Apextrin from Ruditapes philippinarum functions as pattern recognition receptor and modulates NF-κB pathway

Identification and characterization of a novel ApeC-containing transmembrane protein family in parasitic flatworms

The Apextrin C-terminal (ApeC) domain is widely distributed across various animal clades. Several ApeC domains have been identified as carbohydrate-binding domains, contributing to extracellular adhesion and mucosal immunity. However, the functions and evolutionary history of most ApeC-containing protein (ACP) families remain largely unexplored. In this study, we identified 213 ACPs in flatworms (Platyhelminthes), with each species containing one to two such proteins. All flatworm ACPs belong to a unique transmembrane protein family, characterized by a length of 1700-2200 amino acids and a distinctive domain architecture (SP-[Kringle]1-2-[ApeC]7-[EGF]1-4-TM) unlike any found in other phyla. This ACP is conserved across all major parasitic flatworm lineages, including flukes (Trematoda), tapeworms (Cestoda) and monogeneans (Monogenea), despite their diverse morphologies and habitats. Notably, it is also present in one group of free-living flatworms, the planarians (Tricladida), suggesting that this ACP originated in the free-living ancestor of parasitic flatworms. This ACP contains seven consecutive ApeC domains, an unparalleled number among known animal proteins. Five of these ApeC domains are highly divergent, necessitating the definition of a new domain model (ApeC_Pla; Pfam: PF24148) for accurate classification. Structural predictions indicate that these ApeC domains adopt a conserved three β-sheet structure. Furthermore, transcriptomic analysis revealed that flatworm ACPs, along with several important serpins and proteases, are predominantly expressed in parenchymal cells and feeding organs, suggesting that ACPs serve as novel marker genes for parenchymal tissue and may be involved in cell adhesion, oral immunity, and parasite-host interactions. Taken together, our findings indicate that this flatworm ACP represents a promising target for vaccine development and provides key insights into the physiology of the parenchyma, a unique flatworm tissue that functions as a substitute for a body cavity.

DOPA Decarboxylase (DDC) in Pacific Oysters: Characterization and Role in Tyrosine Metabolism and Melanogenesis

DOPA decarboxylase (DDC) plays a crucial role in the physiological functions of animals by participating in the dopaminergic system. However, the functions of DDC in shellfish remain poorly understood. The Pacific oyster (Crassostrea gigas) is an extensively cultivated shellfish. In this study, we characterized a DDC gene, designated CgDDC, from C. gigas. The CgDDC gene encodes a protein that contains a Pyridoxal_deC domain, which features specific binding sites for pyridoxal-5'-phosphate (PLP) and L-DOPA. CgDDC exhibits a significantly higher expression level in the black shell oyster strain than the white strain. In vitro enzymatic reaction assays demonstrated that CgDDC catalyzes the conversion of L-DOPA to dopamine. In vivo experiments revealed that inhibiting CgDDC activity reduced the expression of genes associated with tyrosine metabolism. Furthermore, the knockdown of CgDDC caused a decline in cAMP level and reduced transcription of genes involved in the cAMP-mediated melanogenesis. Additionally, treatment with L-α-DOPA inhibited CgDDC enzyme activity and cAMP-mediated melanogenesis; however, dopamine supplementation countered this inhibition, maintaining gene expression and melanin content at baseline levels. Collectively, our findings suggest that CgDDC is intricately involved in regulating tyrosine metabolism and melanogenesis in C. gigas.

Identification and function analysis of Toll-like receptor 4 (TLR4) from Manila clam (Ruditapes philippinarum)

Toll-like receptor 4 (TLR4) is a pattern recognition receptor that activates innate immunity in response to pathogen infection. However, the role of TLR4 in pathogen-induced apoptosis and host immunity in mollusks remains largely unknown. In this study, the TLR4 of the Manila clam Ruditapes philippinarum (RpTLR4) was cloned. The open reading frame of RpTLR4 encodes a protein of 734 amino acids, containing a conserved TIR domain. Phylogenetic analysis revealed that RpTLR4 clusters closely with TLR4s from mollusks. RpTLR4 mRNA was detected in all tested tissues, with notably high expression in hemocytes (428-fold) and gills (657-fold). Subcellular localization showed that RpTLR4 is expressed on the cell membrane. qRT-PCR and western blot analyses demonstrated that RpTLR4 expression was induced in Manila clams after treatment with Vibrio parahaemolyticus. Overexpression of RpTLR4 significantly increased apoptosis levels and the expression of apoptosis-related genes. Conversely, silencing RpTLR4 markedly reduced the apoptosis rate in hemocytes induced by V. parahaemolyticus, indicating that V. parahaemolyticus-induced hemocyte apoptosis depends on RpTLR4 expression. Overall, these findings confirm that RpTLR4 plays a pro-apoptotic role in the response of Manila clams to V. parahaemolyticus infection. This study provides a theoretical foundation for understanding the molecular mechanisms underlying mollusk responses to pathogen infection.

Novel ApeC-containing protein mediates the recognition and internalization of Vibrio splendidus in Apostichopus japonicus

Pattern recognition receptors (PRRs) mediate the innate immune responses and play a crucial role in host defense against pathogen infections. Apextrin C-terminal (ApeC)-containing proteins (ACPs), a newly discovered class of PRRs specific to invertebrates, recognize pathogens through their ApeC domain as intracellular or extracellular effectors. However, the other immunological functions of ACPs remain unclear. In this study, a membrane-localized ACP receptor was identified in the sea cucumber Apostichopus japonicus (denoted as AjACP1). The ApeC domain of AjACP1, which was located outside of its cell membrane, exhibited the capability to recognize and aggregate Vibrio splendidus. AjACP1 was upregulated upon V. splendidus infection, internalizing into the cytoplasm of coelomocytes. AjACP1 overexpression enhanced the phagocytic activity of coelomocytes against V. splendidus, while knockdown of AjACP1 by RNA interfere inhibited coelomocyte endocytosis. Inhibitor experiments indicated that AjACP1 regulated coelomocyte phagocytosis through the actin-dependent endocytic signaling pathway. Further investigation revealed that AjACP1 interacted with the subunit of the actin-related protein 2/3 complex ARPC2, promoting F-actin polymerization and cytoskeletal rearrangement and thereby affecting the coelomocyte phagocytosis of V. splendidus via the actin-dependent endocytic signaling pathway. As a novel membrane PRR, AjACP1 mediates the recognition and phagocytic activity of coelomocytes against V. splendidus through the AjACP1-ARPC2-F-actin polymerization and cytoskeletal rearrangement pathway.

Transcriptome analysis provides new insights into the immune response of Ruditapes philippinarum infected with Vibrio alginolyticus

Manila clam (Ruditapes philippinarum) is a bivalve species with commercial value, but it is easily infected by pathogenic microorganisms in aquaculture, which restricts the shellfish industry. Notably, the impact of Vibrio alginolyticus on clam culture is obvious. In this study, RNA-seq was performed to analyze clam hepatopancreas tissue in 48 h (challenge group, G48h) and 96 h (challenge group, G96h) after infection with V. alginolyticus and 0 h after injection of PBS (control group, C). The results showed that a total of 1670 differentially expressed genes were detected in the G48h vs C group, and 1427 differentially expressed genes were detected in the G96h vs C group. In addition, KEGG analysis showed that DEGs were significantly enriched in pathways such as Lysosome and Mitophagy. Moreover, 15 immune related DEGs were selected for qRT-PCR analysis to verify the accuracy of RNA-seq, and the results showed that the expression level of DEGs was consistent with that of RNA-seq. Therefore, the results obtained in this study provides a preliminary understanding of the immune defense of R. philippinarum and molecular insights for genetic breeding of V. alginolyticus resistance in Manila clam.

Integrated evidence of transcriptional, metabolic, and intestinal microbiota changes in Ruditapes philippinarum due to perfluorooctanoic acid-induced immunotoxicity

Perfluorooctanoic acid (PFOA) is a toxic pollutant that bioaccumulates and is a significant public health concern due to its ubiquitous and persistent occurrence in global environments. Few studies have evaluated the adverse effects of PFOA on immune system, and this is particularly true for mollusks. Here, the PFOA-associated effects on immune system were evaluated in Ruditapes philippinarum using integrated analysis of metabolomes, microbiomes, and transcriptomes, providing evidence for possible mechanisms related to immunotoxicity. PFOA exposure caused clear variation in several important metabolites related to immune regulatory function within the haemolyph from R. philippinarum, while also altering key metabolic pathways, including those of lipids, unsaturated fatty acids (UFAs), and bile acids (BAs). After exposure to PFOAs, intestinal bacterial communities also clearly changed, with the predominant microflora becoming Mycoplasma and Bacteroidetes that are related to intestinal inflammation. Molecular analyses provided consistent results, wherein the expression of immune-related genes was significantly altered. Integration of the multi-'omics' analyses suggested that the TLR/MyD88/NF-kB pathway, along with PI3K-Akt-mTOR pathway, PPAR-mediated lipid metabolism and the autophagy signaling pathway, likely play important roles in initiating immunotoxic effects in R. philippinarum after PFOA exposure. These results provide further evidence that PFOA exposure can lead to immunologic dysfunction and also provide new insights into the mechanisms of PFAS alteration of bivalve immune function.

Bioconcentration, biotransformation, and transcriptomic impact of the UV-filter 4-MBC in the manila clam Ruditapes philippinarum

Ultraviolet filters (UV-filters) are compounds extensively used in personal care products. These compounds are produced at increasing rates and discharged into marine ecosystems in unknown quantities and with no regulation, making them emerging contaminants. Among those, the UV-filter 4-Methylbenzylidene camphor (4-MBC) is used in a variety of personal care products such as sunscreens, soaps, or lipsticks. This high consumption has resulted in its presence in various environmental matrices at in concentrations ranging from ng to μg L-1. Very little is known, however, about the possible adverse effects in exposed non-target organisms. Our study presents novel data on the bioconcentration, toxicokinetics, and molecular effects of 4-MBC in a marine bivalve species of commercial interest, Ruditapes philippinarum (Manila clam). Organisms were exposed at two different concentrations (1.34 and 10.79 μg L-1) of 4-MBC for 7 days, followed by a 3-day depuration period (clean sea waters). Bioconcentration factors (BCF) were 3562 and 2229 L kg-1 for the low and high exposure concentrations, respectively, making this pollutant bioaccumulative according to REACH criteria. Up to six 4-MBC biotransformation products (BTPs)were identified, 2 of them for the first time. Transcriptomic analysis revealed between 658 and 1310 differently expressed genes (DEGs) after 4-MBC exposure. Functional and enrichment analysis of the DEGs showed the activation of the detoxification pathway to metabolize and excrete the bioconcentrated 4-MBC, which also involved energy depletion and caused an impact on the metabolism of carbohydrates and lipids and in the oxidative phosphorylation pathways. Oxidative stress and immune response were also evidenced through the activation of cathepsins and the complement system. Such elucidation of the mode of action of a ubiquitous pollutant such as 4-MBC at the molecular level is valuable both from an environmental point of view and for the sustainable production of Manila clam, one of the most cultivated mollusk species worldwide.

Mussel antiviral transcriptome response and elimination of viral haemorrhagic septicaemia virus (VHSV)

As filter-feeding bivalves, mussels have been traditionally studied as possible vectors of different bacterial or viral pathogens. The absence of a known viral pathogen in these bivalves makes it particularly interesting to study the interaction of the mussel innate immune system with a virus of interest. In the present work, mussels were challenged with viral haemorrhagic septicaemia virus (VHSV), which is a pathogen in several fish species. The viral load was eliminated after 24 h and mussels evidenced antiviral activity towards VHSV, demonstrating that the virus was recognized and eliminated by the immune system of the host and confirming that mussels are not VHSV vectors in the marine environment. The transcriptome activating the antiviral response was studied, revealing the involvement of cytoplasmic viral sensors with the subsequent activation of the JAK-STAT pathway and several downstream antiviral effectors. The inflammatory response was inhibited with the profound downregulation of MyD88, shifting the immune balance towards antiviral functions. High modulation of retrotransposon activity was observed, revealing a mechanism that facilitates the antiviral response and that had not been previously observed in these species. The expression of several inhibitors of apoptosis and apoptosis-promoting genes was modulated, although clear inhibition of apoptosis in bivalves after severe viral infection and subsequent disease was not observed in this study. Finally, the modulated expression of several long noncoding RNAs that were correlated with genes involved in the immune response was detected.

Two novel mollusk short-form ApeC-containing proteins act as pattern recognition proteins for peptidoglycan

The Apextrin C-terminal (ApeC) domain is a new protein domain largely specific to aquatic invertebrates. In amphioxus, a short-form ApeC-containing protein (ACP) family is capable of binding peptidoglycan (PGN) and agglutinating bacteria via its ApeC domain. However, the functions of ApeC in other phyla remain unknown. Here we examined 130 ACPs from gastropods and bivalves, the first and second biggest mollusk classes. They were classified into nine groups based on their phylogenetics and architectures, including three groups of short-form ACPs, one group of apextrins and two groups of ACPs of complex architectures. No groups have orthologs in other phyla and only four groups have members in both gastropods and bivalves, suggesting that mollusk ACPs are highly diversified. We selected one bivalve ACP (CgACP1; from the oyster Crossostrea gigas) and one gastropod ACP (BgACP1; from the snail Biomphalaria glabrata) for functional experiments. Both are highly-expressed, secreted short-form ACPs and hence comparable to the amphioxus ACPs previously reported. We found that recombinant CgACP1 and BgACP1 bound with yeasts and several bacteria with different affinities. They also agglutinated these microbes, but showed no inhibiting or killing effects. Further analyses show that both ACPs had high affinities to the Lys-type PGN from S. aureus but weak or no affinities to the DAP-type PGN from Bacillus subtilis. Both recombinant ACPs displayed weak or no affinities to other microbial cell wall components, including lipopolysaccharide (LPS), lipoteichoic acid (LTA), zymosan A, chitin, chitosan and cellulose, as well as to several PGN moieties, including muramyl dipeptide (MDP), N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc). Besides, CgACP1 had the highest expression in the gill and could be greatly up-regulated quickly after bacterial challenge. This is reminiscent of the amphioxus ACP1/2 which serve as essential mucus lectins in the gill. Taken together, the current findings from mollusk and amphioxus ACPs suggest several basic common traits for the ApeC domains, including the high affinity to Lys-type PGN, the bacterial binding and agglutinating capacity, and the role as mucus proteins to protect the mucosal surface.