Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Exposure to cadmium alters metabolic pathways in the hepatic proteome of a neotropical catfish","authors":"Ana Carolina Felipe da Silva ,&nbsp;Letícia da Silva Pereira ,&nbsp;Rodrigo Soares Caldeira Brant ,&nbsp;Maiara Vicentini ,&nbsp;Helena Cristina Silva de Assis","doi":"10.1016/j.cbd.2025.101564","DOIUrl":"10.1016/j.cbd.2025.101564","url":null,"abstract":"<div><div>Cadmium (Cd) is a non-essential metal known for its potential to biomagnify and bioaccumulate in organisms, raising concerns about the toxic effects on aquatic environments and human beings. However, Cd toxicity effects seem variable across species, and its mechanisms of toxicity remain poorly understood, particularly in native Neotropical fish species. This study aimed to evaluate proteomic alterations in the livers of male <em>Rhamdia quelen</em> exposed to environmentally relevant concentrations of Cd. For this, fish were maintained in 60 L tanks under laboratory conditions and exposed to different CdCl₂ concentrations: 0.1, 1, 10, and 100 μg/L for 15 days. Fish were anesthetized and after euthania their livers were samples for subsequent proteomic analysis using the UniProtKB database, which is most suitable for this species. From the initial 1366-expressed protein, 117 were statistically significant, with most belonging to the group of animals exposed to 10 μg/L. These differentially expressed proteins were mainly related to metabolic pathways concerning energy production, carbohydrate metabolism, protein synthesis and degradation, immune responses, and detoxification. Nonetheless, the concentration of 10 μg/L exhibited the most pronounced changes and holds major biological relevance, given that this concentration is commonly detected in freshwater ecosystems and can affect several metabolic processes. This study provides crucial information about the mechanism of Cd toxicity in the <em>R. quelen</em> catfish liver, highlighting protein targets affected after exposure. Furthermore, the study supports a protocol standardization for proteomic analysis in this native species with ecotoxicological relevance.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101564"},"PeriodicalIF":2.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144263073","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}

{"title":"Effects of Spirulina platensis as a substitute for fishmeal on the liver of zig-zag eel (Mastacembelus armatus) infected with Aeromonas hydrophila","authors":"Chong Wang ,&nbsp;Di Sun ,&nbsp;Xiaodi Hu ,&nbsp;Wei Chen ,&nbsp;Chenhao Zou ,&nbsp;Jixing Zou","doi":"10.1016/j.cbd.2025.101563","DOIUrl":"10.1016/j.cbd.2025.101563","url":null,"abstract":"<div><div>With the development of economy, there is an increasing demand for higher value fish such as Zig-zag eel (<em>Mastacembelus armatus</em>). However, <em>M. armatus</em>, as a carnivorous fish, needs to be trained to feed during the juvenile period in order to save the culture cost, so as to improve its culture efficiency. However, with the increasing price of fishmeal and the higher amount of harmful bacteria in the water body, the development of <em>M. armatus</em> aquaculture is seriously constrained. Therefore, in this experiment, different proportions of <em>Spirulina platensis</em> (0, 5 %,10 %, 15 %, 20 %, 25 %) were used to replace fishmeal and fed to <em>M. armatus</em> seedlings during the period of dietary transition. Finally, <em>M. armatus</em> was infected with <em>Aeromonas hydrophila</em> to investigate the effect of <em>S. platensis</em> on the immunity of <em>M. armatus</em>. The results showed that <em>S. platensis</em> significantly reduced the damage caused by <em>A. hydrophila</em> to the liver of <em>M. armatus</em>. <em>S. platensis</em> could improve the antioxidant capacity of the organism by increasing the activities of T-SOD, GSH-px and T-AOC, as well as decreasing the activity of MDA. The transcriptome showed that <em>S. platensis</em> could activate the hepatic activation of Glycolysis/Gluconeogenesis and AMPK signaling pathway. In the Glycolysis/Gluconeogenesis pathway, the <em>gpi</em>, <em>pfkl</em> and <em>pfkp</em> genes had the strongest correlation with other genes. Metabolomic results showed that <em>S. platensis</em> activates pathways such as Nicotinate and nicotinamide metabolism and Arginine and proline metabolism. In conclusion, <em>S. platensis</em> can effectively improve the infection tolerance of <em>M. armatus</em> against <em>A. hydrophila</em>. This suggests that <em>S. platensis</em> has great potential in promoting liver metabolism and boosting the body's immunity, which is of great value for application.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101563"},"PeriodicalIF":2.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144213336","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}

{"title":"Genome-wide identification of 14-3-3 gene family and their expression profiles under low temperature stress in noble scallop Chlamys nobilis","authors":"Jingwen Deng ,&nbsp;Qingyao Lu ,&nbsp;Yetao Zeng ,&nbsp;Yaoting Liu ,&nbsp;Beiyu Yan ,&nbsp;Huiqi Li ,&nbsp;Meizhen Chen ,&nbsp;Hongquan Li ,&nbsp;Jingyao Lu ,&nbsp;Qiying Tang ,&nbsp;Hongkuan Zhang ,&nbsp;Huaiping Zheng","doi":"10.1016/j.cbd.2025.101562","DOIUrl":"10.1016/j.cbd.2025.101562","url":null,"abstract":"<div><div>The <em>14-3-3</em> family genes, highly conserved regulatory factors in eukaryotes, play critical roles in cellular regulation and stress adaptation. Despite extensive research in vertebrates and some aquatic species, the functional roles of <em>14-3-3</em> genes in bivalves remain underexplored. In this study, we identified and characterized five <em>14-3-3</em> genes (<em>Cn14-3-3a</em> to <em>Cn14-3-3e</em>) in the noble scallop <em>Chlamys nobilis</em>. Phylogenetic and motif analyses confirmed their high conservation, consistent with their roles in essential biological processes. Tissue-specific expression profiling revealed that these genes are predominantly expressed in immune-related tissues such as the blood, gills, and intestine, suggesting their involvement in immune responses. Furthermore, their expression dynamics under acute and chronic low-temperature stress highlighted distinct regulatory patterns: acute cold exposure from 25 °C to 9 °C elicited significant upregulation of all <em>Cn14-3-3</em> genes (<em>P</em> &lt; 0.05), while under chronic cold stress conditions, the expression profiles of <em>Cn14-3-3</em> family members exhibited distinct patterns. Specifically, the expression levels of <em>Cn14-3-3a</em> and <em>Cn14-3-3b</em> initially showed a slight upregulation at 17 °C. However, as the temperature continued to decline, their expression gradually diminished. In contrast, the expression of <em>Cn14-3-3c</em> displayed a continuous downward trend with decreasing temperature. Notably, the expression of <em>Cn14-3-3d</em> and <em>Cn14-3-3e</em> remained relatively stable, showing no significant changes in response to temperature decreased. These findings provide novel insights into the functional roles of <em>14-3-3</em> genes in the cold adaptation and immune responses of bivalves, offering a foundation for strategies to enhance cold tolerance in aquaculture systems.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101562"},"PeriodicalIF":2.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144306974","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}

{"title":"Multi-omics reveals dynamic molecular characteristics in the ovarian development of Chinese longsnout catfish Leiocassis longirostris","authors":"Fan Liu ,&nbsp;Hujun Gao ,&nbsp;Feng Qin ,&nbsp;Shengfu Zhao ,&nbsp;Bo Zhou ,&nbsp;Jian Zhou ,&nbsp;Ronghua Wu ,&nbsp;Hui Luo ,&nbsp;Zhongwei Wang ,&nbsp;Hua Ye","doi":"10.1016/j.cbd.2025.101551","DOIUrl":"10.1016/j.cbd.2025.101551","url":null,"abstract":"<div><div><em>Leiocassis longirostris</em> (<em>L. longirostris</em>) is a significant freshwater fish species in China. Due to the decline in natural populations, its market demand is now largely met through artificial breeding. However, the complex and prolonged ovarian maturation process has rendered current artificial breeding methods limited. Additionally, the molecular mechanisms underlying ovarian development in L. <em>longirostris</em> remain poorly understood. In this study, we conducted RNA and protein sequencing of L. <em>longirostris</em> ovarian samples across five developmental stages, categorized based on histological staining results. To uncover the dynamic characteristics of ovarian development, we identified differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) by comparing gene and protein expression profiles stage-by-stage (stage I to II, II to III, III to IV, and IV to V). GO and KEGG enrichment analyses of these profiles revealed significant enrichment in terms and pathways related to the endocrine system, signal transduction, and lipid metabolism, with dynamic changes observed across stages. The nine-quadrant analysis further elucidated the regulatory characteristics of DEGs and DEPs, highlighting differences in mRNA and protein-level regulation of genes and proteins involved in fat and protein digestion and absorption. Protein-protein interaction networks were further constructed from shared DEGs and DEPs profiles to evacuate candidate proteins involved in L. <em>longirostris</em> ovarian development. Moreover, we clustered DEGs and DEPs into ten clusters based on their expression trend. KEGG enrichment analysis of clusters showed pathways such as FoxO and MAPK signaling pathways were significantly enriched in cluster 4, where the expression increased as ovarian development. qPCR validation confirmed differential expression of genes associated with oocyte meiosis and steroid hormone biosynthesis, consistent with RNA-seq results. This study provides a foundation for understanding yolk lipids metabolism, paracrine factors, and endocrine system regulation during ovarian development and offers insights into developing efficient artificial breeding strategies for L. <em>longirostris</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101551"},"PeriodicalIF":2.2,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144213335","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}

{"title":"Liver transcriptome analysis reveals genes and pathways involved in the ovarian development in spotted scat (Scatophagus argus)","authors":"Mei-Zhen Zhang ,&nbsp;Jing Zheng ,&nbsp;Li-Ting Cai ,&nbsp;Wan-Xin Li ,&nbsp;Zhi-Yuan Li ,&nbsp;Gang Shi ,&nbsp;Hong-Juan Shi ,&nbsp;Hua-Pu Chen ,&nbsp;Si-Ping Deng ,&nbsp;Yu-Cong Hong ,&nbsp;Guang-Li Li ,&nbsp;Dong-Neng Jiang","doi":"10.1016/j.cbd.2025.101550","DOIUrl":"10.1016/j.cbd.2025.101550","url":null,"abstract":"<div><div><em>Scatophagus argus</em> is a highly valuable aquaculture fish. Its artificial breeding faces problems in the induction of high quality eggs, thus necessitating studies on the regulation of ovarian development. As the centre of nutrient metabolism in fish, the liver provides the material basis for ovarian development. However, the molecular mechanism of the liver in ovarian development in <em>S. argus</em> is still unclear. In this study, a transcriptome analysis of adult <em>S. argus</em> livers at different stages of ovarian development (stages II, III and IV) was performed. 410, 1025 and 1867 differentially expressed genes (DEGs) were obtained between stages II and III, stages II and IV and stages III and IV, respectively. In GO and KEGG analyses, DEGs were mostly involved in vitellogenesis and egg envelope formation (<em>e.g.</em>, <em>erα</em>, <em>erβ1</em>, <em>vtga</em>, <em>vtgb</em>, <em>vtgc</em>, <em>zp3</em>, <em>zp4a</em> and <em>zp4b</em>), lipid metabolism and energy metabolism (<em>e.g.</em>, <em>dagt1</em>, <em>dagt2</em>, <em>lpl</em>, <em>apob</em>, <em>hk1</em>, <em>acly</em>, <em>ogdh</em>, <em>pc</em>, and <em>fbp1</em>), and hormone signaling (<em>e.g.</em>, <em>lepa</em> and <em>igfbp1</em>). Additionally, genes that were significantly upregulated in the liver at stage IV of ovarian development, compared to stages II and III, were markedly enriched in steroid biosynthesis and metabolism pathways. These findings provide clues to understanding the mechanisms of liver action in teleost ovarian development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101550"},"PeriodicalIF":2.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144213334","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}

{"title":"Multi-omics analysis of Pacific oyster “Haida No. 1” strain and wild population reveals growth-related genes and transcription regulatory network","authors":"Kunyin Jiang ,&nbsp;Boyang Hu ,&nbsp;Yu Wang ,&nbsp;Qi Li","doi":"10.1016/j.cbd.2025.101549","DOIUrl":"10.1016/j.cbd.2025.101549","url":null,"abstract":"<div><div>Selective breeding has significantly enhanced the growth properties of Pacific oysters (<em>Crassostrea gigas</em>), but the molecular mechanisms behind these improvements remain largely unclear. In this study, we performed a comparative analysis of the adductor muscle transcriptome and proteome of the 10th-generation Pacific oyster strain “Haida No.1” and wild populations. Combining multi-omics analysis with published whole-genome resequencing and LC-MS metabolomics data of the “Haida No.1” strain and wild populations, we identified growth-related genes and transcription regulatory networks in <em>C. gigas</em>. Transcriptome analysis revealed 4110 differentially expressed genes (DEGs), significantly enriched in 49 pathways. Proteome analysis showed 105 differentially expressed proteins (DEPs) between “Haida No.1” and wild populations, which were enriched in 30 relevant pathways, including metabolic pathways, oxidative phosphorylation, ribosomes, phagosomes, and amino acid biosynthesis. Multi-omics analysis grouped these DEGs, DEPs, and selected genes (from Fst and XP_CLR analyses of previous whole-genome resequencing results) into 13 categories. The shared pathways were classified into five main classes: signal transduction, metabolism &amp; biosynthesis, disease, cellular processes, and cellular components. Multi-generation selection has influenced the cellular behaviors and physiological processes of “Haida No.1”, which might explain its faster growth compared to wild populations. These findings provide novel insights into oyster growth regulation and offer candidate genes for oyster breeding programs.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101549"},"PeriodicalIF":2.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189651","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}

{"title":"Genomics profile of ocular toxicity in zebrafish exposed to environmental contaminants","authors":"Rajesh Pamanji ,&nbsp;Ragothaman Prathiviraj ,&nbsp;Yashwanth Bomma ,&nbsp;Ashok Sundar Venkateswaran ,&nbsp;Gisha Sivan","doi":"10.1016/j.cbd.2025.101544","DOIUrl":"10.1016/j.cbd.2025.101544","url":null,"abstract":"<div><div>Environmental contaminants present a significant and growing threat to aquatic ecosystems, with a particularly notable impact on the visual systems of aquatic organisms, including zebrafish. Zebrafish (<em>Danio rerio</em>) are increasingly used in toxicological research because of their genetic and physiological similarities to humans, making them an ideal model for studying the effects of environmental toxins. Among the most frequently observed and studied ocular malformations in zebrafish exposed to toxicants are microphthalmia, cyclopia, and coloboma, all of which involve developmental abnormalities of the eyes. A comprehensive review of over 500 scientific articles was conducted to identify the genes and molecular pathways implicated in these ocular defects. The main focus of this review is to explore how a single ocular malformation can be influenced by multiple genes and how these genes interact within complex molecular networks. Through detailed network analysis of microphthalmia, coloboma and cyclopia, we pinpointed 3 key “hub genes” aldh1a3, vsx2, and stra6 which play central roles in all the three ocular malformations. These hub genes include those that exhibit overexpression, downregulation, as well as those affected by knockout, knockdown, and mutations. Furthermore, an effort was made to connect the gene networks underlying different ocular malformations to identify common genetic factors that may be shared across various conditions. Surprisingly the same hub genes identified are the key players in toxicant induced ocular phenotypes. This approach could help uncover genetic pathways that are critical not only for understanding the specific ocular malformations but also for providing insights into the broader mechanisms through which environmental contaminants disrupt ocular development. This review highlights the interconnected nature of genetic factors influencing eye malformations and emphasizes the need for a more integrated view of how these genes contribute to ocular health in the context of toxicant exposure.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101544"},"PeriodicalIF":2.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154485","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}

{"title":"Identification of the changes of immune response, morphology, and gene expressions in hepatopancreas of Macrobrachium nipponense under the treatment of alkalinity exposure","authors":"Shubo Jin ,&nbsp;Hongtuo Fu ,&nbsp;Yiwei Xiong ,&nbsp;Hui Qiao ,&nbsp;Wenyi Zhang ,&nbsp;Sufei Jiang","doi":"10.1016/j.cbd.2025.101546","DOIUrl":"10.1016/j.cbd.2025.101546","url":null,"abstract":"<div><div><em>Macrobrachium nipponense</em> exhibits limited alkali tolerance, restricting its cultivation in the predominant saline-alkaline water resources of China. Understanding the molecular and physiological mechanisms underlying alkaline acclimation is critical for enhancing its environmental adaptability through genetic improvement. This study comprehensively examines the hepatopancreatic responses of <em>M. nipponense</em> to alkaline stress (10 mmol/L) through integrated analyses of antioxidant enzyme activities, histological alterations, and transcriptomic profiling analysis. Results demonstrate that alkali stress significantly elevates the activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), total antioxidant capacity (T-AOC), and Na+/K + -ATPase, suggesting their crucial role in mitigating oxidative damage, caused by the alkaline exposure. Histopathological analysis reveals structural alterations in the hepatopancreas after 96 h of exposure, particularly in luminal integrity, vacuolization, and storage cell morphology. Transcriptomic profiling analysis indicates minimal differential gene expression at this alkalinity; however, KEGG analysis identifies key enriched metabolic pathways, including fatty acid biosynthesis, fatty acid metabolism, insulin signalling pathway, and AMPK signalling pathway, as central to the adaptive response. These pathways are closely associated with energy metabolism, implying their regulatory significance in alkali acclimation. Quantitative real-time PCR validation confirms the transcriptomic data, ensuring methodological reliability. This study provides novel insights into the physiological and molecular adaptations of <em>M. nipponense</em> under alkaline stress, offering a foundation for future functional studies and marker-assisted breeding. Further research will focus on characterizing candidate genes and identifying associated single nucleotide polymorphisms (SNPs) to advance genetic enhancement in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101546"},"PeriodicalIF":2.2,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188658","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}

{"title":"The LRR domain of internalin gene regulates Streptococcus agalactiae crossing the intestinal barrier and intestinal immunity in tilapia","authors":"Yinhui Peng ,&nbsp;Xin Lu ,&nbsp;Ming Liu ,&nbsp;Lulu Liu ,&nbsp;Peng Xu ,&nbsp;Jing Fang ,&nbsp;Xiaohui Cai ,&nbsp;Shuanghu Cai","doi":"10.1016/j.cbd.2025.101545","DOIUrl":"10.1016/j.cbd.2025.101545","url":null,"abstract":"<div><div>To investigate the effect of the LRR domain of the <em>internalin</em> gene on its role in the invasion of <em>S. agalactiae</em> into tilapia through the intestine and the impact on host immunity. In this study, the LRR domain deletion mutant strain of TOS01 was firstly constructed by homologous recombination. The results of biological characteristics showed no significant difference in growth rate between TOS01ΔLRR and TOS01 (<em>P</em> &gt; 0.05). However, compared with TOS01, the capsular polysaccharide of TOS01ΔLRR was significantly thickened, the chain was significantly shortened, and the ability of invasion and adhesion to PCK cells was significantly decreased (<em>P</em> &lt; 0.05). In addition, the animal oral challenge test results showed that compared with TOS01, the strain TOS01ΔLRR significantly reduced the tissue bacterial load of experimental animals at 24 h, suggesting a role of the LRR domain in mediating bacterial crossing intestinal barriers. However, the virulence did not change, which was also confirmed by comparative transcriptome analysis of TOS01ΔLRR and TOS01. To further explore the effect of the LRR domain of the <em>internalin</em> gene of <em>S. agalactiae</em> on host intestinal immunity, we used RNA-seq to examine tissue expression patterns in tilapia after stimulation with TOS01ΔLRR and TOS01. RNA-seq results displayed 1255 genes were differentially expressed, with 521 genes up-regulated and 734 genes down-regulated. KEGG enrichment showed that differentially expressed genes were mainly concentrated in cell adhesion, invasion and immune-related aspects, such as lysosome, phagosome, apoptosis, cell adhesion molecules (CAMs), cytokine-cytokine receptor interaction, intestinal immune network for IgA production, and PPAR signaling pathwayetc. Among them, the cytokine-cytokine receptor interaction, cellular senescence, PPAR signaling pathway and NOD-like receptor signaling pathway were significantly up-regulated and the lysosome and apoptosis was significantly down-regulated. This suggested that LRR domain inhibited innate immune-related pathways to evade host immunity during <em>S. agalactiae</em> invasion. In summary, the LRR domain of the <em>internin</em> gene is a critical component for <em>S. agalactiae</em> to invade and adhere to host cells. Its deletion reduces the ability of the strain to cross the intestinal barrier, and the LRR domain of <em>internin</em> suppresses the host's innate immunity to promote <em>S. agalactiae</em> colonization in the gut.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101545"},"PeriodicalIF":2.2,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188659","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}

{"title":"Signaling pathways underlying extracellular trap formation induced by Vibrio alginolyticus in Strongylocentrotus intermedius","authors":"Haoyu Zhang ,&nbsp;Wei Chen ,&nbsp;Xiaochen Zhang ,&nbsp;Yijing Han ,&nbsp;Wan Liu ,&nbsp;Yan Li ,&nbsp;Xiaona Wang ,&nbsp;Deyang Tian ,&nbsp;Dong Xu ,&nbsp;Weizhong Wang ,&nbsp;Junsong YangLi ,&nbsp;Yaqiong Liu ,&nbsp;Xiaotong Wang","doi":"10.1016/j.cbd.2025.101547","DOIUrl":"10.1016/j.cbd.2025.101547","url":null,"abstract":"<div><div>Extracellular traps (ETs), comprising a DNA-protein network, are widespread and function as an innate immune defense in many species. Notably, <em>Strongylocentrotus intermedius</em> solely depend on innate immunity for disease resistance. This study investigated the formation and preliminary mechanism of ETs in the coelomocytes of the <em>S. intermedius</em> under the stimulation of bacterium <em>Vibrio alginolyticus</em>. These results revealed that as the concentration of <em>V. alginolyticus</em> increased, the formation of ETs became more significant. Flow cytometry analysis showed that the formation process of ETs was accompanied by changes in mitochondrial indicators, suggesting that mitochondria may be involved in the formation process of <em>V. alginolyticus</em>-induced ETs. Transcriptome analysis indicated that the ETs production by coelomocytes of the <em>S. intermedius</em> was related to glycolysis and ATP synthesis. A total of 2631 differentially expressed genes (DEGs) were screened in this transcriptome. We then screened 34 immune-related DEGs from 16 signaling pathways to construct the PPI network, and defined hub proteins corresponding to genes such as ATP6, ND2, G3PDH, MAPK7 and other related genes. These genes are related to mitochondrial function, glycolytic pathways, and immune pathways. Additionally, the formation of ETs led to alterations in multiple immune regulators, such as TNF, NF-κB, MAPK, PI3K-AKT, and mTOR, implying its role in cellular immunomodulation. Quantitative real-time PCR experiment revealed that the expression changes of some DEGs identified and validated in ET-formation coelomocytes matched transcriptome analysis results. This study provided insights into <em>S. intermedius</em> aquaculture, elucidated marine organism immune mechanisms, and advanced invertebrate innate immunity understanding.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101547"},"PeriodicalIF":2.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144164243","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}