A comparative proteomic study on the effects of metal pollution in oysters Crassostrea hongkongensis

Transcriptomic investigation and biomarker discovery for zinc response in oysters Crassostrea gasar

In an era of unprecedented industrial and agricultural growth, metal contamination in marine environments is a pressing concern. Sentinel organisms such as the mangrove oyster Crassostrea gasar provide valuable insights into these environments' health. However, a comprehensive understanding of the molecular mechanisms underlying their response to metal exposure remains elusive. To address this gap, we reanalyzed the 454-sequencing data of C. gasar, utilizing an array of bioinformatics workflow of CDTA (Combined De Novo Transcriptome Assembly) to generate a more representative assembly. In parallel, C. gasar individuals were exposed to two concentrations of zinc (850 and 4500 μg L-1 Zn) for 48 h to understand their molecular responses. We utilized Trinotate workflow for the 11,684-CDTA unigenes annotation, with most transcripts aligning with the genus Crassostrea. Our analysis indicated that 67.3% of transcript sequences showed homology with Pfam, while 51.4% and 54.5%, respectively had GO and KO terms annotated. We identified potential metal pollution biomarkers, focusing on metal-related genes, such as those related to the GSH biosynthesis (CHAC1 and GCLC-like), to zinc transporters (ZNT2-like), and metallothionein (MT-like). The evolutionary conservation of these genes within the Crassostrea genus was assessed through phylogenetic analysis. Further, these genes were evaluated by qPCR in the laboratory exposed oysters. All target genes exhibited significant upregulation upon exposure to Zn at both 850 and 4500 μg L-1, except for GCLC-like, which showed upregulation only at the higher concentration of 4500 μg L-1. This result suggests distinct activation thresholds and complex interactions among these genes in response to varying Zn concentrations. Our study provides insights into the molecular responses of C. gasar to Zn, adding valuable tools for monitoring metal pollution in marine ecosystems using the mangrove oyster as a sentinel organism.

Cytosolic distribution of copper in the gills of field-collected oysters with different copper bioaccumulation

Oysters can hyper-accumulate copper (Cu) without apparent toxicity, but the mechanism of sequestering excessive cytosolic Cu in oysters remains unclear. We here investigated the Cu distribution in the cytosolic proteins (CPs) in the gills of oysters (Crassostrea hongkongensis) through size-exclusion chromatography coupled to inductively coupled plasma mass spectrometry (SEC-ICP-MS). Oysters collected from the southern coast of China contained a gradient of gill Cu concentrations ranging from 132 to 3540 μg g-1 (dry weight), with 7-41 % of Cu distributed in the CPs fraction. The CPs-Cu concentrations were 8.6 times higher in oysters with high Cu concentrations compared to low concentrations. In the CPs, Cu was dispersed with a broad range of molecular weight, suggesting the involvement of various cytosolic proteins in Cu binding. Among the 10 major Cu peaks, peaks 2 (>600 kDa) and peak 8 (18 kDa) contained substantial Cu and showed obvious differences in response to the variation of CPs-Cu levels. Peak 8 contained metallothionein-like proteins that decreased their role in Cu binding as CPs-Cu concentrations increased. LC-MS/MS analysis revealed that peak 2 contained macromolecular protein complexes (MPCs), which played a critical role in binding excess Cu. The comparison with other bivalve species further suggested that sequestering excess CPs-Cu in MPCs was a special strategy employed by oysters in response to high Cu accumulation. This study provides valuable insights into the mechanism of hyper-accumulation and sequestration of Cu in oysters and helps to better understand Cu biomonitoring by oysters.

Proteomic analysis of zebrafish (Danio rerio) embryos exposed to benzyl benzoate

Benzyl benzoate (BB) is widely used in the food, cosmetics, agriculture, and pharmaceutical industries and is discharged into the aquatic environment via various water sources, including wastewater. Research on the bioaccumulation and possible toxicity of BB has been conducted, but the biochemical responses to BB toxicity are not fully understood, and the specific molecular pathways by which BB causes toxicity remain unknown. In this study, label-free quantitative proteomics based on mass spectrometry was applied to investigate protein profiles in zebrafish (Danio rerio) embryos exposed to BB (1 µg/mL) for 7 days. A total of 83 differentially expressed proteins (DEPs) were identified, including 49 up-regulated and 34 down-regulated proteins. The biological functions of proteins regulated by BB were grouped into functional categories and subcategories, including the biosynthesis of organonitrogen compound biosynthetic process, translation, amide biosynthetic process, lipid transport, stress response, and cytoskeletal activity. The results provide novel insight into the molecular basis of the ecotoxicity of BB in aquatic ecosystems.

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.

Protein molecular responses of field-collected oysters Crassostrea hongkongensis with greatly varying Cu and Zn body burdens

The oyster Crassostrea hongkongensis is an ideal biomonitor due to its widespread distribution along the coast of Southern China and the ability to hyperaccumulate metals including Cu and Zn. In this study, we conducted the first investigation of the molecular responses to metal hyperaccumulation based on quantitative shotgun proteomics technique and genome information. Gill tissue of oysters collected from the uncontaminated environment (Site 1, 59.6 μg/g and 670 μg/g dry weight for Cu and Zn) displayed significant protein profile differentiation compared to those from a moderately contaminated (Site 2, 1,465 μg/g and 10,170 μg/g for Cu and Zn) and a severely contaminated environment (Site 3, 3,899 μg/g and 39,170 μg/g for Cu and Zn). There were 626 proteins identified to be differentially expressed at Site 3 but only 247 proteins at Site 2. Oysters from a moderately contaminated estuary (Site 2) displayed fewer effects as compared to oysters under severe contamination, with fluctuated small molecule metabolism and enhanced translation process. At Site 3, the induction of reactive oxygen species (ROS) was the main toxicity under the extremely high level of metal stress, which resulted in protein damage. Additionally, the impaired structure of cytoskeleton and modified membrane tracking process at Site 3 oysters led to the blockage or less efficient protein or macromolecule distribution within cells. Nonetheless, proteomic analysis in this study revealed that oysters could partly alleviate the adverse metal effects by boosting the translation process, enhancing the ability to recycle the misfolded proteins, and enhancing the potential to eliminate the excess ROS. Our study demonstrated an adaptive potential of oysters at the protein level to survive under conditions of metal hyper-accumulation.

Can proteomics contribute to biomonitoring of aquatic pollution? A critical review

Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.

Oxidative Damage of Mussels Living in Seawater Enriched with Trace Metals, from the Viewpoint of Proteins Expression and Modification

The impact of metals bioaccumulation in marine organisms is a subject of intense investigation. This study was designed to determine the association between oxidative stress induced by seawater enriched with trace metals and protein synthesis using as a model the mussels Mytilus galloprovincialis. Mussels were exposed to 40 μg/L Cu, 30 μg/L Hg, or 100 μg/L Cd for 5 and 15 days, and the pollution effect was evaluated by measuring established oxidative biomarkers. The results showed damage on the protein synthesis machine integrity and specifically on translation factors and ribosomal proteins expression and modifications. The exposure of mussels to all metals caused oxidative damage that was milder in the cases of Cu and Hg and more pronounced for Cd. However, after prolonged exposure of mussels to Cd (15 days), the effects receded. These changes that perturb protein biosynthesis can serve as a great tool for elucidating the mechanisms of toxicity and could be integrated in biomonitoring programs.

Molecular responses of an estuarine oyster to multiple metal contamination in Southern China revealed by RNA-seq

The estuarine oysters Crassostrea hongkongensis hyper-accumulate many metals and survive under high levels of metal exposure. In the present study, three natural populations of oysters with various levels of accumulated metals (mainly Cu and Zn) were collected from Southern China. The morphological characteristics and metal concentrations revealed their phenotypic differentiation. Further transcripts sequences acquired from their gill tissues were analyzed and 44,801 genes (with effective reads) were obtained via de novo assembly. The principal component analysis (PCA) revealed that the gene expression patterns also displayed differentiation among the three populations. A total of 3,199 differentially expressed genes (DEGs) was identified in the contaminated oysters as compared to the 'clean' oysters, which were used to explain the molecular mechanisms of metal accumulation and toxicity. GO and KEGG enrichment analysis revealed that energy production and cytoskeleton metabolism-related genes were particularly enriched in the contaminated sites during chronic metal exposure. Besides, increasing expressions of Zn/Cu transporters and metallothionein may explain their high accumulation in contaminated populations. We showed that oysters with less metal accumulation tended to cope with metal stress actively, but severe contamination destroyed part of the normal function. Our study analyzed the gene expression patterns of C. hongkongensis in Southern China and demonstrated the phenotypic differentiation of oysters under chronical metal exposure in the field.

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.

Assessment of trace elements pollution in the sea ports of New South Wales (NSW), Australia using oysters as bioindicators

In this study Sydney rock oysters (S. glomerata) from six major sea ports of NSW, Australia were used as bioindicators to assess the distribution and levels of trace element accumulation in the ports. Substantial enrichment of Cu, Pb and Zn in the oysters of the sea ports were detected when compared to their background samples and the US Environmental Protection Agency (USEPA) provisional tolerable intake standard. Enrichment of As, Al, Fe, Mn, Br, Sr were also found in the oysters at the port areas. The bioconcentration ratios of the trace elements illustrated significant Fe, Cu, Zn, As, Mn, Al, Pb and Cr accumulation in S. glomerate. The biota sediment accumulation factor suggested Cu, Mn and Zn accumulation at two of the ports (Port Yamba and Botany), indicating availability of these metals in the oysters as strong metal accumulators. In addition, integrated metal contamination illustrated notable Fe, Zn, Cu and Al contamination at port environment, whereas cluster analysis portrayed interconnection between the contaminants and the study sites.

The evolution of ependymin-related proteins

Background

Ependymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood.

Results

We undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar.

Conclusions

Our results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.

Trace metals in oysters: molecular and cellular mechanisms and ecotoxicological impacts

Oysters are important benthic bivalves in coastal and estuarine environments. They are widely farmed due to their rapid growth and taste; they are also widely applied in environmental monitoring of coastal pollution due to their accumulation of contaminants. Most importantly, oysters are among the few marine organisms that are considered to be hyper-accumulators of many toxic metals, such as cadmium, copper and zinc. As such, there is a tremendous call to study the interactions between metals and oysters, especially due to the increasing metal pollution in many coastal and estuarine waters. Over the past decades, many studies have focused on metal accumulation in oysters as well as the ecotoxicological effects of metals on oysters. In this review, we summarize the recent progress in our understanding of the molecular and cellular mechanisms of metal accumulation, sequestration and toxicity in oysters. Applications of modern technologies such as omics and nanoscale imaging have added significantly to our knowledge of metal biology in oysters. Variations between different metals also demonstrate the diversity of the interactions between oysters and metals. Despite this recent progress, however, there is a need for further study of the molecular mechanisms of metal uptake and toxicity as well as the joint effects of metal mixtures on oyster populations. Oysters have higher numbers of stress responsive genes than most animals, which may have been induced by gene duplication during the evolution of their intertidal environmental adaptations. The divergent expression of stress responsive genes may explain the different tolerances for metals among different species. These fundamental studies may eventually provide promising solutions for reducing toxic metal concentrations in oysters for safe consumption by humans. To conclude, the complexity of life history and metal chemistry of oysters coupled with emerging pollution and application of modern techniques represents an important and exciting research area in modern ecotoxicology.

Heavy metal concentrations in some gastropods and bivalves collected from the fishing zone of South India

The present study investigates heavy metal concentrations in gastropods and bivalves collected from major fishing centers in South India. Three gastropods, Bursa spinosa, Tibia curta, and Murex trapa, and two bivalves, Perna viridis and Villoritta cyprinoids, were collected for the analysis of heavy metals. The metals in the present study followed the order Mg>Ca>Zn>Fe>Cu>Mn>Cr>Pb>Ni>Co>Cd. Trace metal concentrations in the soft tissue of the molluscs varied as follows: for Cd: 0.04-5.33, Co: 0.09-0.87, Cr: 2.18-7.59, Cu: 9.54-37.02, Mn: 1.30-8.50, Ni: 0.94-3.21, Pb: 1.16-2.64 and Zn: 68.16-113.64mgkg^-1. Metal concentrations in all the species were below the limits proposed by the World Health Organization, except for Pb and Cd. This baseline study suggests that the levels of toxic metals in M. trapa, T. curta, and B. spinosa should be continuously monitored to assess the fate and effects of these metals in this fragile ecosystem.