Pub Date : 2026-01-20DOI: 10.1016/j.cbd.2026.101756
Yufei Liu , Zonglin Yang , Min Zhang , Xiaowu Chen , Xiaodong Jiang
The Chinese mitten crab (Eriocheir sinensis) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected E. sinensis to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, E. sinensis maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of E. sinensis to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.
{"title":"Response mechanisms of hepatopancreatic metabolism and gut microbiota in Chinese mitten crab (Eriocheir sinensis) under chronic high-pH stress","authors":"Yufei Liu , Zonglin Yang , Min Zhang , Xiaowu Chen , Xiaodong Jiang","doi":"10.1016/j.cbd.2026.101756","DOIUrl":"10.1016/j.cbd.2026.101756","url":null,"abstract":"<div><div>The Chinese mitten crab (<em>Eriocheir sinensis</em>) is a commercially important aquaculture species in China, with its survival highly vulnerable to abnormal water pH. This study subjected <em>E. sinensis</em> to chronic high-pH stress (control: pH = 8; experimental groups: pH = 9 and pH = 10) and integrated hepatopancreas transcriptomic/metabolomic analyses with intestinal microbiota 16S rRNA sequencing to explore its adaptive mechanisms. The results revealed distinct adaptive strategies across stress phases: under short-term (15 days) high-pH stress, <em>E. sinensis</em> maintained somatic homeostasis mainly via rapid regulation of carbohydrate, lipid, protein metabolism, and energy allocation. In contrast, long-term (30 days) stress drove a strategic shift toward accelerated lipid catabolism, enhanced energy metabolism, and activated immune-related pathways. Additionally, high-pH stress significantly altered the intestinal microbiota community structure, marked by increased abundances of Proteobacteria and Pseudomonas, indicating a potential risk of microbial dysbiosis. Collectively, these findings elucidate the physiological adaptation mechanisms of <em>E. sinensis</em> to high-pH environments and lay a theoretical foundation for improving the sustainability of its aquaculture under extreme pH conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101756"},"PeriodicalIF":2.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.cbd.2026.101758
Na Sheng , Yongchuang Li , Yongqing Wang , Zheyan Chen , Xilei Li , Xianji Tao , Jiale Li , Jianbin Feng
The red swamp crayfish, Procambarus clarkii, is a commercially significant crustacean species for aquaculture globally. Growth traits are of great importance for economic efficiency in the aquaculture of the species. However, the molecular mechanisms of regulating growth rate in P. clarkii remain poorly understood. Here, to identify the hub genes and key pathways related to growth rate, transcriptome sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted on the gill, heart, hepatopancreas, intestine, and muscle from P. clarkii with different growth rate in three full-sib families. A total of 906 differentially expressed genes (DEGs) in the gill (95 up-regulated and 811 down-regulated), 1042 DEGs in the heart (45 up-regulated and 997 down-regulated), 257 DEGs in the hepatopancreas (80 up-regulated and 177 down-regulated), 691 DEGs in the intestine (174 up-regulated and 517 down-regulated), and 158 DEGs in the muscle (30 up-regulated and 128 down-regulated) were identified, respectively. The DEGs were annotated into 101 GO terms, which mainly involved in chitin binding, structural components of the stratum corneum, extracellular region and extracellular space. Nine key pathways including the Wnt signaling pathway, autophagy-animal, phagosome, amino sugar and nucleotide sugar metabolism, TGF-β signaling pathway, drug metabolism-other enzymes, mTOR signaling pathway, lysine degradation, and lysosome pathway were identified based on the KEGG enrichment analysis. A hub module was identified by WGCNA analysis. The hub genes related to structural composition, such as cuticle protein 7-like and pro-resilin, as well as genes involved in various cellular processes, like ataxin-2 homolog were identified based on the PPI network analysis. Overall, the results would provide valuable insights into understanding the molecular regulatory mechanisms of growth rate of P. clarkii.
{"title":"Identification of candidate hub genes and key pathways related to growth rate of the red swamp crayfish based on WGCNA analysis","authors":"Na Sheng , Yongchuang Li , Yongqing Wang , Zheyan Chen , Xilei Li , Xianji Tao , Jiale Li , Jianbin Feng","doi":"10.1016/j.cbd.2026.101758","DOIUrl":"10.1016/j.cbd.2026.101758","url":null,"abstract":"<div><div>The red swamp crayfish, <em>Procambarus clarkii</em>, is a commercially significant crustacean species for aquaculture globally. Growth traits are of great importance for economic efficiency in the aquaculture of the species. However, the molecular mechanisms of regulating growth rate in <em>P. clarkii</em> remain poorly understood. Here, to identify the hub genes and key pathways related to growth rate, transcriptome sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted on the gill, heart, hepatopancreas, intestine, and muscle from <em>P. clarkii</em> with different growth rate in three full-sib families. A total of 906 differentially expressed genes (DEGs) in the gill (95 up-regulated and 811 down-regulated), 1042 DEGs in the heart (45 up-regulated and 997 down-regulated), 257 DEGs in the hepatopancreas (80 up-regulated and 177 down-regulated), 691 DEGs in the intestine (174 up-regulated and 517 down-regulated), and 158 DEGs in the muscle (30 up-regulated and 128 down-regulated) were identified, respectively. The DEGs were annotated into 101 GO terms, which mainly involved in chitin binding, structural components of the stratum corneum, extracellular region and extracellular space. Nine key pathways including the Wnt signaling pathway, autophagy-animal, phagosome, amino sugar and nucleotide sugar metabolism, TGF-β signaling pathway, drug metabolism-other enzymes, mTOR signaling pathway, lysine degradation, and lysosome pathway were identified based on the KEGG enrichment analysis. A hub module was identified by WGCNA analysis. The hub genes related to structural composition, such as <em>cuticle protein 7-like</em> and <em>pro-resilin</em>, as well as genes involved in various cellular processes, like <em>ataxin-2 homolog</em> were identified based on the PPI network analysis. Overall, the results would provide valuable insights into understanding the molecular regulatory mechanisms of growth rate of <em>P. clarkii</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101758"},"PeriodicalIF":2.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.cbd.2026.101753
Tao Zhu , Zhu Zhu , Shengjie Li , Jing Tian , Caixia Lei , Jinxing Du , Hongmei Song
Salinity profoundly impacts fish survival, distribution, and physiological functions. Grass carp (Ctenopharyngodon idella), a vital aquaculture species, offers a representative model to investigate salinity adaptation mechanisms, providing crucial theoretical support for aquaculture practices. While the liver is a key metabolic organ in fish salinity adaptation, its specific regulatory role in the high-salinity tolerance of grass carp remains unclear. In this study, we investigated the effects of long-term salinity stress (0parts per thousand [ppt], 4 ppt, and 8 for one month) on grass carp liver. At 4 ppt salinity, mild hepatocyte edema and acinar cell hyperplasia were observed, while at 8 ppt salinity, irregular hepatocyte shapes, dilated hepatic sinusoids, and focal inflammatory cell infiltration were detected. Transcriptome sequencing showed that increasing salinity led to significant upregulation of genes involved in steroid synthesis, lipid metabolism, and cholesterol synthesis, while immune-related gene expression trended downward. Notably, LOC127523424 (carbonic anhydrase 4), igfbp7 (insulin-like growth factor-binding protein 7), and taurine transporter genes (slc6a6b, slc6a6a) all increased with rising salinity, suggesting their involvement in enhancing hyperosmotic stress adaptation. In conclusion, our findings confirm a significant impact of salinity on the grass carp liver. Long-term high-salinity adaptation appears to reduce immunity, while the liver enhances high-salinity tolerance through increased steroid synthesis and metabolism.
{"title":"Hepatic physiological and transcriptomic responses of grass carp (Ctenopharyngodon idella) to long-term salinity stress","authors":"Tao Zhu , Zhu Zhu , Shengjie Li , Jing Tian , Caixia Lei , Jinxing Du , Hongmei Song","doi":"10.1016/j.cbd.2026.101753","DOIUrl":"10.1016/j.cbd.2026.101753","url":null,"abstract":"<div><div>Salinity profoundly impacts fish survival, distribution, and physiological functions. Grass carp (<em>Ctenopharyngodon idella</em>), a vital aquaculture species, offers a representative model to investigate salinity adaptation mechanisms, providing crucial theoretical support for aquaculture practices. While the liver is a key metabolic organ in fish salinity adaptation, its specific regulatory role in the high-salinity tolerance of grass carp remains unclear. In this study, we investigated the effects of long-term salinity stress (0parts per thousand [ppt], 4 ppt, and 8 for one month) on grass carp liver. At 4 ppt salinity, mild hepatocyte edema and acinar cell hyperplasia were observed, while at 8 ppt salinity, irregular hepatocyte shapes, dilated hepatic sinusoids, and focal inflammatory cell infiltration were detected. Transcriptome sequencing showed that increasing salinity led to significant upregulation of genes involved in steroid synthesis, lipid metabolism, and cholesterol synthesis, while immune-related gene expression trended downward. Notably, <em>LOC127523424</em> (carbonic anhydrase 4), <em>igfbp7</em> (insulin-like growth factor-binding protein 7), and taurine transporter genes (<em>slc6a6b</em>, <em>slc6a6a</em>) all increased with rising salinity, suggesting their involvement in enhancing hyperosmotic stress adaptation. In conclusion, our findings confirm a significant impact of salinity on the grass carp liver. Long-term high-salinity adaptation appears to reduce immunity, while the liver enhances high-salinity tolerance through increased steroid synthesis and metabolism.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101753"},"PeriodicalIF":2.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.cbd.2026.101755
Qiang Wang , Siyi Li , Yu Yang , Rubiao Xie , Lingbin Wang , Weijun Wang , Jianmin Yang , Guohua Sun
Heat temperature caused by changes in the global environment have significant impacts on marine organisms. Apostichopus japonicus (A. japonicus) is an economically important benthic species in China's shallow-sea aquaculture. However, its growth and survival are easily affected by rising seawater temperatures. Therefore, it is necessary to explore its response to environmental high temperature. Endoplasmic reticulum (ER)stressserves as an important regulatory strategy for organisms to respond to environmental changes. It acts as the core hub connecting stress and immunity. In this study, we analyzed the histology, ultrastructure, and transcriptome of the digestive tract of A. japonicus at three temperatures: normal (18 °C), aestivation (25 °C), and lethal (32 °C) temperatures, to explore the role of ER stress in response to high temperature. Histological and ultrastructural results indicate that high temperature caused morphological changes in the digestive tract and that the structure and morphology of the ER exhibit alterations and even varying degrees of damage. A total of 603 and 4615 differentially expressed genes (DEGs) were identified by transcriptome sequencing in the T25-vs-T18 and the T32-vs-T25 group comparisons, respectively. The GO results showed that DEGs were significantly enriched in GO terms related to protein folding, such as chaperone-mediated protein folding in both comparison groups. Additionally, KEGG enrichment analysis showed that both groups activated the pathway of protein processing in the ER and induced the ER stress response. The ER molecular chaperones, including BiP, GRP94, and HSP70, were all upregulated in expression. In addition to the aforementioned ER molecular chaperones, downstream factors in the unfolded protein response, such as S1P, TRAF2, and XBP, were also significantly upregulated in T32-vs-T25 group comparisons, indicating that UPR signaling pathways had enhanced expression. Our findings have characterized the internal molecular regulatory process of A. japonicus under high temperature from the perspective of ER stress and provides clues regarding immune response and homeostatic regulation in invertebrates under environment stress. These findings can provide a reference for the formulation of management measures to mitigate the impact of climate change on aquaculture.
{"title":"Different degrees of environmental high temperature induce varying endoplasmic reticulum stress responses in Apostichopus japonicus","authors":"Qiang Wang , Siyi Li , Yu Yang , Rubiao Xie , Lingbin Wang , Weijun Wang , Jianmin Yang , Guohua Sun","doi":"10.1016/j.cbd.2026.101755","DOIUrl":"10.1016/j.cbd.2026.101755","url":null,"abstract":"<div><div>Heat temperature caused by changes in the global environment have significant impacts on marine organisms. <em>Apostichopus japonicus (A. japonicus)</em> is an economically important benthic species in China's shallow-sea aquaculture. However, its growth and survival are easily affected by rising seawater temperatures. Therefore, it is necessary to explore its response to environmental high temperature. <em>Endoplasmic reticulum (</em>ER<em>)</em> <strong>stress</strong> <em>serves as an important regulatory strategy for organisms to respond to environmental changes. It acts as the core hub connecting stress and immunity</em>. In this study, we analyzed the histology, ultrastructure, and transcriptome of the digestive tract of <em>A. japonicus</em> at three temperatures: normal (18 °C), aestivation (25 °C), and lethal (32 °C) temperatures, to explore the role of ER stress in response to high temperature. Histological and ultrastructural results indicate that high temperature caused morphological changes in the digestive tract and that the structure and morphology of the ER exhibit alterations and even varying degrees of damage. A total of 603 and 4615 differentially expressed genes (DEGs) were identified by transcriptome sequencing in the T25-vs-T18 and the T32-vs-T25 group comparisons, respectively. The GO results showed that DEGs were significantly enriched in GO terms related to protein folding, such as chaperone-mediated protein folding in both comparison groups. Additionally, KEGG enrichment analysis showed that both groups activated the pathway of protein processing in the ER and induced the ER stress response. The ER molecular chaperones, including <em>BiP</em>, <em>GRP94</em>, and <em>HSP70</em>, were all upregulated in expression. In addition to the aforementioned ER molecular chaperones, downstream factors in the unfolded protein response, such as <em>S1P</em>, <em>TRAF2</em>, and <em>XBP</em>, were also significantly upregulated in T32-vs-T25 group comparisons, indicating that UPR signaling pathways had enhanced expression. Our findings have characterized the internal molecular regulatory process of <em>A. japonicus</em> under high temperature from the perspective of ER stress and provides clues regarding immune response and homeostatic regulation in invertebrates under environment stress. These findings can provide a reference for the formulation of management measures to mitigate the impact of climate change on aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101755"},"PeriodicalIF":2.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146069474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-16DOI: 10.1016/j.cbd.2026.101754
Janki A. Bhalodi , Joachim M. Surm , Adam M. Reitzel
Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, Nematostella vectensis. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of N. vectensis HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.
{"title":"Transcription dynamics and regulation of heat shock protein genes during stress and development in the estuarine cnidarian Nematostella vectensis","authors":"Janki A. Bhalodi , Joachim M. Surm , Adam M. Reitzel","doi":"10.1016/j.cbd.2026.101754","DOIUrl":"10.1016/j.cbd.2026.101754","url":null,"abstract":"<div><div>Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, <em>Nematostella vectensis</em>. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of <em>N. vectensis</em> HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101754"},"PeriodicalIF":2.2,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146020932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-15DOI: 10.1016/j.cbd.2026.101748
Jingyang Li , Ruijian Sun , Tongxuan Zhao , Xiaojian Tang , Bo Gao , Guangping Xu , Yue Wang , Han Yu , Qian Meng , Zhiwei Zhang
Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (Acanthopagrus schlegelii), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.
{"title":"Proteomic analysis reveals the mechanism of cold tolerance in black porgy (Acanthopagrus schlegelii) via ribosome hibernation, metabolic remodeling, and antioxidant coordination","authors":"Jingyang Li , Ruijian Sun , Tongxuan Zhao , Xiaojian Tang , Bo Gao , Guangping Xu , Yue Wang , Han Yu , Qian Meng , Zhiwei Zhang","doi":"10.1016/j.cbd.2026.101748","DOIUrl":"10.1016/j.cbd.2026.101748","url":null,"abstract":"<div><div>Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (<em>Acanthopagrus schlegelii</em>), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101748"},"PeriodicalIF":2.2,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The bark beetle Acanthotomicus suncei is an emerging destructive pest of the introduced American sweetgum (Liquidambar styraciflua) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of A. suncei. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with A. suncei clustering closely with Dendroctonus species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of A. suncei provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. styraciflua. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.
{"title":"Comprehensive transcriptomic analysis reveals detoxification gene expansion and adaptive genetic variation in the emerging pest Acanthotomicus suncei","authors":"Lulu Dai, Jiao Li, Weiyi Pan, Fangyuan Shen, Dejun Hao","doi":"10.1016/j.cbd.2026.101749","DOIUrl":"10.1016/j.cbd.2026.101749","url":null,"abstract":"<div><div>The bark beetle <em>Acanthotomicus suncei</em> is an emerging destructive pest of the introduced American sweetgum (<em>Liquidambar styraciflua</em>) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of <em>A. suncei</em>. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with <em>A. suncei</em> clustering closely with <em>Dendroctonus</em> species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of <em>A. suncei</em> provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. <em>styraciflua</em>. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101749"},"PeriodicalIF":2.2,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1016/j.cbd.2026.101752
Dehui Sun , Xiuke Ouyang , Ruili Zheng , Jing Cao, Lisha Wei, Meng Xu, Guxin Wang
The heat stress and Vibrio infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and Vibrio infection on the survival of the clam Cyclina sinensis. The clams C. sinensis were separately cultivated at 26 °C (low temperature) or 30 °C (high temperature) and subjected to Vibrio infection experiment. The results showed that dual challenges aggravated the mortality of clam. To further investigate the underlying mechanisms, the hepatopancreas of clam C. sinensis under varying thermal conditions were separately sampled at different infection phases, including pre-infection, 8 days post-infection (dpi) and 12 dpi. Transcriptomic analysis revealed that the dual challenges significantly decreased the expression level of genes related to immunity, antioxidation, and energy metabolism, while upregulating genes associated with apoptosis and endoplasmic reticulum stress compared to the control group (26 °C and non-infection). The functional analysis indicated that downregulated differentially expressed genes (DEGs), identified in the dual challenges groups compared with the control group, were primarily involved in lysosome, phagosome, peroxisome, carbohydrate metabolism and regulation of oxidoreductase activity. The qRT-PCR validation of 15 DEGs corroborated the RNA-seq findings. We further demonstrated that the combined stress increased the content of MDA and decreased the activity of antioxidant enzymes (SOD, CAT) and immune enzymes (ACP, LZM) in hepatopancreas. Taken together, these findings suggest that immunosuppression, oxidative damage and deficiencies in carbohydrate metabolism were potential contributors to the mass summer mortality of clams. This study provides valuable data resources and critical information for revealing the molecular response of C. sinensis to combined stress of high temperature and Vibrio infection.
{"title":"Transcriptomics analysis provides insights into the molecular response of the clam Cyclina sinensis to Vibrio infection under heat stress","authors":"Dehui Sun , Xiuke Ouyang , Ruili Zheng , Jing Cao, Lisha Wei, Meng Xu, Guxin Wang","doi":"10.1016/j.cbd.2026.101752","DOIUrl":"10.1016/j.cbd.2026.101752","url":null,"abstract":"<div><div>The heat stress and <em>Vibrio</em> infection are considered as the key factors contributing to the mass mortality of clams in summer. In this study, we explored the combined effects of high temperature and <em>Vibrio</em> infection on the survival of the clam <em>Cyclina sinensis</em>. The clams <em>C. sinensis</em> were separately cultivated at 26 °C (low temperature) or 30 °C (high temperature) and subjected to <em>V</em>ibrio infection experiment. The results showed that dual challenges aggravated the mortality of clam. To further investigate the underlying mechanisms, the hepatopancreas of clam <em>C. sinensis</em> under varying thermal conditions were separately sampled at different infection phases, including pre-infection, 8 days post-infection (dpi) and 12 dpi. Transcriptomic analysis revealed that the dual challenges significantly decreased the expression level of genes related to immunity, antioxidation, and energy metabolism, while upregulating genes associated with apoptosis and endoplasmic reticulum stress compared to the control group (26 °C and non-infection). The functional analysis indicated that downregulated differentially expressed genes (DEGs), identified in the dual challenges groups compared with the control group, were primarily involved in lysosome, phagosome, peroxisome, carbohydrate metabolism and regulation of oxidoreductase activity. The qRT-PCR validation of 15 DEGs corroborated the RNA-seq findings. We further demonstrated that the combined stress increased the content of MDA and decreased the activity of antioxidant enzymes (SOD, CAT) and immune enzymes (ACP, LZM) in hepatopancreas. Taken together, these findings suggest that immunosuppression, oxidative damage and deficiencies in carbohydrate metabolism were potential contributors to the mass summer mortality of clams. This study provides valuable data resources and critical information for revealing the molecular response of <em>C. sinensis</em> to combined stress of high temperature and <em>Vibrio</em> infection.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101752"},"PeriodicalIF":2.2,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-12DOI: 10.1016/j.cbd.2026.101750
Fujun Xuan , Xinyue Zhang , Jinghao Hu , Xuguang Li , Yuchen Chen , Aiming Zhang , Ruifang Wang , Qian Ren , Tao Wu , Weibing Guan , Yongxu Cheng , Jun Zhou , Rongchen Liu
Eriocheir sinensis (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a “low consumption–high storage” metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., PTGS1, TPI1, POR) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in E. sinensis, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.
{"title":"Multi-omics dissection of large-size formation in Eriocheir sinensis: Insights from RNA, metabolite profiling, and ceRNA regulatory networks","authors":"Fujun Xuan , Xinyue Zhang , Jinghao Hu , Xuguang Li , Yuchen Chen , Aiming Zhang , Ruifang Wang , Qian Ren , Tao Wu , Weibing Guan , Yongxu Cheng , Jun Zhou , Rongchen Liu","doi":"10.1016/j.cbd.2026.101750","DOIUrl":"10.1016/j.cbd.2026.101750","url":null,"abstract":"<div><div><em>Eriocheir sinensis</em> (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a “low consumption–high storage” metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., <em>PTGS1</em>, <em>TPI1</em>, <em>POR</em>) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in <em>E. sinensis</em>, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101750"},"PeriodicalIF":2.2,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-10DOI: 10.1016/j.cbd.2026.101751
Guoliang Chang , Fanqian Kong , Songyue Gao , Huajie Cai , Long Wang , Huaiyu Ding , Yongxu Cheng , Jiayao Li
The carapace coloration is of great significance to Procambarus clarkii, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of P. clarkii. This study identified many genes (such as tyrosinase, APOD) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in P. clarkii by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of P. clarkii. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of P. clarkii, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.
{"title":"Comparative transcriptome analysis reveals molecular mechanism of temperature effect on body color of red swamp crayfish (Procambarus clarkii)","authors":"Guoliang Chang , Fanqian Kong , Songyue Gao , Huajie Cai , Long Wang , Huaiyu Ding , Yongxu Cheng , Jiayao Li","doi":"10.1016/j.cbd.2026.101751","DOIUrl":"10.1016/j.cbd.2026.101751","url":null,"abstract":"<div><div>The carapace coloration is of great significance to <em>Procambarus clarkii</em>, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of <em>P. clarkii</em>. This study identified many genes (such as <em>tyrosinase</em>, <em>APOD</em>) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in <em>P. clarkii</em> by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of <em>P. clarkii</em>. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of <em>P. clarkii</em>, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101751"},"PeriodicalIF":2.2,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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