Proteomic analysis reveals the important roles of alpha-5-collagen and ATP5β during skin ulceration syndrome progression of sea cucumber Apostichopus japonicus

Comparative proteomic analysis of the protein profile in the cuttlefish Sepia pharaonis associated with skin ulceration syndrome

Skin ulceration syndrome (SUS) is becoming a severe problem in the breeding and culturing process of the cuttlefish Sepia pharaonis. However, limited knowledge is available about the occurrence of this devastating disease. In this study, proteomic analysis was used to identify the differentially expressed proteins (DEPs) and the biological pathways enriched in SUS-diseased S. pharaonis. Both the healthy group and diseased group were analyzed in triplicate, with 4 cuttlefish in each replicate. The results showed that 85 DEPs were identified between the two groups, including 36 upregulated proteins and 49 downregulated proteins in the diseased group compared to the healthy group. GO enrichment analysis revealed that the DEPs were mainly enriched in cellular component organization or biogenesis, nucleus and ion binding processes. The results of the KEGG pathway analysis indicated that extracellular matrix (ECM)-receptor interaction was the most enriched upregulated pathway. Real-time reverse transcriptase PCR was used to identify the expression of two differentially expressed matrix metalloproteinases (MMPs), and the results showed that the mRNA expression of MMP14 and MMP19 was significantly upregulated in the skin tissue of the diseased group. Furthermore, the protease activity of the diseased group was higher than that of the healthy group. Our results offer basic knowledge on the changes in protein profiles during the occurrence of SUS in the cuttlefish S. pharaonis.

Bacillus licheniformis reduces mortality, improves symptoms, and controls residual pathogenicity in juvenile sea cucumbers Apostichopus japonicus infected with skin ulceration syndrome

Mass mortality caused by skin ulceration syndrome (SUS) is the bottle-neck for the sustainable aquaculture of the sea cucumber Apostichopus japonicus. In the present study, probiotic Bacillus licheniformis (0.25 × 109 CFU/g) was used as the treatment for A. japonicus infected with the SUS that caused by Vibrio harveyi. We found that B. licheniformis significantly reduced the number of infected sea cucumbers 5 days and 7 days after the treatment (group B), compared to those without B. licheniformis treatment (group C) (P < 0.001; P < 0.001). Further, the sea cucumbers fed B. licheniformis had significantly lower mortality at the end of the experiment (<10%) than that of those without the B. licheniformis treatment (>60%) (P < 0.001). These results suggest that the treatment of B. licheniformis is an effective method to reduce the mass mortality resulted from SUS in sea cucumber aquaculture. Further, 3-5 days of treatment significantly improved the adverse symptoms of SUS on the physiology and behavior of sea cucumbers, including the righting behavior, adhesion behavior, food consumption, fecal output and mobility. This indicates B. licheniformis treatment has the advantage in the recovery of sea cucumbers after SUS. Moreover, there was no significant difference observed in the physiology and behavior of sea cucumbers between the SUS infected sea cucumbers after the 7-day treatment of B. licheniformis and the healthy individuals. SUS infected sea cucumbers effectively returned to a stage of normalcy. Further, we found a significantly lower infected rate in sea cucumbers exposed to the culture water of group B (∼5%) than that of those in exposure to the culture water of group C (∼60%). This indicates that the treatment of B. licheniformis efficiently controls the residual pathogenicity of SUS in culture water. The present study demonstrated the effectiveness of B. licheniformis treatment as an environmentally friendly approach to reducing mortality, improving symptoms, and controlling residual pathogenicity in sea cucumber aquaculture.

TMT-based proteomics analysis of growth advantage of triploid Apostichopus japonicus

Polyploid breeding can produce new species with a faster growth rate, higher disease resistance, and higher survival rate, and has achieved significant economic benefits. This study investigated the protein differences in the body wall of triploid Apostichopus japonicus and diploid A. japonicus using isotope-labeled relative and absolute quantitative Tandem Mass Tag technology. A total of 21,096 independent peptides and 4621 proteins were identified. Among them, there were 723 proteins with significant expression differences, including 413 up-regulated proteins and 310 down-regulated proteins. The differentially expressed proteins (DEPs) were enriched in 4519 Gene Ontology enrichment pathways and 320 Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Twenty-two key DEPs related to important functions such as growth and immunity of triploid A. japonicus were screened from the results, among which 20 were up-regulated, such as cathepsin L2 cysteine protease and fibrinogen-like protein A. Arylsulfatase A and zonadhesin were down-regulated. The up-regulated proteins were mainly involved in oxidative stress response, innate immune response, and collagen synthesis in triploid A. japonicus, and the down-regulated proteins were mainly associated with the sterility of triploid A. japonicus. In addition, the transcriptome and proteome were analyzed jointly to support proteome data. In this study, the differences in protein composition between triploid and diploid A. japonicus were analyzed for the first time, and the results revealed the underlying reasons for the growth advantage of triploid A. japonicus.

Functions of lysin motif (LysM)-containing protein in antibacterial responses of sea cucumbers, Apostichopus japonicus

The lysin motif (LysM)-containing protein is one of widespread pattern-recognition receptors in prokaryotes and eukaryotes. Numerous LysM-containing gene sequences are present in gene databases; however, few have been well characterized, especially in echinoderms. In this study, the full-length cDNA of a novel LysM-containing gene was obtained from the sea cucumber Apostichopus japonicus, named AjLysM-1, using polymerase chain reaction (PCR) combined with rapid amplification of cDNA ends. We prepared and expressed recombinant AjLysM-1 protein (rAjLysM-1) and determined its pathogen-recognition ability by enzyme-linked immunosorbent and immunofluorescence assays. We also analyzed the tissue expression pattern and response to immune challenges of AjLysM-1 using quantitative real-time reverse transcription-PCR and in situ hybridization. The AjLysM-1 protein was predicted to be an intracellular non-secreted LysM-containing protein, highly homologous to the same protein in other marine echinoderms. AjLysM-1 transcripts were highest expressed in coelomocytes and were strikingly induced by challenge with representative bacterial and fungal polysaccharides. rAjLysM-1 showed weak binding to mannan, Pseudoalteromonas nigrifaciens, and Shewanella baltica, implying that AjLysM-1 might provide inadequate defense against Gram-negative bacteria and fungi. Notably, rAjLysM-1 also interacted with tyrosine protein kinase and filamin-B, indicating that it could be involved in focal adhesion in A. japonicus. These findings improve our understanding of the functions of LysM-containing proteins in marine echinoderms.

Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota

Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology.

IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.

Proteomics reveals gender differences in physiological characteristics of the gonads and tube feet of the sea cucumber, Apostichopus japonicus

The sea cucumber Apostichopus japonicus is an important aquaculture species in China because of its high nutritional and medicinal values. Gender, as a factor affecting the physiology of organisms, is always considered when improving the breeding efficiency of economically important animals. In the present study, protein expression profiles of the gonads and tube feet of male and female A. japonicus were investigated using a comparative proteomics approach. A set of 7499 proteins were identified, which covered a broad range of functions based on function annotations. A significant difference in protein expression profiles was observed between the gonads and tube feet of A. japonicus; gonads showed more apparent gender differences than tube feet. Moreover, the findings revealed that male A. japonicus had more specific functions and most of these functions were associated with energy consumption. Further analyses suggested that the regulation of ERK activity and the capacity of tyrosine production and virus immunity might be more powerful in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. Overall, our study provides new insights into the understanding of molecular mechanisms underlying gender-based physiological differences in A. japonicus. SIGNIFICANCE: The current study aimed to reveal gender differences in the physiological characteristics of gonads and tube feet of the sea cucumber A. japonicus. To the best of our knowledge, this is the first proteomics study to analyze the differences in the protein expression profiles of external organs between male and female A. japonicus. The analysis revealed gender differences in the protein expression profiles of both gonads and tube feet of A. japonicus, and the gender differences in gonads were quite apparent. Moreover, according to the recognition of differentially expressed proteins and the enrichment analyses based on Kyoto Encyclopedia of Genes and Genomes, a draft view of how the physiological functions of A. japonicus were affected by gender was obtained. Male A. japonicus could have more specific functions related to energy consumption than females. The regulation of ERK activity and virus immunity might be more robust in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. The findings presented here will improve the understanding of researchers about the molecular mechanisms underlying gender-based differences in A. japonicus and contribute to the meticulous breeding of A. japonicus.

Uncovering proteome variations of differently heat-treated sea cucumber (Apostichopus japonicus) by label-free mass spectrometry

The effects of heat treatment on the proteome of Apostichopus japonicus have been evaluated using label-free quantitative proteomics by ultrahigh performance liquid chromatography-quadrupole/time of flight (UHPLC-Q/TOF) mass spectrometry with sequential window acquisition of all the theoretical fragment ion (SWATH) acquisition mode. Chemometric tools are integrated to reveal proteomic changes by mining the protein quantitation data from fresh and differently heat-treated samples. SWATH allows the quantitation of 548 proteins, of which 24 proteins are significantly sensitive to heat treatment and 13 proteins vary significantly responding to different heat procedures (boiling, steaming, and microwave heating), and 5 of them are sharing proteins. Gene ontology (GO) annotation of the differentiating proteins highlights most of them are relevant to molecular functions. The results can be favorable to evaluate the effects of heat treatment on the nutrition and function of processed sea cucumbers and facilitate the selection of an optimal thermal treatment.

Insights into the DNA methylation of sea cucumber Apostichopus japonicus in response to skin ulceration syndrome infection

DNA methylation is an important epigenetic modification that regulates gene expression in many biological processes, including immune response. In this study, whole-genome bisulfite sequencing (WGBS) was carried out on healthy body wall (HB) and skin ulceration syndrome (SUS) infected body wall (SFB) to gain insights into the epigenetic regulatory mechanism in sea cucumber Apostichopus japonicus. After comparison, a total of 116,522 differentially methylated regions (DMRs) were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs (p < 0.05, FDR < 0.001). GO enrichment analysis indicated that regulation of DNA-templated transcription (GO: 0006355), where DNA methylation occurred, was the most significant term in the biology process. The integration of methylome and transcriptome analysis revealed that 10,499 DMRs were negatively correlated with 496 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were enriched in the phosphoinositide 3-kinase-protein kinase B (PI3K/Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Interestingly, two serine/threonine-protein kinases, nemo-like kinase (NLK) and mTOR, were highlighted after functional analysis. The variations of methylation in these two genes were associated with SUS infection and immune regulation. They regulated gene expression at different levels and showed interaction during response process. The validation of methylation sites showed high consistency between pyrosequencing and WGBS. WGBS analysis not only revealed the changes of DNA methylation, but also presented important information about the regulation of key genes after SUS infection in A. japonicus.

A real-time isothermal amplification based portable microfluidic system for simple and reliable detection of Vibrio splendidus

The spread of infectious diseases among aquaculture species has a serious impact on the aquaculture industry. Simple, specific and low-cost detection methods are urgently needed for early diagnosis and timely treatment, particularly for on-site identifying and tracking of pathogens. Vibrio splendidus (V. splendidus) is regarded as one of the main pathogenic bacteria causing skin ulcerative syndrome in cultured sea cucumbers, leading to massive mortality and severe economic losses. We herein present a microfluidic-based real-time fluorogenic loop-mediated isothermal amplification (LAMP) system for simple and reliable detection of V. splendidus. A LAMP primer set with six primers (arsB1) specifically targeting the arsB gene of V. splendidus was successfully designed and tested on the portable microfluidic system for the first time. Only a single step of sample loading using a pipette is required to fill an array of reaction wells (with 10 or 18 wells) in a disposable chip for multiplex detection. A dedicated plastic shell is then utilized to tightly seal the openings of the chip by buckling to prevent contamination and evaporation. Up to four chips (one sample per chip) can be held in the stand-alone and inexpensive microdevice simultaneously, enabling on-demand detection of multiple samples in a single run. Reproducible (relatively low intra- and inter-chip variability) and sensitive (as few as ∼20 CFU, Colony-Forming Units, per reaction well) on-chip arsB1-LAMP assay was demonstrated by using diluted lysate of V. splendidus. A linear standard curve (R2 > 0.98) was attained over the template concentration range of 5 × 103 to 5 × 106 CFU mL-1. V. splendidus can be detected in samples containing different bacteria, indicating the feasibility of the portable microfluidic LAMP system for parallel detection of multiple bacterial pathogens. The proposed on-chip LAMP assay is simple to operate, reliable for amplification, flexible in detection and cost-effective in instrumentation and testing, holding great potential for on-site rapid detection and routine monitoring of aquaculture pathogens.

Divergent proteomics response of Apostichopus japonicus suffering from skin ulceration syndrome and pathogen infection

Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease that affects the stable development of Apostichopus japonicus in the culture industry. The part of sea cucumber that suffers from major injury and is directly observed is the body wall, in which protein variations should be the most direct evidence of the disease. To understand the response mechanisms of A. japonicus in SUS progression, we investigated protein changes in the body wall of diseased A. japonicus induced by Vibrio splendidus and individuals with natural diseases by isobaric tags for relative and absolute quantification (iTRAQ). About 119 proteins were identified in the two iTRAQ groups. A comparison of the protein expression profiles among two SUS conditions revealed that the mode of action induced by V. splendidus (Vs-SUS) was completely different from those in individuals with natural disease (ND-SUS). Most of the differentially expressed proteins (DEPs) (33 in 37 DEPs) were significantly depressed in the Vs-SUS group. Only 13 proteins in 27 DEPs showed similar trend to those in the ND-SUS group. Many important proteins involved in major intercellular signaling pathways associated with SUS disease were identified based on the KEGG and GO database search. Many proteins were located in the mitochondria and mainly involved in the oxidative stress pathway. Glutathione metabolism pathway was associated with reactive oxygen (ROS) production in the ND-SUS group. In the Vs-group, most of the proteins were concentrated in the cytoplasm and were related to immunity and extracellular matrix stability. In the ND-SUS group, the activity of key enzymes (CAT, GPx) that eliminate mitochondrial ROS production and structural stable protein (HSP60, HSP10) decreased, whereas those of complement proteins (C3, C3-2) that promoted ROS production was upregulated. This finding supported that oxidative damage caused by ROS might be the main effector for SUS in the ND-SUS group. The challenge with V. splendidus led to the breakdown of the defense capability of sea cucumber and suppressed the expression of immune-related proteins, such as C-type lectin, caspase, STAT, and cystatin. The downregulation of TIMP led to MMP1 overexpression. Members of the MMP family could directly degrade the extracellular matrix, which may be the main reason for the cell matrix degradation and induced SUS disease in the Vs-SUS group. Hence, ROS and extracellular matrix degradation enzymes could play important roles in the formation of SUS in sea cucumber. Results provide insights into the complex molecular mechanism of SUS in sea cucumber.