RNA-Seq Transcriptome Profiling of the Queen Scallop (Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia

Coordination regulation of enhanced performance reveals the tolerance mechanism of Chlamys farreri to azaspiracid toxicity

Azaspiracids (AZAs) are lipid biotoxins produced by the marine dinoflagellates Azadinium and Amphidoma spp. that can accumulate in shellfish and cause food poisoning in humans. However, the mechanisms underlying the tolerance of shellfish to high levels of such toxins remain poorly understood. This study investigated the combined effects of detoxification metabolism and stress-related responses in scallops Chlamys farreri exposed to AZA. Scallops accumulated a maximum of 361.81 μg AZA1 eq/kg and 41.6 % AZA residue remained after 21 days of exposure. A range of AZA2 metabolites, including AZA19, AZA11, and AZA23, and trace levels of AZA2-GST, were detected. Total hemocyte counts significantly increased and ROS levels remained consistently high until gradually decreasing. Immune system activation mediated mitochondrial dysfunction and severe energy deficiency. DEGs increased over time, with key genes CYP2J6 and GPX6 contributing to AZA metabolism. These transcriptome and metabolic results identify the regulation of energy metabolism pathways, including inhibition of the TCA cycle and activation of carbohydrates, amino acids, and lipids. AZA also induced autophagy through the MAPK-AMPK signaling pathways, and primary inhibited PI3K/AKT to decrease mTOR pathway expression. Our results provide additional insights into the resistance of C. farreri to AZA, characterized by re-establishing redox homeostasis toward a more oxidative state.

Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance

One-third of protein domains in the CATH database contain a recently discovered tertiary topological motif: non-covalent lasso entanglements, in which a segment of the protein backbone forms a loop closed by non-covalent interactions between residues and is threaded one or more times by the N- or C-terminal backbone segment. Unknown is how frequently this structural motif appears across the proteomes of organisms. And the correlation of these motifs with various classes of protein function and biological processes have not been quantified. Here, using a combination of protein crystal structures, AlphaFold2 predictions, and Gene Ontology terms we show that in E. coli, S. cerevisiae and H. sapiens that 71%, 52% and 49% of globular proteins contain one-or-more non-covalent lasso entanglements in their native fold, and that some of these are highly complex with multiple threading events. Further, proteins containing these tertiary motifs are consistently enriched in certain functions and biological processes across these organisms and depleted in others, strongly indicating an influence of evolutionary selection pressures acting positively and negatively on the distribution of these motifs. Together, these results demonstrate that non-covalent lasso entanglements are widespread and indicate they may be extensively utilized for protein function and subcellular processes, thus impacting phenotype.

Tissue-specific antioxidative response and metabolism of paralytic shellfish toxins in scallop (Chlamys farreri) mantle with Alexandrium dinoflagellate exposure

Bivalves show remarkable capacity to acclimate paralytic shellfish toxins (PSTs) produced by dinoflagellates, severely affecting fishery industry and public health. Here, transcriptomic response to PSTs-producing dinoflagellate (Alexandrium minutum) was investigated in Zhikong scallop (Chlamys farreri) mantle. The PSTs accumulated in C. farreri mantle continually increased during the 15 days exposure, with "oxidation-reduction" genes induced compared to the control group at the 1st and 15th day. Through gene co-expression network analysis, 16 PSTs-responsive modules were enriched with up- or down-regulated genes. The concentration of GTXs, major PSTs in A. minutum and accumulated in scallops, was correlated with the up-regulated magenta module, enriching peroxisome genes as the potential mantle-specific PSTs biomarker. Moreover, Hsp70B2s were inhibited throughout the exposure, which together with the expanded neurotransmitter transporter SLC6As, may play essential roles on neurotransmitter homeostasis in scallop mantle. These results paved the way for a comprehensive understanding of defensive mechanism and homeostatic response in scallop mantle against PSTs.

Comparative study of domoic acid accumulation, isomer content and associated digestive subcellular processes in five marine invertebrate species

Despite the deleterious effects of the phycotoxin domoic acid (DA) on human health, and the permanent threat of blooms of the toxic Pseudo-nitzschia sp. over commercially important fishery-resources, knowledge regarding the physiological mechanisms behind the profound differences in accumulation and depuration of this toxin in contaminated invertebrates remain very scarce. In this work, a comparative analysis of accumulation, isomer content, and subcellular localization of DA in different invertebrate species was performed. Samples of scallops Pecten maximus and Aequipecten opercularis, clams Donax trunculus, slippersnails Crepidula fornicata, and seasquirts Asterocarpa sp. were collected after blooms of the same concentration of toxic Pseudo-nitzschia australis. Differences (P < 0.05) in DA accumulation were found, wherein P. maximus showed up to 20-fold more DA in the digestive gland than the other species. Similar profiles of DA isomers were found between P. maximus and A. opercularis, whereas C. fornicata was the species with the highest biotransformation rate (∼10 %) and D. trunculus the lowest (∼4 %). DA localization by immunohistochemical analysis revealed differences (P < 0.05) between species: in P. maximus, DA was detected mainly within autophagosome-like vesicles in the cytoplasm of digestive cells, while in A. opercularis and C. fornicata significant DA immunoreactivity was found in post-autophagy residual bodies. A slight DA staining was found free within the cytoplasm of the digestive cells of D. trunculus and Asterocarpa sp. The Principal Component Analysis revealed similarities between pectinids, and a clear distinction of the rest of the species based on their capabilities to accumulate, biotransform, and distribute the toxin within their tissues. These findings contribute to improve the understanding of the inter-specific differences concerning the contamination-decontamination kinetics and the fate of DA in invertebrate species.

Exploration of anti-stress mechanisms in high temperature exposed juvenile golden cuttlefish (Sepia esculenta) based on transcriptome profiling

Sepia esculenta is a cephalopod widely distributed in the Western Pacific Ocean, and there has been growing research interest due to its high economic and nutritional value. The limited anti-stress capacity of larvae renders challenges for their adaptation to high ambient temperatures. Exposure to high temperatures produces intense stress responses, thereby affecting survival, metabolism, immunity, and other life activities. Notably, the molecular mechanisms by which larval cuttlefish cope with high temperatures are not well understood. As such, in the present study, transcriptome sequencing of S. esculenta larvae was performed and 1,927 differentially expressed genes (DEGs) were identified. DEGs were subjected to functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The top 20 terms of biological processes in GO and 20 high-temperature stress-related pathways in KEGG functional enrichment analysis were identified. A protein-protein interaction network was constructed to investigate the interaction between temperature stress-related genes. A total of 30 key genes with a high degree of participation in KEGG signaling pathways or protein-protein interactions were identified and subsequently validated using quantitative RT-PCR. Through a comprehensive analysis of the protein-protein interaction network and KEGG signaling pathway, the functions of three hub genes (HSP90AA1, PSMD6, and PSMA5), which belong to the heat shock protein family and proteasome, were explored. The present results can facilitate further understanding of the mechanism of high temperature resistance in invertebrates and provide a reference for the S. esculenta industry in the context of global warming.

Transcriptomic analysis reveals the genes involved in tetrodotoxin (TTX) accumulation, translocation, and detoxification in the pufferfish Takifugu rubripes

Tetrodotoxin (TTX) is a potent marine neurotoxin that exists in a variety of aquatic and terrestrial organisms. Pufferfish in different habitats show great variation in their TTX contents. Exploring the genes involved in TTX metabolism could contribute to our understanding of the molecular mechanisms underlying TTX accumulation, translocation, and detoxification in pufferfish. In this study, transcriptomic analysis was used to identify the functional genes related to TTX metabolism in the blood, liver, and muscle of the toxic and non-toxic tiger puffer (Takifugu rubripes). A total of 6101 differentially expressed genes (DEGs) were obtained after transcriptomic analysis; of these, 2401 were identified in the blood, 2262 in the liver, and 1438 in the muscle. After enrichment analysis, fourteen genes encoding glutathione S-transferases (GSTs), glutathione peroxidase (GPx), thioredoxins (TXNs), superoxide dismutase (SOD), ATP-binding cassettes (ABCs), apolipoproteins (APOs), inhibitors of apoptosis protein (IAP), and solute carrier (SLC), which are mainly antioxidant enzymes, membrane transporters, or anti-apoptotic factors, were revealed in the blood. Thirty-six genes encoding SLCs, ABCs, long-chain-fatty-acid-CoA ligases (ACSLs), interleukin 6 cytokine family signal transducer (IL6ST), endoplasmic reticulum (ER), and heat shock protein family A (Hsp70) were involved in transmembrane transporter activity and innate immune response. Notably, a large number of slc genes were found to play critical and diverse roles in TTX accumulation and translocation in the liver of T. rubripes. Nine genes from the slc, hsp70, complement C5 (c5), acsl, er, and serpin peptidase inhibitor (serpin) gene families were found to participate in the regulation of protein processing and anti-apoptosis. These results reflect the diverse functions of genes closely related to TTX accumulation, translocation, and detoxification in T. rubripes.

Occurrence and Seasonal Monitoring of Domoic Acid in Three Shellfish Species from the Northern Adriatic Sea

As filter feeders, bivalves and ascidians can accumulate contaminants present in the environment and pass them on to higher food chain levels as vectors. The consumption of bivalves contaminated with the potent neurotoxin domoic acid (DA) can cause amnesic shellfish poisoning in humans. The aim of this study was to determine seasonal differences in occurrence and accumulation of this phycotoxin in European oysters (Ostrea edulis Linnaeus, 1758) (n = 46), Queen scallops (Aequipecten opercularis Linnaeus, 1758) (n = 53), and edible ascidians of the Microcosmus spp. (n = 107), originating from the same harvesting area in the Northern Adriatic Sea. The quantification was performed using ultra-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) preceded by derivatization with dansyl chloride. DA was found in very low concentrations throughout the year, with a maximum value of 810 μg/kg in Queen scallops. This study reveals differences in the occurrence and accumulation of DA between Queen scallops and the other two investigated species (oysters and ascidians) and the highest concentrations during the colder part of the year. Even though DA was detected in all of them, Queen scallops showed higher DA accumulation compared to the other two (p < 0.001), hence representing a sentinel species suitable for the monitoring of DA level in seafood.

Marine Neurotoxins' Effects on Environmental and Human Health: An OMICS Overview

Harmful algal blooms (HAB), and the consequent release of toxic metabolites, can be responsible for seafood poisoning outbreaks. Marine wildlife can accumulate these toxins throughout the food chain, which presents a threat to consumers’ health. Some of these toxins, such as saxitoxin (STX), domoic acid (DA), ciguatoxin (CTX), brevetoxin (BTX), tetrodotoxin (TTX), and β-N-methylamino-L-alanine (BMAA), cause severe neurological symptoms in humans. Considerable information is missing, however, notably the consequences of toxin exposures on changes in gene expression, protein profile, and metabolic pathways. This information could lead to understanding the consequence of marine neurotoxin exposure in aquatic organisms and humans. Nevertheless, recent contributions to the knowledge of neurotoxins arise from OMICS-based research, such as genomics, transcriptomics, proteomics, and metabolomics. This review presents a comprehensive overview of the most recent research and of the available solutions to explore OMICS datasets in order to identify new features in terms of ecotoxicology, food safety, and human health. In addition, future perspectives in OMICS studies are discussed.

Physiological role of CYP17A1-like in cadmium detoxification and its transcriptional regulation in the Pacific oyster, Crassostrea gigas

Cadmium (Cd) is one of the most harmful heavy metals due to its persistence and bioaccumulation through the food chains, posing health risks to human. Oysters can bioaccumulate and tolerate high concentrations of Cd, providing a great model for studying molecular mechanism of Cd detoxification. In a previous study, we identified two CYP genes, CYP17A1-like and CYP2C50, that were potentially involved in Cd detoxification in the Pacific oyster, Crassostrea gigas. In this work, we performed further investigations on their physiological roles in Cd detoxification through RNA interference (RNAi). After injection of double-stranded RNA (dsRNA) into the adductor muscle of oysters followed by Cd exposure for 7 days, we observed that the expressions of CYP17A1-like and CYP2C50 in interference group were significantly suppressed on day 3 compared with control group injected with PBS. Moreover, the mortality rate and Cd content in the CYP17A1-like dsRNA interference group (dsCYP17A1-like) was significantly higher than those of the control on day 3. Furthermore, the activities of antioxidant enzymes, including SOD, CAT, GST, were significantly increased in dsCYP17A1-like group, while were not changed in dsCYP2C50 group. More significant tissue damage was observed in gill and digestive gland of oysters in RNAi group than control group, demonstrating the critical role of CYP17A1-like in Cd detoxification. Dual luciferase reporter assay revealed three core regulatory elements of MTF-1 within promoter region of CYP17A1-like, suggesting the potential transcriptional regulation of CYP17A1-like by MTF-1 in oysters. This work demonstrated a critical role of CYP17A1-like in Cd detoxification in C. gigas and provided a new perspective toward unravelling detoxification mechanisms of bivalves under heavy metal stress.

Nanoplastic-Induced Genotoxicity and Intestinal Damage in Freshwater Benthic Clams (Corbicula fluminea): Comparison with Microplastics

With the wide application of plastics in daily life, nanoplastics (NPs) are ubiquitous in freshwater environments. However, to date, few studies have focused on the mechanism underlying the toxicity of NPs, and the differences between this mechanism and that governing the toxicity of MPs have also not been thoroughly characterized. In this study, the genotoxicity, intestinal damage, and intestinal flora in Corbicula fluminea exposed to micro/nanoplastics were investigated through RNA sequencing, histopathology, and 16S rRNA sequencing, respectively. Significant differences in differentially expressed genes (DEGs) were observed between MP and NP exposure groups. It was observed that NPs preferentially elicited the process related to cellular components and triggered the apoptosis through the mitochondrial pathway in various tissues, especially in indirectly contacted tissues, while MPs induced the innate immune response and activated the complement and coagulation cascades (complement system) pathway. Both MPs and NPs can induce an inflammatory response and cause epithelial damage in the intestines, and they can notably change the gut microbial community structure. However, the abundance of pathogenic bacteria (e.g., Mycoplasma) was observed to increase only in the MP-treated group, which exacerbated intestinal damage. Unlike MPs, the effect of NPs on the intestinal microflora was highly limited, while NPs elicited more severe damage to the intestinal mucosal barrier. The results of this study may help to elucidate the toxicity mechanisms governing the responses of bivalves to MPs and NPs and to evaluate the detriment of MPs and NPs to the benthic ecosystem.

Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid

Some diatom species of the genus Pseudo-nitzschia produce the toxin domoic acid. The depuration rate of domoic acid in Pecten maximus is very low; for this reason, king scallops generally contain high levels of domoic acid in their tissues. A transcriptomic approach was used to identify the genes differentially expressed in the P. maximus digestive gland after the injection of domoic acid. The differential expression analysis found 535 differentially expressed genes (226 up-regulated and 309 down-regulated). Protein–protein interaction networks obtained with the up-regulated genes were enriched in gene ontology terms, such as vesicle-mediated transport, response to stress, signal transduction, immune system process, RNA metabolic process, and autophagy, while networks obtained with the down-regulated genes were enriched in gene ontology terms, such as response to stress, immune system process, ribosome biogenesis, signal transduction, and mRNA processing. Genes that code for cytochrome P450 enzymes, glutathione S-transferase theta-1, glutamine synthase, pyrroline-5-carboxylate reductase 2, and sodium- and chloride-dependent glycine transporter 1 were among the up-regulated genes. Therefore, a stress response at the level of gene expression, that could be caused by the domoic acid injection, was evidenced by the alteration of several biological, cellular, and molecular processes.

Host Defense Effectors Expressed by Hemocytes Shape the Bacterial Microbiota From the Scallop Hemolymph

The interaction between host immune response and the associated microbiota has recently become a fundamental aspect of vertebrate and invertebrate animal health. This interaction allows the specific association of microbial communities, which participate in a variety of processes in the host including protection against pathogens. Marine aquatic invertebrates such as scallops are also colonized by diverse microbial communities. Scallops remain healthy most of the time, and in general, only a few species are fatally affected on adult stage by viral and bacterial pathogens. Still, high mortalities at larval stages are widely reported and they are associated with pathogenic Vibrio. Thus, to give new insights into the interaction between scallop immune response and its associated microbiota, we assessed the involvement of two host antimicrobial effectors in shaping the abundances of bacterial communities present in the scallop Argopecten purpuratus hemolymph. To do this, we first characterized the microbiota composition in the hemolymph from non-stimulated scallops, finding both common and distinct bacterial communities dominated by the Proteobacteria, Spirochaetes and Bacteroidetes phyla. Next, we identified dynamic shifts of certain bacterial communities in the scallop hemolymph along immune response progression, where host antimicrobial effectors were expressed at basal level and early induced after a bacterial challenge. Finally, the transcript silencing of the antimicrobial peptide big defensin ApBD1 and the bactericidal/permeability-increasing protein ApLBP/BPI1 by RNA interference led to an imbalance of target bacterial groups from scallop hemolymph. Specifically, a significant increase in the class Gammaproteobacteria and the proliferation of Vibrio spp. was observed in scallops silenced for each antimicrobial. Overall, our results strongly suggest that scallop antimicrobial peptides and proteins are implicated in the maintenance of microbial homeostasis and are key molecules in orchestrating host-microbiota interactions. This new evidence depicts the delicate balance that exists between the immune response of A. purpuratus and the hemolymph microbiota.

Transcriptome analysis of Catarina scallop (Argopecten ventricosus) juveniles treated with highly-diluted immunomodulatory compounds reveals activation of non-self-recognition system

Marine bivalve hatchery productivity is continuously challenged by apparition and propagation of new diseases, mainly those related to vibriosis. Disinfectants and antibiotics are frequently overused to prevent pathogen presence, generating a potential negative impact on the environment. Recently, the use of highly diluted compounds with immunostimulant properties in marine organisms has been trailed successfully to activate the self-protection mechanisms of marine bivalves. Despite their potential as immunostimulants, little is known about their way of action. To understand their effect, a comparative transcriptomic analysis was performed with Argopecten ventricosus juveniles. The experimental design consisted of four treatments formulated from pathogenic Vibrio lysates at two dilutions: [(T1) Vibrio parahaemolyticus and Vibrio alginolyticus 1D; (T2) V. parahaemolyticus and V. alginolyticus 7C]; minerals [(T3) PhA+SiT 7C], scorpion venom [(T4) ViT 31C]; and one control (C1) hydro-alcoholic solution (ethanol 1%). The RNA sequencing (RNAseq) analysis showed a higher modulation of differentially expressed genes (DEG) in mantle tissue compared to gill tissue. The scallops that showed a higher number of DEG related to immune response in mantle tissue corresponded to T1 (V. parahaemolyticus and V. alginolyticus lysate) and T3 (Silicea terra® - Phosphoric acid®). The transcriptome analysis allowed understanding some interactions between A. ventricosus juveniles and highly-diluted treatments.

Solute carriers in scallop genome: Gene expansion and expression regulation after exposure to toxic dinoflagellate

The solute carriers (SLCs) are membrane proteins that transport many endogenous and exogenous substances such as xenobiotic toxins. Bivalve mollusks, mainly feeding on microalgae, show marked capacity to accumulate paralytic shellfish toxins (PSTs), the most common and hazardous marine biotoxins produced by dinoflagellates. Exploring the SLCs related to PST accumulation in bivalve could benefit our understanding about the mechanisms of PST bioavailability in bivalve and the adaptations of these species. Herein, we provided the first systematic analysis of SLC genes in mollusks, which identified 673 SLCs (PySLCs, 48 subfamilies) in Yesso scallop (Patinopecten yessoensis), 510 (48 subfamilies) in Pacific oyster (Crassostrea gigas), and 350 (47 subfamilies) in gastropod owl limpet (Lottia gigantea). Significant expansion of subfamilies SLC5, SLC6, SLC16, and SLC23 in scallop, and SLC46 subfamily in both scallop and oyster were revealed. Different PySLC members were highly expressed in the developmental stages and adult tissues, and hepatopancreas harboured more specifically expressed PySLCs than other tissues/organs. After feeding the scallops with PST-producing dinoflagellate, 131 PySLCs were regulated and more than half of them were from the expanded subfamilies. The trend of expression fold change in regulated PySLCs was consistent with that of PST changes in hepatopancreas, implying the possible involvement of these PySLCs in PST transport and homeostasis. In addition, the PySLCs from the expanded subfamily were revealed to be under positive selection, which might be related to lineage-specific adaptation to the marine environments with algae derived biotoxins.

Effects of Marine Toxin Domoic Acid on Innate Immune Responses in Bay Scallop Argopecten irradians

Domoic acid (DA) is an amnesic shellfish poisoning toxin produced by some species of the genera Pseudo-nitzschia and Nitzschia. This toxin has harmful effects on various species, especially scallops. This study aimed to investigate the effects of DA exposure on the immune and physical responses of bay scallop, Argopecten irradians. Various immunological and physical parameters were assessed (acid phosphatase (ACP), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), lipid peroxide (LPO), nitric oxide (NO), and the total protein content) in the haemolymph of scallops at 3, 6, 12, 24, and 48 h post-exposure to DA at different concentrations (10, 50, and 100 ng/mL). Moreover, the expression of immune-related genes (CLT-6, FREP, HSP90, MT, PGRP, and PrxV) was assessed. The activities of ACP, ALP, and LDH and the total protein content and LPO increased upon exposure to DA at different concentrations, while NO levels were decreased. Furthermore, immune-related genes were assessed upon DA exposure. Our results showed that exposure to DA negatively impacts immune function and disrupts physiological activities in bay scallops.