Effect of seasonal high temperature on the immune response in Apostichopus japonicus by transcriptome analysis

Sea cucumber physiological response to abiotic stress: Emergent contaminants and climate change

The ocean is facing a multitude of abiotic stresses due to factors such as climate change and pollution. Understanding how organisms in the ocean respond to these global changes is vital to better predicting consequences. Sea cucumbers are popular echinoderms with multiple ecological, nutritional, and pharmaceutical benefits. Here, we reviewed the effects of environmental change on an ecologically important echinoderm of the ocean, aiming to understand their response better, which could facilitate healthy culture programs under environmental changes and draw attention to knowledge gaps. After screening articles from the databases, 142 studies were included on the influence of emergent contaminants and climate variation on the early developmental stages and adults of sea cucumbers. We outlined the potential mechanism underlying the physiological response of sea cucumbers to emerging contaminants and climate change. It can be concluded that the physiological response of sea cucumbers to emergent contaminants differs from their response to climate change. Sea cucumbers could accumulate pollutants in their organs but are aestivated when exposed to extreme climate change. Research showed that the physiological response of sea cucumbers to pollutants indicates that these pollutants impair critical physiological processes, particularly during the more susceptible early phases of development compared to adults, and the accumulation of these pollutants in adults is often observed. For climate change, sea cucumbers showed gradual adaptation to the slight variation. However, sea cucumbers undergo aestivation under extreme conditions. Based on this review, critical suggestions for future research are presented, and we call for more efforts focusing on the co-occurrence of different stressors to extend the knowledge regarding the effects of environmental changes on these economically and ecologically important species.

Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata

To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.

Gills de novo assembly reveals oxidative stress, unfolded protein, and immune response on red cusk-eel (Genypterus chilensis) under thermal stress

The heat waves on the South Pacific coast could lead to thermal stress in native fish. The red cusk-eel (Genypterus chilensis) is relevant for Chilean artisanal fisheries and aquaculture diversification. This study examined the effect of high-temperature stress in the gills of G. chilensis in control (14 °C) and high-temperature stress (19 °C) conditions. High-temperature stress induces a significant increase in gills cortisol levels. Additionally, oxidative damage was observed in gills (protein carbonylation and lipoperoxidation). RNA-seq data was used to build the first transcriptome assembly of gills in this species (23,656 annotated transcripts). A total of 1138 down-regulated and 1531 up-regulated transcripts were observed in response to high-temperature stress in gills. The enrichment analysis showed immune response and replication enriched processes (on down-regulated transcripts), and processes related to the folding of proteins, endoplasmic reticulum, and transporter activity (on up-regulated transcripts). The present study showed how gills could be affected by high-temperature stress.

Alterations in mitochondrial structure and function in response to environmental temperature changes in Apostichopus japonicus

Global temperatures have risen as a result of climate change, and the resulting warmer seawater will exert physiological stresses on many aquatic animals, including Apostichopus japonicus. It has been suggested that the sensitivity of aquatic poikilothermal animals to climate change is closely related to mitochondrial function. Therefore, understanding the interaction between elevated temperature and mitochondrial functioning is key to characterizing organisms' responses to heat stress. However, little is known about the mitochondrial response to heat stress in A. japonicus. In this work, we investigated the morphological and functional changes of A. japonicus mitochondria under three representative temperatures, control temperature (18 °C), aestivation temperature (25 °C) and heat stress temperature (32 °C) temperatures using transmission electron microscopy (TEM) observation of mitochondrial morphology combined with proteomics and metabolomics techniques. The results showed that the mitochondrial morphology of A. japonicus was altered, with decreases in the number of mitochondrial cristae at 25 °C and mitochondrial lysis, fracture, and vacuolization at 32 °C. Proteomic and metabolomic analyses revealed 103 differentially expressed proteins and 161 differential metabolites at 25 °C. At 32 °C, the levels of 214 proteins and 172 metabolites were significantly altered. These proteins and metabolites were involved in the tricarboxylic acid (TCA) cycle, substance transport, membrane potential homeostasis, anti-stress processes, mitochondrial autophagy, and apoptosis. Furthermore, a hypothetical network of proteins and metabolites in A. japonicus mitochondria in response to temperature changes was constructed based on proteomic and metabolomic data. These results suggest that the dynamic regulation of mitochondrial energy metabolism, resistance to oxidative stress, autophagy, apoptosis, and mitochondrial morphology in A. japonicus may play important roles in the response to elevated temperatures. In summary, this study describes the response of A. japonicus mitochondria to temperature changes from the perspectives of morphology, proteins, and metabolites, which provided a better understanding the mechanisms of mitochondrial regulation under environment stress in marine echinoderms.

Transcriptomic Response of the Atlantic Surfclam (Spisula solidissima) to Acute Heat Stress

There is clear evidence that the oceans are warming due to anthropogenic climate change, and the northeastern coast of USA contains some of the fastest warming areas. This warming is projected to continue with serious biological and social ramifications for fisheries and aquaculture. One species particularly vulnerable to warming is the Atlantic surfclam (Spisula solidissima). The surfclam is a critically important species, linking marine food webs and supporting a productive, lucrative, and sustainable fishery. The surfclam is also emerging as an attractive candidate for aquaculture diversification, but the warming of shallow coastal farms threatens the expansion of surfclam aquaculture. Little is known about the adaptive potential of surfclams to cope with ocean warming. In this study, the surfclam transcriptome under heat stress was examined. Two groups of surfclams were subjected to heat stress to assess how artificial selection may alter gene expression. One group of clams had been selected for greater heat tolerance (HS) and the other was composed of random control clams (RC). After a 6-h exposure to 16 or 29 °C, gill transcriptome expression profiles of the four temperature/group combinations were determined by RNA sequencing and compared. When surfclams experienced heat stress, they exhibited upregulation of heat shock proteins (HSPs), inhibitors of apoptosis (IAPs), and other stress-response related genes. RC clams differentially expressed 1.7 times more genes than HS clams, yet HS clams had a stronger response of key stress response genes, including HSPs, IAPs, and genes involved with mitigating oxidative stress. The findings imply that the HS clams have a more effective response to heat stress after undergoing the initial selection event due to genetic differences created by the selection, epigenetic memory of the first heat shock, or both. This work provides insights into how surfclams adapt to heat stress and should inform future breeding programs that attempt to breed surfclam for greater heat tolerance, and ultimately bring greater resiliency to shellfish farms.

Transcriptomic Responses of a Lightly Calcified Echinoderm to Experimental Seawater Acidification and Warming during Early Development

Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised under combinations of two temperatures (19 °C or 22 °C) and two pCO2 levels (400 or 1000 μatm) that reflect the current and end-of-21st-century projected ocean scenarios. The investigation focused on assessing larval development and identifying differences in gene expression patterns at four crucial embryo-larval stages (blastula, gastrula, auricularia, and doliolaria) of sea cucumbers, using RNA-seq. Results showed the detrimental effect of OA on the early development and body growth of A. japonicus larvae and a reduction in the expression of genes associated with biomineralization, skeletogenesis, and ion homeostasis. This effect was particularly pronounced during the doliolaria stage, indicating the presence of bottlenecks in larval development at this transition phase between the larval and megalopa stages in response to OA. OW accelerated the larval development across four stages of A. japonicus, especially at the blastula and doliolaria stages, but resulted in a widespread upregulation of genes related to heat shock proteins, antioxidant defense, and immune response. Significantly, the negative effects of elevated pCO2 on the developmental process of larvae appeared to be mitigated when accompanied by increased temperatures at the expense of reduced immune resilience and increased system fragility. These findings suggest that alterations in gene expression within the larvae of A. japonicus provide a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.

Ajpacifastin-like is involved in the immune response of Apostichopus japonicus challenged by Vibrio splendidus

Pacifastin proteins are previously found to regulate the phenoloxidase system in invertebrates and arthropods. In this study, the immune response that was regulated by Ajpacifastin-like in the sea cucumber Apostichopus japonicus was determined. RNA interference was used to knock down the expression of the Ajpacifastin-like gene in A. japonicus, followed by challenge with Vibrio splendidus, and the colony count showed that the survival of V. splendidus in the si-Ajpacifastin group increased 4.64-fold compared to that of the control group. The purified recombinant Ajpacifastin-like showed an inhibitory effect on the extracellular protease activity of the supernatant collected from the V. splendidus culture. Consequently, a comparative transcriptome analysis of the coelomocytes from the control group and the si-Ajpacifastin group was performed to explore the global regulatory effect of the Ajpacifastin-like. A total of 1486 differentially expressed genes (DEGs) were identified, including 745 upregulated genes and 741 downregulated genes. GO enrichment showed that the DEGs were mainly enriched in translation, cytosolic ribosomal subunit and structural constituent of ribosome. KEGG analysis showed that the DEGs were significantly enriched in the retinoic acid-inducible gene I (RIG-I)-like receptor signaling pathway, antigen processing and presentation, toll-like receptor signaling pathway, mitogen-activated protein kinase signaling pathway, nuclear factor-kappa B signaling pathway and other immune-related pathways. Furthermore, real-time reverse transcriptase PCR was used to determine the RNA levels of six DEGs, i.e., cathepsinB, CYLD, caspase8, TRAF6, hsp90 and FADD, to verify the RNA-seq results. Overall, our results specified the immune response and pathways of A. japonicus in which Ajpacifastin-like was involved in.

Oxidative stress responses in the respiratory tree and the body wall of sea cucumber Apostichopus japonicus (Selenka) to high temperature

Sea cucumber Apostichopus japonicas (Selenka) is one of the important aquaculture species distributed in northern China. In recent years, global warming caused frequent high temperature weather in summer in northern China, resulting in dramatic losses of the sea cucumber aquaculture industry. In the present study, we focused on the effect of oxidative stress in Apostichopus japonicus (Selenka) subjected to high temperature stress. Sea cumbers were exposed to the control (16 °C), and high temperature treatments (20 °C, 24 °C, and 28 °C) for 7 days. Then, reactive oxygen species (ROS) level, superoxide dismutase (SOD) activity, catalase (CAT) activity, peroxidase (POD) activity, reduced glutathione (GSH) content, malondialdehyde (MDA) content and 8-hydroxy-2'-deoxyguanosine (8-OHdG) level in the respiratory tree and body wall were detected, respectively. Results showed that 24 °C and 28 °C acute exposure induced the elevation of ROS level, SOD, CAT, POD activities, GSH content, MDA content and 8-OHdG level in the respiratory tree of sea cucumber. In contrast, no significant changes were observed for ROS and 8-OHdG levels in the body wall of sea cucumber, while the antioxidants including SOD, CAT, POD, and GSH decreased to some extent. Moreover, MDA content exhibited a noticeable increase in the body wall, similarly to that in the respiratory tree, indicating that high temperature could induce severe lipid peroxidation in two tissues. Considering the differences in various biomarkers measured in two tissues, respiratory tree might be more susceptible to the high temperature changes compared to the body wall. Our findings may help understand the oxidative stress response to high temperature in the respiratory tree and the body wall in A. japonicus.

Expression Regulation Mechanisms of Sea Urchin (Strongylocentrotus intermedius) Under the High Temperature: New Evidence for the miRNA-mRNA Interaction Involvement

In the context of global warming and continuous high temperatures in the northern part of China during summer, the mortality rate of our main breeding species, Strongylocentrotus intermedius, reached 80% in 2020. How sea urchins respond to high temperatures is of great concern to academia and industry. In this study, we examined the antioxidant enzyme activities of different color tube-footed sea urchins under heat stress and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. The results showed that the antioxidant enzyme activities of sea urchins were altered by thermal stress, and the changes in peroxidase activities of red tube-footed sea urchins were particularly significant. Investigations revealed that 1,079 differentially expressed genes (DEGs), 11 DE miRNAs, and 104 “DE miRNA-DEG” pairs in total were detected in sea urchins under high temperature stress. Several mRNA and miRNAs were significantly changed (e.g. HSP70, DnaJ11, HYAL, CALR, miR-184-p5, miR-92a, miR-92c, and miR-124-p5), suggesting these genes and miRNAs exerted important functions in response to high temperature. At the transcriptional level, red tube-footed sea urchins were found to be more sensitive to high temperature and could respond to high temperature rapidly. DE miRNA-mRNA network showed that miR-92b-3p and PC-5p-7420 were the most corresponding miRNAs. Five mRNAs (DnaJ11, SAR1B, CALR, HYOU1, TUBA) may be potential markers of sea urchin response to high temperature. Possible interaction between miRNA-mRNA could be linked to protein folding in the endoplasmic reticulum, Phagosomes, and calcium transport. This study provides a theoretical basis for the molecular mechanism of sea urchin heat tolerance and information that will aid in the selection and breeding of sea urchins with high temperature tolerance.

Comparative transcriptome analysis reveals changes in gene expression in sea cucumber (Holothuria leucospilota) in response to acute temperature stress

Ambient temperature is an important abiotic factor that influences growth performance and physiological functions in sea cucumbers. To understand the molecular responses of the sea cucumber Holothuria leucospilota to acute temperature stress, we performed a de novo transcriptome analysis of body wall tissue from H. leucospilota exposed to 2 hoursh of acute heat (35 ± 1 °C) and cold stress (15 ± 1 °C). A total of 99,015 unigenes were obtained after assembly of the sequenced reads. Compared with a control group maintained at 25.0 ± 1 °C, 1169 differentially expressed unigenes (DEGs) were identified after heat stress, 781 were up-regulated and 388 were down-regulated. After cold stress, 1464 DEGs were identified; 900 were up-regulated and 564 were down-regulated. The annotation of DEGs revealed that heat shock proteins play important roles in protecting H. leucospilota from high temperature stress. Furthermore, KEGG pathway enrichment analysis showed that the categories: "Ribosome" and "Protein processing in endoplasmic reticulum" were strongly affected by heat stress. These two pathways are associated with biosynthesis and processing of proteins, and refolding of misfolded proteins. The lipid metabolism pathways "Sphingolipid metabolism" and "Ether lipid metabolism", were affected by cold stress. The RNA-Seq results for eight selected DEGs were verified the expression by quantitative real-time PCR analysis. Our results will improve the understanding of the molecular response mechanisms of H. leucospilota to ambient temperature stress.

Transcriptome analysis reveals roles of polian vesicle in sea cucumber Apostichopus japonicus response to Vibrio splendidus infection

Polian vesicle is originally regarded as a hematopoietic and inflammatory response organ in sea cucumber by the operations of cell depletion and heterogeneous cells injection, respectively. In the present study, to reveal the role and immune mechanisms of polian vesicle in response to pathogen, Vibrio splendidus, we first performed a comparative transcriptome analysis for the cells from polian vesicle wall in V. splendidus-challenged Apostichopus japonicus through RNA high-throughput sequencing technology. Briefly, 465,356,848 clean reads were obtained after cleaning up low-quality reads in total. Approximately 73% of the sequenced reads could be aligned to the reference genome of A. japonicus. The DEGs of CG (control group) vs TG 24 h (24 h post-infection group), CG vs TG 72 h (72 h post-infection group) and TG 24 h vs TG 72 h were 3762, 1391 and 3258, respectively. Gene Ontology (GO) annotation assay revealed that those genes associated with the processes such as cell process, cell, binding and catalytic activity were significantly induced in all three groups post V. splendidus infection. KEGG enrichment analysis suggested the DEGs in TG 24 h were enriched in Toll-like receptor (TLR) signaling pathway, complement and coagulation cascades, antigen processing and presentation and IL-17 signaling pathway compared with that in CG, while the pathways including ribosome biogenesis in eukaryotes, DNA replication, and cell cycle related with cell proliferation were mainly enriched in TG 72 h than that of CG. Furthermore, six important DEGs were chosen and showed the consistent expression patterns with the results of RNA-seq by qPCR. Overall, our analysis towards the current data demonstrates that polian vesicle may play an essential role in the regulation of immune response in A. japonicus and provide new insights into hematopoietic function of polian vesicle in response to pathogen infection.

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus

Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.

Combined Effects of Elevated Temperature and Crude Oil Pollution on Oxidative Stress and Apoptosis in Sea Cucumber (Apostichopus japonicus, Selenka)

Currently, global climate change and oil pollution are two main environmental concerns for sea cucumber (Apostichopus japonicus) aquaculture. However, no study has been conducted on the combined effects of elevated temperature and oil pollution on sea cucumber. Therefore, in the present study, we treated sea cucumber with elevated temperature (26 °C) alone, water-accommodated fractions (WAF) of Oman crude oil at an optimal temperature of 16 °C, and Oman crude oil WAF at an elevated temperature of 26 °C for 24 h. Results showed that reactive oxygen species (ROS) level and total antioxidant capacity in WAF at 26 °C treatment were higher than that in WAF at 16 °C treatment, as evidenced by 6.03- and 1.31-fold-higher values, respectively. Oxidative damage assessments manifested that WAF at 26 °C treatment caused much severer oxidative damage of the biomacromolecules (including DNA, proteins, and lipids) than 26 °C or WAF at 16 °C treatments did. Moreover, compared to 26 °C or WAF at 16 °C treatments, WAF at 26 °C treatment induced a significant increase in cellular apoptosis by detecting the caspase-3 activity. Our results revealed that co-exposure to elevated temperature and crude oil could simulate higher ROS levels and subsequently cause much severer oxidative damage and cellular apoptosis than crude oil alone on sea cucumber.

Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus

Heat stress (HS) is an important factor for the survival of the marine organism Apostichopus japonicus. Lysine acetylation is a pivotal post-translational modification that modulates diverse physiological processes including heat shock response (HSR). In this study, 4028 lysine acetylation sites in 1439 proteins were identified in A. japonicus by acetylproteome sequencing. A total of 13 motifs were characterized around the acetylated lysine sites. Gene Ontology analysis showed that major acetylated protein groups were involved in “oxidation–reduction process”, “ribosome”, and “protein binding” terms. Compared to the control group, the acetylation quantitation of 25 and 41 lysine sites changed after 6 and 48 h HS. Notably, lysine acetyltransferase CREB-binding protein (CBP) was identified to have differential acetylation quantitation at multiple lysine sites under HS. Various chaperones, such as caseinolytic peptidase B protein homolog (CLBP), T-complex protein 1 (TCP1), and cyclophilin A (CYP1), showed differential acetylation quantitation after 48 h HS. Additionally, many translation-associated proteins, such as ribosomal proteins, translation initiation factor (IF), and elongation factors (EFs), had differential acetylation quantitation under HS. These proteins represented specific interaction networks. Collectively, our results offer novel insight into the complex HSR in A. japonicus and provide a resource for further mechanistic studies examining the regulation of protein function by lysine acetylation.