZK-C22 could not perform its fungicidal activity by inhibiting DNA repair. Target screening by drug-affinity-responsive target stability (DARTS) showed that pyruvate kinase (PK), a key enzyme in the glycolytic pathway, was the potent new fungicidal target of YZK-C22. Fifty-eight differentially expressed proteins (DEPs) primarily involved in the metabolic process were identified by isobaric tags for relative and absolute quantification analysis (iTRAQ) in S. cerevisiae, and protein expression in the citrate cycle decreased with treatment of 5 mg/L YZK-C22, which was consistent with the results of DARTS. Molecular-docking analysis further validated that YZK-C22 could dock into the active center of PK instead of phosphoenolpyruvate. The enzyme activity of PK from S. cerevisiae was competitively inhibited with a K_i of 3.33 ± 0.28 μmol/L, and the cell-growth inhibition of S. cerevisiae was released by supplementation with pyruvic acid, whereas the growth of S. cerevisiae was not recovered by adding PK's substrate (phosphoenolpyruvate) or allosteric regulator (fructose-1,6-bisphosphate). The present studies uncovered and validated the primary target of the new, potent fungicidal candidate YZK-C22; our results provide a successful, valuable, and applicable case of target discovery and identification for novel-fungicide development.

An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide

The use of integrative molecular approaches can aid in a comprehensive understanding of the effects of toxicants at different levels of biological organization, also supporting risk assessment. The present study aims to unravel the toxicity mechanisms of a widely used herbicide to the arthropod Folsomia candida exposed in a natural soil, by linking effects on reproduction, proteomics and genome-wide gene expression. The EC50 effects on reproduction over 4 weeks was 4.63 mg glyphosate/kg of soil. The formulation included a polyethoxylated tallowamine as an adjuvant, which at 50% effect on reproduction had an estimated concentration of 0.87-1.49 mg/kg of soil. No effects were observed on survival and reproduction when using the isolated active substance, pointing the toxicity of the formulated product to the co-formulant instead of the active ingredient, glyphosate. RNA sequencing and shotgun proteomics were applied to assess differential transcript and protein expressions between exposed and control organisms in time, respectively. Specific functional categories at protein and transcriptome levels were concordant with each other, despite overall limited correlations between datasets. The exposure to this formulation affected normal cellular respiration and lipid metabolism, inducing oxidative stress and leading to impairment in biological life cycle mechanisms such as molting and reproduction.

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

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

Mode of action characterization for adverse effect of propranolol in Daphnia magna based on behavior and physiology monitoring and metabolite profiling

Studies are underway to gather information about the mode of action (MOA) of emerging pollutants that could guide practical environmental decision making. Previously, we showed that propranolol, an active pharmaceutical ingredient, had adverse effects on Daphnia magna that were similar to its pharmaceutical action. In order to characterize the mode of action of propranolol in D. magna, which is suspected to be organ-specific pharmaceutical action or baseline toxicity, we performed time-series monitoring of behavior along with heart rate measurements and nuclear magnetic resonance (NMR) based metabolite profiling. Principle component analysis (PCA) and hierarchical clustering were used to categorize the mode of action of propranolol among 5 chemicals with different modes of action. The findings showed that the mode of action of propranolol in D. magna is organ-specific and vastly different from those of narcotics, even though metabolite regulation is similar between narcotic and non-narcotic candidates. The method applied in this study seems applicable to rapid characterization of the MOA of other cardiovascular pharmaceutical ingredients.

Transketolase Is Identified as a Target of Herbicidal Substance α-Terthienyl by Proteomics

α-terthienyl is a natural phytotoxin isolated originally from Flaveria bidentis (L.) Kuntze. The bioassay presented here shows the strong herbicidal activity of α-terthienyl on Digitaria sanguinalis, Arabidopsis thaliana and Chlamydomonas reinhardtii. The α-terthienyl-induced response of A. thaliana at the protein level was analyzed at different times. Changes in the protein expression profiles were analyzed by two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry (LC-MS/MS) mass spectrometry. Sixteen protein spots were identified that showed reproducible changes in the expression of at least 2-fold when compared to the control. Among these 16 spots, three were up-regulated and 13 were down-regulated. The decreased expression of several proteins associated with energy production and carbon metabolism suggested that these processes were affected by α-terthienyl. To search for the candidate proteins in this screen, A. thaliana T-DNA mutants of the candidate proteins were used to test their susceptibility to α-terthienyl. Amongst the others, attkl1, a mutant of transketolase, exhibited a significantly lower sensitivity to α-terthienyl when hit compared with Col-0. Based on the identification of the proteins associated with the response to α-terthienyl by proteomics, a candidate target protein transketolase was identified.

Transcriptional and cellular effects of benzotriazole UV stabilizers UV-234 and UV-328 in the freshwater invertebrates Chlamydomonas reinhardtii and Daphnia magna

Benzotriazole ultra violet stabilizers (BZT-UVs) are compounds used in many applications and products to prevent photochemical degradation. Despite their widespread presence in aquatic ecosystems and persistence in the environment, there are very limited data on their effects and toxicity, and their modes of action remain largely unknown. The objectives of the present study were to evaluate the chronic effects of 2 BZT-UVs, 2-(2H-benzotriazol-2-yl)-4,6-bis(1-methyl-1-phenylethyl)phenol (UV-234) and 2-(2H-benzotriazol-2-yl)-4,6-di-tert-pentylphenol (UV-328), on the freshwater green algae Chlamydomonas reinhardtii and the freshwater crustacean Daphnia magna. Organisms were exposed to 0.01 and 10 μg/L of UV-234, UV-328, as well as a mixture of the 2 compounds. Life-history endpoints (viability, reproduction, and growth) and oxidative stress-related biomarkers (gene transcription, reactive oxygen species [ROS] production, and lipid peroxidation) were measured. Daphnia magna growth, reproduction, and gene transcription were not impacted by 21-d individual or mixed exposure. After 96-h of exposure, no differences were observed on the cellular viability of C. reinhardtii for either of the 2 BZT-UVs. In the algae, results showed increased ROS production in response to UV-328 and lipid peroxidation following exposure to UV-234. Synergistic effects of the 2 BZT-UVs were evident at the transcriptional level with 2 to 6 times up-regulation of glutathione peroxidase (gp_x ) in response to the mixture for all treatment conditions. The transcription of superoxide dismutase (sod), catalase (cat), and ascorbic peroxidase (apx) was also regulated by UV-234 and UV-328 in the green algae, most likely as a result of ROS production and lipid peroxidation. Results from the present study suggest potential impacts of UV-234 and UV-328 exposure on the antioxidant defense system in C. reinhardtii. Environ Toxicol Chem 2017;36:3333-3342. © 2017 Crown in the Right of Canada. Published by Wiley Periodicals Inc., on behalf of SETAC.

Oxidative stress in the algae Chlamydomonas reinhardtii exposed to biocides

The toxicity of biocides can be associated with the formation of reactive oxygen species (ROS) and subsequent oxidative damage, interfering with the normal function of photosynthetic organisms. This study investigated the formation and effects of ROS in the unicellular green algae Chlamydomonas reinhardtii exposed to three environmentally relevant biocides, aclonifen, dichlofluanid and triclosan. After a first screening to identify which biocides induced ROS, a 24h multi-endpoint analysis was used to verify the possible consequences. A battery of high-throughput methods was applied in algae for measuring ROS formation, reduced glutathione (GSH), lipid peroxidation (LPO), photosystem (PS) II performance and pigments (chlorophylls a, b and carotenoids). Results show that only aclonifen induced ROS after the first 6h exposure, with the other two biocides not showing any ROS formation. Aclonifen, a Protox and carotenoid inhibitor, induced a concentration-dependent ROS formation, LPO and interfered with algae pigments content, while no alterations were detected in GSH content. A significant effect was also seen in the photosynthetic process, especially a reduction in the maximum and effective quantum yields, accompanied by alterations in energy dissipation in PSII reaction centers and the impairment of the electron transport rate. This study demonstrated the successful use of a battery of high-throughput methods for quickly screening biocides capacity to induce the formation of ROS and the subsequent effects in C. reinhardtii, thus revealing their mode of action (MoA) at concentrations before an impact on growth can become effective.

Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study

Chlamydomonas reinhardtii cells were exposed to a sublethal concentration of the widespread herbicide atrazine for 3h. Physiological cellular parameters, such as chlorophyll a fluorescence and oxidative stress monitored by flow cytometry and pigments levels were altered in microalgal cells exposed to 0.25 μM of atrazine. Furthermore, the effects of this herbicide on C. reinhardtii were explored using "omics" techniques. Transcriptomic analyses, carried out by RNA-Seq technique, displayed 9 differentially expressed genes, related to photosynthesis, between control cultures and atrazine exposed cultures. Proteomic profiles were obtained using iTRAQ tags and MALDI-MS/MS analysis, identifying important changes in the proteome during atrazine stress; 5 proteins related to photosynthesis were downexpressed. The results of these experiments advance the understanding of photosynthetic adjustments that occur during an early herbicide exposure. Inhibition of photosynthesis induced by atrazine toxicity will affect the entire physiological and biochemical states of microalgal cells.

Omics for aquatic ecotoxicology: control of extraneous variability to enhance the analysis of environmental effects

There are multiple sources of biological and technical variation in a typical ecotoxicology study that may not be revealed by traditional endpoints but that become apparent in an omics dataset. As researchers increasingly apply omics technologies to environmental studies, it will be necessary to understand and control the main source(s) of variability to facilitate meaningful interpretation of such data. For instance, can variability in omics studies be addressed by changing the approach to study design and data analysis? Are there statistical methods that can be employed to correctly interpret omics data and make use of unattributed, inherent variability? The present study presents a review of experimental design and statistical considerations applicable to the use of omics methods in systems toxicology studies. In addition to highlighting potential sources that contribute to experimental variability, this review suggests strategies with which to reduce and/or control such variability so as to improve reliability, reproducibility, and ultimately the application of omics data for systems toxicology.

Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns

Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.

Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

Understanding mechanistic and cellular events underlying a toxicological outcome allows the prediction of impact of environmental stressors to organisms living in different habitats. A systems-based approach aids in characterizing molecular events, and thereby the cellular pathways that have been perturbed. However, mapping only adverse outcomes of a toxicant falls short of describing the stress or adaptive response that is mounted to maintain homeostasis on perturbations and may confer resistance to the toxic insult. Silver is a potential threat to aquatic organisms because of the increasing use of silver-based nanomaterials, which release free silver ions. The effects of silver were investigated at the transcriptome, proteome, and cellular levels of Chlamydomonas reinhardtii. The cells instigate a fast transcriptome and proteome response, including perturbations in copper transport system and detoxification mechanisms. Silver causes an initial toxic insult, which leads to a plummeting of ATP and photosynthesis and damage because of oxidative stress. In response, the cells mount a defense response to combat oxidative stress and to eliminate silver via efflux transporters. From the analysis of the perturbations of the cell's functions, we derived a detailed mechanistic understanding of temporal dynamics of toxicity and adaptive response pathways for C. reinhardtii exposed to silver.

Oxidative stress induced by inorganic nanoparticles in bacteria and aquatic microalgae--state of the art and knowledge gaps

Nanotechnology has revolutionised many areas of modern life, technology and research, which is reflected in the steadily increasing global demand for and consumption of engineered nanomaterials and the inevitable increase of their release into the environment by human activity. The overall long-term impact of engineered nanomaterials on ecosystems is still unknown. Various inorganic nanoparticles have been found to exhibit bactericidal properties and cause growth inhibition in model aquatic microalgae, but the mechanisms of toxicity are not yet fully understood. The causal link between particle properties and biological effects or reactive oxygen species generation is not well established and represents the most eminent quest of nanoecotoxicological investigation. In this review, the current mechanistic understanding of the toxicity of inorganic metal and metal oxide engineered nanomaterials towards bacterial and aquatic microalgal model organisms based on the paradigm of oxidative stress is presented along with a detailed compilation of available literature on the major toxicity factors and research methods.

Omics methods for probing the mode of action of natural and synthetic phytotoxins

For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.