Proteomic and metabolomic analysis on the toxicological effects of As (III) and As (V) in juvenile mussel Mytilus galloprovincialis

Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

Survival strategies in arsenic-contaminated environments: Comparative insights from native and exotic aquatic species

The aim of this work was to study the sublethal effects, biokinetics, subcellular partitioning and detoxification of arsenic in two native Chinses species, Bellamya quadrata and Cipangopaludina cathayensis, as well as an exotic South American species, Pomacea canaliculata. The exotic species exhibited higher tolerance than native species. Physiologically based pharmacokinetic model results showed that the exotic species P. canaliculata exhibited a lower bioaccumulation rate and a greater metabolism capacity of As. Subcellular partitioning of As revealed that P. canaliculata exhibits superior As tolerance compared to the native species B. quadrata and C. cathayensis. This is attributed to P. canaliculata effective management of the metal sensitive fraction and enhanced accumulation of As in the biologically detoxified metal fraction. Under As stress, the biochemical parameters (superoxide dismutase, malondialdehyde, glutathione and glutathione S-transferase) of the exotic species P. canaliculata changed less in the native species, and they returned to normal levels at the end of depuration period. Our study provides evidence of the superior survival capability of the exotic species P. canaliculata compared to the native species B. quadrata and C. cathayensis under environmentally relevant levels of As contamination.

Analyze the toxicities of benzalkonium chloride as a COVID-19 disinfectant in physiological goldfish (Carassius auratus)

Background and Aims

Coronavirus disease-2019 (COVID-19) impacts increasing the use of disinfectants (benzalkonium chloride), which indirectly accumulate in water. The disinfectant accumulation in waters has been studied, but there has been no study of its impact on aquatic commodities, especially fish with a high sensitivity, one of which is goldfish (Carassius auratus). Benzalkonium chloride can potentially affect several body proteins, including the cytoskeleton, nervous and endocrine systems, and fish physiology. This study aimed to determine the impact of benzalkonium chloride as a disinfectant on the level of color brightness, growth, gill histopathology, and mortality in goldfish. This investigation provides input into the impact of using disinfectants to prevent COVID-19 on aquatic commodities.

Materials and Methods

This study utilized goldfish specimens sourced from Tulungagung, East Java, Indonesia. The experiment involved different concentration levels of benzalkonium chloride: (T1) 0 mg/L, (T2) 0.03 mg/L, (T3) 0.06 mg/L, (T4) 0.09 mg/L, and (T5) 0.12 mg/L. The research data were subjected to an analysis of variance for analysis. In cases where significant differences were observed, Duncan's test was conducted for color brightness, growth, and mortality data. Furthermore, if the gill histopathological data yielded significant differences, additional tests were applied (Kruskal-Wallis and Mann-Whitney test).

Results

The findings of this study demonstrated significant differences (p < 0.05) in the level of color brightness, growth, gill histopathology, and mortality in goldfish in response to varying concentrations of benzalkonium chloride. The relationship between the length and weight of the goldfish was analyzed using regression coefficients (b values), which were determined as 4.86, -0.04, -0.2, 0.8, and -0.07, respectively. Notably, the brightness level in the T2 group exhibited positive color results with a hue value of 11.55°, while optimal growth was observed in the T4 group, as evidenced by b value of 0.8. The gill histopathological data showed significant differences (p < 0.05). The scoring of histopathological damage in the goldfish gills ranged from 0 to 10, with higher scores indicating more severe damage. The highest total score of 10 was observed in the T5 group exposed to a concentration of 0.12 mg/L, resulting in an 85% mortality rate. This indicates that benzalkonium chloride, with its toxic compounds, can disrupt the respiratory system of fish and lead to death.

Conclusion

The effects of benzalkonium chloride were evident even at a concentration of 0.03 mg/L. With increasing concentration, there was an increase in mortality rate, a decrease in growth, and a rise in histopathological damage to the gills. These findings highlight the negative impact of using conventional disinfectants on water and its organisms, emphasizing the need for further research on environmentally friendly alternatives.

Structural and evolutionary insights into astacin metallopeptidases

The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.

Analyzing toxicological effects of AsIII and AsV to Chlamys farreri by integrating transcriptomic and metabolomic approaches

Inorganic arsenic (iAs) is a widespread contaminant in marine environments, which is present in two different oxidation states (arsenate (AsV) and arsenite (AsIII)) that have complex toxic effects on marine organisms. The scallop Chlamys farreri (C. farreri) accumulates high levels of As and is a suitable bioindicator of As. In this report, we integrated transcriptomics and metabolomics to investigate genetic and metabolite changes and functional physiological disturbances in C. farreri exposured to inorganic arsenic. Physiological indicators antioxidant factors and cell apoptosis analysis macroscopically corroborated the toxic effects of inorganic arsenic revealed by omics results. Toxic effects of inorganic arsenic on C. farreri were signaling-mediated, causing interference with a variety of cell growth and small molecule metabolism. The results provide evidence that inorganic arsenic disrupts the physiological functions of bivalves, highlighting the correlations between different metabolic pathways and providing new insights into the toxic effects of environmental pollutants on marine organisms.

The draft genome and multi-omics analyses reveal new insights into geo-herbalism properties of Citrus grandis 'Tomentosa'

Citrus grandis 'Tomentosa' (CGT) (Huajuhong, HJH) is a widely used medicinal plant, which is mainly produced in Guangdong and Guangxi provinces of South China. Particularly, HJH from Huazhou (HZ) county of Guangdong province has been well-regarded as the best national product for geo-herbalism. But the reasons for geo-herbalism property in HJH from HZ county remains a mystery. Therefore, a multi-omics approach was applied to identify the nature of the geo-herbalism in CGT from three different regions. The comprehensive screening of differential metabolites revealed that the Nobiletin content was significantly different in HZ region compared to other regions, and could be employed as a key indicator to determine the geo-herbalism. Furthermore, the high-quality genome (N50 of 9.12 Mb), coupled with genomics and transcriptomics analyses indicated that CGT and Citrus grandis are closely related, with a predicted divergence time of 19.1 million years ago (MYA), and no recent WGD occurred in the CGT, and the bioactive ingredients of CGT were more abundant than that of Citrus grandis. Interestingly, Nobiletin (Polymethoxyflavones) content was identified as a potential indicator of geo-herbalism, and O-methyltransferase (OMT) genes are involved in the synthesis of Polymethoxyflavones. Further multi-omics analysis led to the identification of a novel OMT gene (CtgOMT1) whose transient overexpression displayed significantly higher Nobiletin content, suggesting that CtgOMT1 was involved in the synthesis of Nobiletin. Overall, our findings provide new data resources for geo-herbalism evaluation, germplasm conservation and insights into Nobiletin biosynthesis pathways for the medicinal plant C. grandis 'Tomentosa'.

Metabolomics as a valid analytical technique in environmental exposure research: application and progress

BACKGROUND

In recent years, studies have shown that exposure to environmental pollutants (e.g., radiation, heavy metal substances, air pollutants, organic pollutants) is a leading cause of human non-communicable diseases. The key to disease prevention is to clarify the harmful mechanisms and toxic effects of environmental pollutants on the body. Metabolomics is a high-sensitivity, high-throughput omics technology that can obtain detailed metabolite information of an organism. It is a crucial tool for gaining a comprehensive understanding of the pathway network regulation mechanism of the organism. Its application is widespread in many research fields such as environmental exposure assessment, medicine, systems biology, and biomarker discovery.

AIM OF REVIEW

Recent findings show that metabolomics can be used to obtain molecular snapshots of organisms after environmental exposure, to help understand the interaction between environmental exposure and organisms, and to identify potential biomarkers and biological mechanisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review focuses on the application of metabolomics to understand the biological effects of radiation, heavy metals, air pollution, and persistent organic pollutants exposure, and examines some potential biomarkers and toxicity mechanisms.

Finding Biomarkers in Antioxidant Molecular Mechanisms for Ensuring Food Safety of Bivalves Threatened by Marine Pollution

Aquaculture production as an important source of protein for our diet is sure to continue in the coming years. However, marine pollution will also likely give rise to serious problems for the food safety of molluscs. Seafood is widely recognized for its high nutritional value in our diet, leading to major health benefits. However, the threat of marine pollution including heavy metals, persistent organic pollutants and other emerging pollutants is of ever-growing importance and seafood safety may not be guaranteed. New approaches for the search of biomarkers would help us to monitor pollutants and move towards a more global point of view; protocols for the aquaculture industry would also be improved. Rapid and accurate detection of food safety problems in bivalves could be carried out easily by protein biomarkers. Hence, proteomic technologies could be considered as a useful tool for the discovery of protein biomarkers as a first step to improve the protocols of seafood safety. It has been demonstrated that marine pollutants are altering the bivalve proteome, affecting many biological processes and molecular functions. The main response mechanism of bivalves in a polluted marine environment is based on the antioxidant defense system against oxidative stress. All these proteomic data provided from the literature suggest that alterations in oxidative stress due to marine pollution are closely linked to robust and confident biomarkers for seafood safety.

Ingestion of nano/micro plastic particles by the mussel Mytilus coruscus is size dependent

Plastic particles are thought to accumulate in aquatic organisms and cause potential physiological effects. The uneven sizes of plastic particles may affect the ingestion by marine filter feeding bivalves and may lead to differential further physiological effects. To tackle this scientific question, we investigated the size dependent ingestion and dynamic accumulation of nano/micro plastic particles with different diameters (0.07, 0.5, 5, 10 and 100 μm) in the thick shell mussel Mytilus coruscus. The accumulation of particles in gill, digestive tract and mantle of mussels was measured after 3, 15, 87 h exposure and following 87 h depuration. The results showed that particle ingestion was negatively size dependant and positively related to time in digestive tract. In mantle, particles accumulated over the depuration time with a delay, indicating the translocation of particles. Moreover, our results showed that gill was not a target tissue for steady particle accumulation but the digestive tract was. This study showed size dependent and dynamic ingestion of nano/micro particles in mussels which are one of the main marine organisms for accumulating microplastics.

A new perspective on the toxicity of arsenic-contaminated soil: Tandem mass tag proteomics and metabolomics in earthworms

The toxicity of low-level arsenic (As)-contaminated soil is not well understood. An integrated proteomic and metabolomic approach combined with morphological examination was used to investigate the potential biological toxicity of As-contaminated soil based on an exposure experiment with the earthworm Eisenia fetida. The results showed that the earthworm hindgut accumulated high As concentrations resulting in injury to the intestinal epithelia, chloragogenous tissues and coelom tissues. Furthermore, As-contaminated soil induced a significant increase in betaine levels and a decrease in dimethylglycine and myo-inositol levels in the earthworms, suggesting that the osmoregulatory metabolism of the earthworms may have been disturbed. The significantly altered levels of asparagine and dimethylglycine were proposed as potential biomarkers of As-contaminated soil. The upregulation of soluble calcium-binding proteins and profilin, the downregulation of sodium/potassium-transporting ATPase, and the proteins changes identified by gene ontology enrichment analysis confirmed that the earthworms suffered from osmotic stress. In addition, the significant changes in glycine-tRNA ligase activity and coelomic tissue injury revealed that As accumulation may disturb the earthworm immune system. This work provided new insight into the proteomic and metabolic toxicity of low-level As-contaminated soil ecosystems in earthworms, extended our knowledge of dual omics and highlighted the mechanisms underlying toxicity.

Proteomic analysis of whole-body responses in medaka (Oryzias latipes) exposed to benzalkonium chloride

Benzalkonium chloride (BAC) is a cationic surfactant commonly used as a disinfectant, and is discharged into the aquatic environment by various water sources such as wastewater. BAC may also interact with potentially toxic substances such as persistent organic chemicals. Although studies of BAC contamination toxicity and bioaccumulation have been widely reported, the biochemical responses to BAC toxicity remain incompletely understood, and the detailed molecular mechanisms are largely unknown. In this study, two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry-based proteomic approaches were applied to investigate the protein profiles in Oryzias latipes (medaka) chronically exposed to BAC. Fish were exposed to three different concentrations of BAC, 0.05, 0.1, and 0.2 mg/L, for 21 days. A total of 20 proteins involved in the cytoskeleton, the oxidative stress response, the nervous and endocrine systems, signaling pathways, and cellular proteolysis were significantly upregulated by BAC exposure. The proteomic information obtained in the present study will be useful in identification of potential biomarkers for BAC toxicity, and begins to elucidate its molecular mechanisms, providing new insights into the ecotoxicity of BAC.

Profiling of microRNAs and mRNAs in marine mussel Mytilus galloprovincialis

MicroRNAs (miRNAs) are a class of noncoding RNA molecules containing 18-24 nucleotides, and those with conserved structures are able to regulate the expression of eukaryotic genes by inhibition or enhancement of mRNA translation. However, miRNAs of the blue mussel, Mytilus galloprovincialis have not been reported. M. galloprovincialis is a primary species distributed along coastal zones worldwide. To reveal the repertoire of miRNAs in M. galloprovincialis, we constructed small RNA libraries prepared from three different mussels, which were then sequenced by Solexa deep sequencing technology. A total of 32,836,817, 33,359,113 and 33,093,562 clean reads from the tissues of the three M. galloprovincialis were obtained. Based on sequence similarities and hairpin structure predictions, 137 M. galloprovincialis miRNAs (mg-miRNA) were identified. Among the mg-miRNAs, 104 were conserved across species, whereas 33 might be novel and specific for M. galloprovincialis. Some of the mg-miRNAs, such as let-7 and the miR-100 family are playing key roles in many metabolic pathways and are worthy of further study. By performing a whole genome-scale characterization of mg-miRNAs and proposing their potential functions, these results provide a foundation for understanding the biological processes of the blue mussel, M. galloprovincialis.

Toxicological effects of As (V) in juvenile rockfish Sebastes schlegelii by a combined metabolomic and proteomic approach

Arsenic (As) is a metalloid element that is ubiquitous in the marine environment and its contamination has received worldwide attention due to its potential toxicity. Arsenic can induce multiple adverse effects, such as lipid metabolism disorder, immune system dysfunction, oxidative stress and carcinogenesis, in animals. Inorganic arsenic includes two chemical forms, arsenite (As (III)) and arsenate (As (V)), in natural environment. As (V) is the dominant form in natural waters. In the present study, metabolomic and proteomic alterations were investigated in juvenile rockfish Sebastes schlegelii exposed to environmentally relevant concentrations of As (V) for 14 d. The analysis of iTRAQ-based proteomics combined with untargeted NMR-based metabolomics indicated apparent toxicological effects induced by As (V) in juvenile rockfish. In details, the metabolites, including lactate, alanine, ATP, inosine and phosphocholine were significantly altered in As-treated groups. Proteomic responses suggested that As (V) could not only affected energy and primary metabolisms and signal transduction, but also influenced cytoskeleton structure in juvenile rockfish. This work suggested that the combined proteomic and metabolomic approach could shed light on the toxicological effects of pollutants in rockfish S. schlegelii.

Changes in protein expression in mussels Mytilus galloprovincialis dietarily exposed to PVP/PEI coated silver nanoparticles at different seasons

Potential toxic effects of Ag NPs ingested through the food web and depending on the season have not been addressed in marine bivalves. This work aimed to assess differences in protein expression in the digestive gland of female mussels after dietary exposure to Ag NPs in autumn and spring. Mussels were fed daily with microalgae previously exposed for 24 h to 10 μg/L of PVP/PEI coated 5 nm Ag NPs. After 21 days, mussels significantly accumulated Ag in both seasons and Ag NPs were found within digestive gland cells and gills. Two-dimensional electrophoresis distinguished 104 differentially expressed protein spots in autumn and 142 in spring. Among them, chitinase like protein-3, partial and glyceraldehyde-3-phosphate dehydrogenase, that are involved in amino sugar and nucleotide sugar metabolism, carbon metabolism, glycolysis/gluconeogenesis and the biosynthesis of amino acids KEGG pathways, were overexpressed in autumn but underexpressed in spring. In autumn, pyruvate metabolism, citrate cycle, cysteine and methionine metabolism and glyoxylate and dicarboxylate metabolism were altered, while in spring, proteins related to the formation of phagosomes and hydrogen peroxide metabolism were differentially expressed. Overall, protein expression signatures depended on season and Ag NPs exposure, suggesting that season significantly influences responses of mussels to NP exposure.

Protein expression profiles in Bathymodiolus azoricus exposed to cadmium

Proteomic changes in the "gill-bacteria complex" of the hydrothermal vent mussel B. azoricus exposed to cadmium in pressurized chambers ((Incubateurs Pressurises pour l'Observation en Culture d'Animaux Marins Profonds - IPOCAMP) were analyzed and compared with the non-exposed control group. 2-D Fluorescence Difference Gel Electrophoresis (2D-DIGE) showed that less than 1.5% of the proteome of mussels and symbiotic bacteria were affected by a short-term (24 h) Cd exposure. Twelve proteins of the more abundant differentially expressed proteins of which six were up-regulated and six were down-regulated were excised, digested and identified by mass spectrometry. The identified proteins included structural proteins (actin/actin like proteins), metabolic proteins (calreticulin/calnexin, peptidyl-prolyl cis-trans isomerase, aminotransferase class-III, electron transfer flavoprotein, proteasome, alpha-subunit and carbonic anhydrase) and stress response proteins (chaperone protein htpG, selenium-binding protein and glutathione transferases). All differently expressed proteins are tightly connected to Cd exposure and are affected by oxidative stress. It was also demonstrated that B. azoricus was well adapted to Cd contamination therefore B. azoricus from hydrothermal vent areas may be considered a good bioindicator.

An integrated metabolomic and proteomic study of toxic effects of Benzo[a]pyrene on gills of the pearl oyster Pinctada martensii

Benzo[a]pyrene (BaP) is one of the most important polycyclic aromatic hydrocarbons (PAHs), which are widely present in the marine environment. Because of its teratogenic, mutagenic, and carcinogenic effects on various organisms, the toxicity of BaP is of great concern. In this study, we focused on the toxic effects of BaP (1 µg/L and 10 µg/L) on gills of the pearl oyster Pinctada martensii using combined metabolomic and proteomic approaches. At the metabolome level, the high concentration of BaP mainly caused abnormal energy metabolism, osmotic regulation and immune response marked by significantly altered metabolites in gills. At the proteome level, both concentrations of BaP mainly induced signal transduction, transcription regulation, cell growth, stress response, and energy metabolism. Overall, the research demonstrated that the combination of proteomic and metabolomic approaches could provide a significant way to elucidate toxic effects of BaP on P. martensii.

Biochemical responses and accumulation patterns of Mytilus galloprovincialis exposed to thermal stress and Arsenic contamination

Organisms in marine systems are exposed to multiple stressors that create a range of associated environmental and ecotoxicological risks. Examples of stressors include alterations related to climate change, such as temperature increase, and the exposure to pollutants arising from human activities. The present study evaluated the impacts of Arsenic exposure (1mg/L) and warming (21°C) in Mytilus galloprovincialis, acting alone and in combination. Our results demonstrated that both Arsenic exposure and warming induced oxidative stress and reduced mussels metabolism, with changes becoming more prominent with the exposure time and when mussels were exposed to both stressors in combination. Furthermore, results obtained showed higher As accumulation in organisms exposed to warming treatments. The present study showed that under warming scenarios, the negative impacts induced by As may be enhanced in ecologically and economically relevant bivalves, with potential impacts on population stocks due to increased sensitivity to pollutants, which may eventually result in biodiversity loss and socio-economic impacts.

Toxic metals biomonitoring based on prey-predator interactions and environmental forensics techniques: A study at the Romanian-Ukraine cross border of the Black Sea

Marine cross-border areas are ideal for monitoring pollutants so as to increase ecosystems protection. This study was conducted at the Romanian-Ukraine border of the Black Sea to reveal evidence of contamination with toxic metals based on biomonitoring of: cadmium, lead, total chromium, nickel and copper at different water depths and prey-predator interactions, combined with environmental forensics techniques of biological sampling and separation in witnesses size groups. The species used were Mytilus galloprovincialis L. and Rapana venosa V. collected at 17.5m, 28m and 35m depth. An atomic absorption spectrometer with a high-resolution continuum source and graphite furnace was used for toxic metals quantification in various samples: sediments, soft tissue, stomach content, muscular leg, hepatopancreas. The best sample type, based on the pathology of metal location and bioaccumulation, is the hepatopancreas from R. venosa that proved a significant decrease of cadmium and lead at lower depths.

The impacts of As accumulation under different pH levels: Comparing Ruditapes decussatus and Ruditapes philippinarum biochemical performance

Marine bivalves have been used to assess environmental As contamination and the effects of seawater acidification when both factors are acting alone, but limited information is available regarding the impacts of both factors acting in combination. The aim of this study was to compare physiological (glycogen) and biochemical (lipid peroxidation, superoxide dismutase, catalase, glutathione-S-transferase and alkaline phosphatase) responses in both native (Ruditapes decussatus) and introduced (R. philippinarum) clams, when exposed to the combined effects of pH (7.8, control; 7.3) and As concentrations (0 and 4mg/L). The combined effect of As and pH on the health risks associated with clam consumption was also analyzed. Results revealed that both species were able to accumulate As under both pH levels, although higher As concentrations where observed under low pH. Thus, predicted pH decrease will potentiate health risks associated with the consumption of such species, since less amount of clams exposed to As is needed for an adult to exceed the provisional tolerable weekly intake (PTWI). Low pH, As exposure and the combination of both factors did not negatively affect the native species, since clams were able to maintain their physiological and biochemical performance among all conditions. On the other hand, R. philippinarum was negatively affected by As exposure at control pH (7.8), inducing biotransformation and antioxidant defense mechanisms against As toxicity. R. philippinarum exposed and non-exposed to As presented similar responses under low pH although at this condition the introduced species accumulated twice the amount of As than R. decussatus.