Molecular cloning and functional characterization of cathepsin B from the sea cucumber Apostichopus japonicus

Adverse effects of polystyrene nanoplastics on sea cucumber Apostichopus japonicus and their association with gut microbiota dysbiosis

The mariculture environment is a sink of microplastics (MPs) due to its enclosed nature and mass use of plastics. Nanoplastics (NPs) are MPs with a diameter <1 μm that have a more toxic effect on aquatic organisms than other MPs. However, little is known about the underlying mechanisms of NP toxicity on mariculture species. Here, we performed a multi-omics investigation to explore gut microbiota dysbiosis and associated health problems induced by NPs in juvenile sea cucumber Apostichopus japonicus, a commercially and ecologically important marine invertebrate. We observed significant differences in gut microbiota composition after 21 days of NP exposure. Ingestion of NPs significantly increased core gut microbes, especially Rhodobacteraceae and Flavobacteriaceae families. Additionally, gut gene expression profiles were altered by NPs, especially those related to neurological diseases and movement disorders. Correlation and network analyses indicated close relationships between transcriptome changes and gut microbiota variation. Furthermore, NPs induced oxidative stress in sea cucumber intestines, which may be associated with intraspecies variation in Rhodobacteraceae in the gut microbiota. The results suggested that NPs were harmful to the health of sea cucumbers, and they highlighted the importance of the gut microbiota in the responses to NP toxicity in marine invertebrates.

Phenotypic and functional characterization of two coelomocyte subsets in Apostichopus japonicus

The hemocytes of invertebrates are composed of different cell subsets with different morphologies and structures. Different cell subsets have different immune functions, which play an important role in innate immune response against pathogens. However, the understanding of the classification of Apostichopus japonicus coelomocytes and the molecular basis of immune function of different cell subsets is very limited. In this study, two coelomocyte subpopulations of A. japonicus were isolated by Percoll density gradient centrifugation. They were identified from their morphological and structural characteristics, namely, spherical cells with a size of 10-12 μm spherical in shape and a large number of small granules inside; lymphocyte-like cells with a size of 4-5 μm spherical or oval in shape, and 1-3 filopodia. Functionally, the phagocytic capacity and lysosomal activity in spherical cells were significantly greater than those in lymphocyte-like cells. The results suggest that spherical cells may play a more critical role in the immune responses. Meanwhile, transcriptome sequencing analysis was performed to further clarify the functional differences between the two cell subsets. The data indicated significantly different gene expression patterns in them. Spherical cells tend to participate in immune defense, whereas lymphocyte-like cells tend to participate in energy metabolism. In addition, lymphocyte-like cells may convert oxidative phosphorylation to glycolysis by changing the manner of energy metabolism to quickly adapt to the energy demand of external stimuli. Spherical cells may respond to LPS stimulation through phagocytosis, and their response time is slower than that of lymphocyte-like cells. The expression of genes involved in endocytosis, phagocytosis, and lysosomal and humoral immunity in spherical cells was significantly higher than that in lymphocyte-like cells. These data provide valuable information for understanding the molecular basis of cellular and humoral immunity in A. japonicus.

Genomic and transcriptomic identification of the cathepsin superfamily in the Mediterranean mussel Mytilus galloprovincialis

Cathepsins are lysosomal enzymes that participate in important physiological processes, such as development, tissue remodelling, senescence and innate and adaptive immunity. The description of these proteins in molluscs is fragmented and incomplete. In the present work, we identified most of the cathepsin family members in the bivalve Mytilus galloprovincialis by screening published genomic and transcriptomic information. In this specie, the cathepsin family is composed of 41 proteins showing a high diversification of cathepsins D, L and F, not previously observed in other taxonomic groups. Specific set of cathepsins are constitutively expressed in the different mussel tissues. Transcriptomic analyses suggested coordinated activity of the different cathepsins and their sequential activation during larval development. Cathepsins also play an important role in the immune response of bivalves, and different immune pathways seem to be activated in response to Vibrio splendidus infection.

Serpin-type serine protease inhibitor mediates coelomocyte apoptosis in Apostichopus japonicus

Serine protease inhibitors (SPIs, serpins) are a protein superfamily involved in almost all physiological processes in all organisms. In this study, a novel serpin was identified from Apostichopus japonicus (Ajserpin) by using high-throughput sequencing and RACE approaches. The full-length cDNA of Ajserpin was 1893 bp with a 5'-untranslated region (UTR) of 130 bp, a 3'-UTR of 587 bp, and an open reading frame of 1176 bp encoding a polypeptide of 391 amino acids with a deduced molecular weight of 43.8 kDa. Ajserpin shares the standard structure of SPI, including three β-sheets and eight α-helices. The deduced amino acid sequences of Ajserpin had no nuclear location signal and signal peptide structure. The phylogenetic tree and immunofluorescence showed that Ajserpin belonged to the clade B subfamily and was mainly located in the cytoplasm and nucleus. Sequence comparison and protein inhibition experiments showed that the active site (P1-P1' site) of Ajserpin was Arginine and Serine, which displayed inhibitory activity toward trypsin in a dose-dependent manner. Tissue distribution analysis showed that Ajserpin transcripts were constitutively expressed in all examined tissues with the peak in the body wall. Ajserpin mRNA transcripts could be induced in Vibrio splendidus-challenged sea cucumber or lipopolysaccharide-exposed coelomocytes. Furthermore, Ajserpin knockdown by small interfering RNAs could inhibit coelomocytes apoptosis. All our results revealed that Ajserpin might serve as an immune regulator in sea cucumber.

The role of matrix metalloprotease (MMP) to the autolysis of sea cucumber (Stichopus japonicus)

BACKGROUND

Sea cucumber (Stichopus japonicus) is easy to autolysis in response to a variety of environmental and mechanical factors. In the current study, collagen fibres were extracted from fresh sea cucumber body wall and then incubated with endogenous matrix metalloprotease (MMP) of sea cucumber. Scanning electron microscopy (SEM), differential scanning calorimetry (DSC), chemical analysis and sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis were utilized to demonstrate the changes in collagen fibres, collagen fibrils and collagen proteins. Moreover, a verification experiment was also carried out to confirm the contribution of MMP to the autolysis of sea cucumber.

RESULTS

Endogenous MMP caused complete depolymerization of collagen fibres into smaller collagen fibril bundles and collagen fibrils due to the fracture of proteoglycan interfibrillar bridges. Meanwhile, endogenous MMP also caused partial degradation of collagen fibrils by releasing soluble hydroxyproline and pyridinium cross-links. Furthermore, the treatment with MMP inhibitor (1,10-phenanthroline) prevented the autolysis of tissue blocks from S. japonicus dermis.

CONCLUSION

Endogenous MMP was the key enzyme in the autolysis of sea cucumber, while its action still focused on high-level structures of collagens especially collagen fibres. © 2019 Society of Chemical Industry.

Effects of collagenase type I on the structural features of collagen fibres from sea cucumber (Stichopus japonicus) body wall

The autolysis of sea cucumber is caused by depolymerisation of collagen fibres and unfolding of fibrils. In order to highlight the role of collagenase in sea cucumber autolysis, collagen fibres from sea cucumber were hydrolysed with collagenase type I. Electron microscopy (EM) results indicated the collagenase caused partial depolymerisation of collagen fibres into fibrils due to the fracture of proteoglycan interfibrillar bridges, as well as uncoiling of collagen fibrils. Chemical analysis and SDS-PAGE both indicated collagenase induced a time-dependent release of glycosaminoglycans (GAGs) and soluble proteins, which further demonstrated the degradation of proteoglycan interfibrillar bridges. Collagenase also degraded collagens by releasing soluble hydroxyproline (Hpy), with the dissolution rate of Hyp reaching 11.11% after 72 h. Fourier transform infrared analysis showed that collagenase caused the reduction of intermolecular interactions and structural order of collagen. Hence, collagenase participated in the autolysis of sea cucumber by deteriorating both macromolecular and monomeric collagens.

A metabolomics and proteomics study of the Lactobacillus plantarum in the grass carp fermentation

Background

Lactobacillus plantarum, a versatile lactic acid-fermenting bacterium, isolated from the traditional pickles in Ningbo of China, was chosen for grass carp fermentation, which could also improve the flavor of grass carp. We here explored the central metabolic pathways of L. plantarum by using metabolomic approach, and further proved the potential for metabolomics combined with proteomics approaches for the basic research on the changes of metabolites and the corresponding fermentation mechanism of L. plantarum fermentation.

Results

This study provides a cellular material footprinting of more than 77 metabolites and 27 proteins in L. plantarum during the grass carp fermentation. Compared to control group, cells displayed higher levels of proteins associated with glycolysis and nucleotide synthesis, whereas increased levels of serine, ornithine, aspartic acid, 2-piperidinecarboxylic acid, and fumarate, along with decreased levels of alanine, glycine, threonine, tryptophan, and lysine.

Conclusions

Our results may provide a deeper understanding of L. plantarum fermentation mechanism based on metabolomics and proteomic analysis and facilitate future investigations into the characterization of L. plantarum during the grass carp fermentation.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1354-x) contains supplementary material, which is available to authorized users.

Identification and expression of cathepsin B from the freshwater mussel Cristaria plicata

Cathepsin B plays crucial roles in host immune defense against pathogen infection. In present study, a cathepsin B gene from the freshwater mussel, Cristaria plicata (CpCathB) was cloned and characterized. The full-length cDNA of CpCathB was 1825 bp, and contained a 5' untranslated region (UTR) of 36 nucleotides, an open reading frame (ORF) of 1044 bp and a 3' UTR of 745 bp with a poly (A) tail. The deduced CpCathB protein was encoded as a preproenzyme with 347 amino acid residues and predicted molecular weight of 38.55 kDa. Sequence alignment revealed that CpCathB protein shared 56% - 60.7% identity comparison with other species. The predicted tertiary structure of CpCathB protein was highly similar to that of human. The CpCathB mRNA was expressed in hemocytes, hepatopancreas, adductor muscle, gills and mantle tissues of healthy mussels, and the highest expression level was in hepatopancreas. The transcripts of CpCathB were increased in hemocytes and hepatopancreas from mussels after Aeromonas hydrophila challenge. Moreover, the recombinant CpCathB was expressed in the Escherichia coli Rosetta-gami (DE3) strain. The maximum titer of the anti-CpCathB polyclonal antibodies was 1:640,000.The CpCathB protein had a higher expression in hepatopancreas and mantle and a lower level in hemocytes.

RNA-seq based transcriptional analysis reveals dynamic genes expression profiles and immune-associated regulation under heat stress in Apostichopus japonicus

In this study, we explored the gene expression profiles in Apostichopus japonicus under continuous heat stress (6 h, 48 h and 192 h) by applying RNA-seq technique. A total of 676, 1010 and 1083 differentially expressed genes were detected at three heat stress groups respectively, which suggested complex regulation of various biological processes. Then we focused on the changing of immune system under HS in sea cucumbers. Key immune-associated genes were involved in heat stress response, which were classified into six groups: heat shock proteins, transferrin superfamily members, effector genes, proteases, complement system, and pattern recognition receptors and signaling. Moreover, the mRNA expression of the immune-associated genes were validated by the real time PCR. Our results showed that an immunological strategy in this species was developed to confront abrupt elevated temperatures in the environment.

Molecular cloning and functional characterization of cathepsin B from Nile tilapia (Oreochromis niloticus)

Cathepsin B (CatB) has been widely known for its hydrolytic ability and involvement in the innate immunity. However, the mechanism of CatB from teleosts participating in immunoregulation remains poorly understood; and the sequence of CatB from Nile tilapia (NtCatB) has not been cloned and characterized. In this study, the coding sequence of NtCatB was cloned, and then characterized by bioinformatic analysis and heterologous expression. The deduced amino acid sequence (330-aa) of NtCatB contains the representative features of CatB. Quantitative real-time PCR revealed the extensive mRNA expression of NtCatB in six tissues of healthy Nile tilapia, and its transcription level was significantly up-regulated after Streptococcus agalactiae challenge. NtCatB may interact with some immunological function proteins and take part in the regulatory pathway. These results suggest that NtCatB is likely to be involved in the immune reaction. The mature region (residues 79-328, mNtCatB) of NtCatB was cloned and transferred to pET-28a for expressing the recombinant protein. The purified recombinant mNtCatB was verified with the activity of 992.34 U mg^-1 min^-1 under the optimal condition using a substrate hydrolyzing assay. The recombinant cystatin-A1-like can effectively inhibit the activity of the recombinant mNtCatB, and their binding form was predicted by molecular docking. Our results contribute to elucidating the immunological functions of NtCatB.

Divergent roles of three cytochrome c in CTSB-modulating coelomocyte apoptosis in Apostichopus japonicus

Cytochrome c plays crucial roles in apoptosis and the immune response. We previously demonstrated that cathepsin B from Apostichopus japonicus (AjCTSB) induces coelomocyte apoptosis. However, the mechanistic explanation and the regulation of this process have not been investigated. In the present study, we identified three cytochrome c cDNAs from A. japonicus (designated Ajcytc1, Ajcytc-1, and Ajcytc-2) using expressed sequence tag- (EST) and RACE-based approaches. The deduced amino acid sequences of the three cytochrome isoforms contained conserved CXXCH motifs, which are involved in binding heme and maintaining proteolytic activity. Time course expression analysis in vitro and in vivo revealed that the three cytochrome isoforms were induced upon pathogen challenge and LPS exposure. More importantly, AjCTSB knockdown by siRNA dramatically increased mitochondrial membrane potential (ΔΨm) in a time-dependent manner based on JC-1 fluorescent probe staining. AjCTSB knockdown also resulted in decreased expression of these three cytochromes 24 h after siAjCTSB transfection. Functional analysis using isoform-specific siRNAs revealed that Ajcytc-1, but not Ajcytc1 or Ajcytc-2, is involved in coelomocyte apoptosis. Moreover, the transcript level of Ajcaspase-3, an apoptosis executioner, was also consistently down-regulated upon silencing of Ajcytc-1 but not Ajcytc1 or Ajcytc-2. Collectively, these results indicate that Ajcytc1, Ajcytc-1, and Ajcytc-2 play distinct roles in mediating the immune response to bacteria according to AjCTSB expression. Moreover, Ajcytc-1 could be released upon dissipation of the ΔΨm, which could further trigger coelomocyte apoptosis through the activation of Ajcaspase-3.

Characterization of NLRP3-like gene from Apostichopus japonicus provides new evidence on inflammation response in invertebrates

Inflammatory/defensive response after pathogen invasion is considered a local defense reaction in vertebrates. Inflammation response in Apostichopus japonicus was hardly determined due to scarce information available for nucleotide binding domain-like receptor family, pyrin domain-containing (NLRP) family. In the present study, invertebrate NLRP homologue was identified from A. japonicus (designated as AjNLRP3-like) by rapid amplification of cDNA ends. Full-length cDNA of AjNLRP3-like measured 2970 bp with 2265 bp open reading frame encoding a 754-amino acid (aa) residue protein. Structural analysis revealed that AjNLRP3-like processed characteristic domains of pyrin (32-102aa) and NACHT (183-339aa). Multiple sequence alignment and phylogenetic analysis supported that AjNLRP3-like belongs to a new member of NLRP3 protein subfamily. Spatial expression analysis revealed that AjNLRP3-like was ubiquitously expressed in all examined tissues with larger magnitude in coelomocytes. Both Vibrio splendidus challenge in vivo and lipopolysaccharide stimulation in vitro significantly upregulated mRNA expression of AjNLRP3-like when compared with the control group. NLRP3-mediated inflammation response depended on release of lysosomal cathepsin B (CTSB) and subsequent activation of high-mobility group box (HMGB) in vertebrates. We investigated expression profiles of AjNLRP3-like and AjHMGB after AjCTSB knock-down and discovered that AjNLRP3-like was depressed by 0.66-fold and 0.47-fold, whereas AjHMGB was depressed by 0.70-fold and 0.50-fold at 24 and 48 h in AjCTSB-silenced group, respectively. Similarly, down-regulation of AjHMGB was also observed after AjNLRP3-like knock-down. This study therefore suggests that A. japonicus feature similar inflammatory events as those in vertebrates, and activation of AjNLRP3-like depends on AjCTSB expression and release of AjHMGB.

Transcriptomic variation of locally-infected skin of Epinephelus coioides reveals the mucosal immune mechanism against Cryptocaryon irritans

Fish skin is the largest immunologically active mucosal organ, providing first-line defense against external pathogens. However, the skin-associated immune mechanisms of fish are still unclear. Cryptocaryon irritans is an obligate ectoparasitic ciliated protozoan that infects almost all marine fish, and is believed to be an excellent pathogen model to study fish mucosal immunity. In this study, a de novo transcriptome assembly of Epinephelus coioides skin post C. irritans tail-infection was performed for the first time using the Illumina HiSeq™ 2500 system. Comparative analyses of infected skin (group Isk) and uninfected skin (group Nsk) from the same challenged fish and control skin (group C) from uninfected control fish were conducted. As a result, a total of 91,082 unigenes with an average length of 2880 base pairs were obtained and among them, 38,704 and 48,617 unigenes were annotated based on homology with matches in the non-redundant and zebrafish database, respectively. Pairwise comparison resulted in 10,115 differentially-expressed genes (DEGs) in the Isk/C group comparison (4,983 up-regulated and 5,132 down-regulated), 2,275 DEGs in the Isk/Nsk group comparison (1,319 up-regulated and 956 down-regulated) and 4,566 DEGs in the Nsk/C group comparison (1,534 up-regulated and 3,032 down-regulated). Seven immune-related categories including 91 differentially-expressed immune genes (86 up-regulated and 5 down-regulated) were scrutinized. Both DEGs and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and immune-related gene expression analysis were used, and both analyses showed that the genes were more significantly altered in the locally-infected skin than in the uninfected skin of the same challenged fish. This suggests the skin's local immune response is important for host defense against this ectoparasite infection. Innate immune molecules, including hepcidin, C-type lectin, transferrin, transferrin receptor protein, serum amyloid A, cathepsin and complement components were significantly up-regulated (fold-change ranged from 3.3 to 12,944) in infected skin compared with control skin. The up-regulation of chemokines and chemokine receptors and activation of the leukocyte transendothelial migration pathway suggested that leucocytes intensively migrated to the local infected sites to mount a local immune defense. Toll-like receptors (TLRs) 1, 2, 5 and 5S were most significantly up-regulated in the infected skin, suggesting that these TLRs may be involved in parasite pathogen-associated molecular pattern (PAMPs) recognition. Up-regulation of the dendritic cell markers CD209 and CD83 and other antigen presentation pathway molecules provided evidence for skin local antigen presentation. Up-regulation of the T cell markers CD4 and CD48, B cell markers CD22 and CD81 and B cell receptor signaling kinase Lyn, showed the presence and population expansion of T/B cells at locally-infected sites, which suggested possible activation of a local specific immune response in the skin. Our results will facilitate in-depth understanding of local immune defense mechanisms in fish skin against ectoparasite infection.