{"title":"Comprehensive analysis of small non-coding RNAs in the liver of Onychostoma macrolepis during overwintering and non-overwintering periods provides insights into the metabolic mechanisms of fish overwintering.","authors":"Chao Zhu, Guofan Peng, Qimin Liu, Xiaolin Wang, Changqing Sun, Hanghang Zhu, Yibin Ding, Shili Liu, Fangxia Yang, Zhilong Chen, Wuzi Dong","doi":"10.1016/j.cbd.2025.101644","DOIUrl":"10.1016/j.cbd.2025.101644","url":null,"abstract":"<p><p>Fish in aquaculture face dual overwintering stressors: low temperature and food scarcity. However, the role of sncRNAs in this process remains unclear. Integrated histopathology, high-throughput sequencing, and bioinformatics analyses was employed to compare hepatic differences in Onychostoma macrolepis (O. macrolepis) liver between overwintering (January, March, and October) and non-overwintering (June). Significant changes were observed in liver morphology (progressive loss of hepatic cord-like organization and nuclear condensation in January and March), sncRNA expression, and tRNA-derived small RNA (tsRNA) splicing patterns between overwintering and non-overwintering periods, with a pronounced bias in tsRNA expression during non-overwintering. Upregulated sncRNAs during overwintering (miR-30-1, tiRNA5-Asp-GTC-1) could be involved in inhibiting mitochondrial and ribosome biogenesis, as well as ATPase and pyruvate kinase activity. In contrast, Upregulated sncRNAs in non-overwintering (let-7-1, tiRNA5-Lys-CTT-1) may activate cell growth/metabolic pathways and promote liver growth, potentially preparing the fish for feeding and reproduction. Functional experiments using fertilized eggs demonstrated that inhibitors of let-7-1 and tiRNA5-Lys-CTT-1 significantly suppressed embryonic development, further demonstrating confirming the accuracy of functional predictions. These results indicate that O. macrolepis can actively regulate relevant sncRNAs in the liver to reduce its own energy metabolism and growth, thereby entering a low-energy metabolic state during overwintering. In conclusion, these findings significantly advance our understanding of the roles of miRNAs and tsRNAs in enabling O. macrolepis to adapt to winter food scarcity and low-temperature stress.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101644"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145310319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparative identification, characterization and high-temperature stress analysis of the fatty acid-binding protein (fabp) genes in largemouth bass (Micropterus salmoides) genome.","authors":"Bowen Lv, Yanpeng Liu, Shuai Li, Debin Zhong, Haolin Mo, Lixin Wang, Jiajia Yu","doi":"10.1016/j.cbd.2025.101646","DOIUrl":"10.1016/j.cbd.2025.101646","url":null,"abstract":"<p><p>Fatty acid binding proteins (Fabps) could participate in multiple biological processes in organisms, such as immune defense, growth, development, metabolism, and stress tolerance. Although the roles of Fabps are well studied, little is known about the stress-induced changes in the Fabp family in largemouth bass. According to genomic analysis, 10 Fabps were detected in the largemouth bass. Phylogenetic and evolutionary analyses suggested that all Fabps could be divided into four clades. According to phylogenetic tree and conserved motif analysis, Fabps were relatively conserved. Real-time quantitative PCR results indicated that 10 fabps showed distinctive expression features in seven tissues, and the transcripts level of 8 fabps in fish liver exhibited marked changes after high-temperature stress. Additionally, a protein-protein interaction analysis revealed that Fabps might participate in responding to high-temperature stress by affecting lipid contents. This study may be the first systematic investigation about Fabps in largemouth bass. It will further deepen our insights into evolutionary processes and provide a critical framework for uncovering the underlying mechanism of Fabps in largemouth bass exposed to high temperature.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101646"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145245952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bofang Zhang, Yuhong Hu, Mingxue Jiao, Zhijun Yu, Kenneth B Storey, Yonggang Niu, Hui Wang
{"title":"Proteomic responses to progressive dehydration and rehydration in Xenopus laevis.","authors":"Bofang Zhang, Yuhong Hu, Mingxue Jiao, Zhijun Yu, Kenneth B Storey, Yonggang Niu, Hui Wang","doi":"10.1016/j.cbd.2025.101654","DOIUrl":"10.1016/j.cbd.2025.101654","url":null,"abstract":"<p><p>Amphibians, notably Xenopus laevis, exhibit remarkable dehydration tolerance, yet the tissue-specific proteomic adaptations remain poorly understood. Here, we used data-independent acquisition-based proteomics to analyze molecular responses in five organs and tissues (heart, kidney, liver, lung, skeletal muscle) of X. laevis during graded dehydration (15 %, 30 %) and rehydration. We identified 844 differentially expressed proteins (DEPs) in heart, 334 in kidney, 1057 in liver, 560 in lung, and 374 in muscle, respectively. DEPs in heart, liver, and kidney were significantly enriched in energy metabolism pathways, highlighting metabolic remodeling in response to dehydration and rehydration stresses. Progressively down-regulated proteins in heart during dehydration were enriched in NAD/NADH and ATP metabolic processes as well as glycolysis, aligning with metabolic rate depression to conserve energy and reduce oxidative stress. Conversely, lung and skeletal muscle prioritized cytoskeletal integrity (actin-myosin reorganization) over metabolic adjustments. Heart tissue exhibited activation of p38-MAPK signaling and up-regulation of MAPKAPK2, which is important in implementing the response to dehydration. Tissue-specific antioxidant responses showed that kidney and muscle catalase were up-regulated during 15 % dehydration, whereas lung delayed induction until rehydration to mitigate ischemia-reperfusion damage. Chaperone dynamics varied, with HSP27 up-regulated in heart and lung during dehydration and HSP60 sustained in liver, which contribute to maintaining the structural integrity of mitochondrial proteins. Moreover, X. laevis up-regulates proteins involved in oxygen transport, blood circulation and blood coagulation in order to counteract dehydration-induced hemoconcentration and hypovolemia. Five conserved DEPs shared in all examined tissues displayed dynamic expression, including Na<sup>+</sup>/K<sup>+</sup>-ATPase, plectin, annexin, electron transfer flavoprotein, and aconitate hydratase, indicating systemic adjustments in ion homeostasis, cytoskeletal stability, and mitochondrial metabolism. Overall, these findings highlight tissue-specific and conserved responses to dehydration stress, elucidate the importance of inhibiting metabolic pathways and eliciting protective mechanisms, and provide valuable insights for future studies exploring animal adaptation to stressful environments.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101654"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145310307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oscar E Juárez, Claudia Ventura-López, Diana Lara-Pérez, Ricardo Gómez-Reyes, Pavel Galindo-Torres, Miguel Tripp-Valdez, Carlos Rosas, Clara E Galindo-Sánchez
{"title":"Key neuropeptide and neuroendocrine pathways of the optic lobe are affected by high temperatures in the female Octopus maya.","authors":"Oscar E Juárez, Claudia Ventura-López, Diana Lara-Pérez, Ricardo Gómez-Reyes, Pavel Galindo-Torres, Miguel Tripp-Valdez, Carlos Rosas, Clara E Galindo-Sánchez","doi":"10.1016/j.cbd.2025.101649","DOIUrl":"10.1016/j.cbd.2025.101649","url":null,"abstract":"<p><p>This study investigated the neuroendocrine role of the optic lobe (OL) in Octopus maya females during reproduction. While previous neuroendocrine research in octopus has focused on the gonads, optic glands, olfactory lobes, and oviducal glands, the role of the OL remains less explored. A transcriptomic approach was used to compare gene expression in the OL across reproductive stages-mating, egg-laying, and senescence-and with other tissues. Additionally, mature females were exposed to a thermal challenge (TC), and their OL transcriptomes were compared to those maintained at optimal temperatures (24 °C). Compared to other octopus' tissues, the OL transcriptome was enriched with genes encoding neuropeptides, neuroendocrine proteins, and neurotransmitter-modifying enzymes, confirming its neuroendocrine functions. Notably, transcripts of the LWamide neuropeptide, which is involved in life-stage transitions, were exclusively detected in the OL. Genes from neuroendocrine and neuropeptide pathways exhibited stable expression patterns throughout the reproductive stages. However, the TC induced stage-specific changes in gene expression. For instance, at the mating stage, transcripts of FMRF-amide, buccalin, and neuropeptide prohormone-4 were upregulated. At the egg-laying stage, apoptotic transcripts were upregulated, while genes encoding the neuroendocrine protein 7B2 and multiple ATPases were downregulated. Finally, at the senescence stage, mitochondrial and metabolic transcripts were downregulated by the TC. Temperature-driven changes in gene expression during the mating and egg-laying stages could be linked to a decrease in the reproductive success of this octopus species. This study confirms the critical role of OL in neuropeptide and neuroendocrine pathways that regulate the physiology and reproduction of octopuses.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101649"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145304966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transcriptomic analysis of the gill and hepatopancreas reveals the thermal adaptation mechanisms of Eriocheir sinensis.","authors":"Hucheng Jiang, Yiyun Zhang, Longlong Fu, Yanhua Zhao, Runbo Li, Xiumei Xing, Yanming Sui, Hui Xue","doi":"10.1016/j.cbd.2025.101650","DOIUrl":"10.1016/j.cbd.2025.101650","url":null,"abstract":"<p><p>Global warming-induced high-temperature stress threatens Eriocheir sinensis aquaculture. This study used transcriptome sequencing combined with histopathological analysis to explore thermal adaptation mechanisms in its gills and hepatopancreas under 38 °C stress. Histopathological results revealed severe tissue damage in the heat-sensitive group (HS). In HS, gills showed distorted and fractured filaments, epithelial detachment, cellular swelling, vacuolation, and nuclear pyknosis, while hepatopancreas exhibited disorganized acinar structures, enlarged intercellular gaps, and extensive nuclear abnormalities. In contrast, heat-tolerant group (HT) displayed milder damage than HS with preserved structural integrity. Transcriptomic analysis identified 869 DEGs in the hepatopancreas and 288 in gills, with 49 shared DEGs enriched in heat shock proteins and antioxidant pathways. Tissue-specific regulation was evident: gills upregulated genes related to ion transport and cell adhesion, while hepatopancreas enhanced fatty acid degradation and detoxification pathways. GSEA further revealed that HT significantly enriched pathways, including protein processing in endoplasmic reticulum, alcoholism in gills, and antigen processing and presentation in hepatopancreas. Key pathways also included MAPK signaling and glutathione metabolism. These findings clarify multi-layered thermal adaptation mechanisms involving tissue-specific transcriptional regulation, synergistic activation of stress-responsive pathways, and structural protection. They provide targets for breeding heat-tolerant strains to mitigate climate change impacts on aquaculture.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101650"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145276971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Man Zhang, Wenhao Nie, Mengke Tang, Yubei Qiu, Youyi Zhang, Yaya Li, Shangliang Xu, Xiaojun Yan, Shaosen Yang, Jiabao Hu, Yajun Wang
{"title":"Effects of low temperature on intestinal microbiota composition of silver pomfret (Pampus argenteus).","authors":"Man Zhang, Wenhao Nie, Mengke Tang, Yubei Qiu, Youyi Zhang, Yaya Li, Shangliang Xu, Xiaojun Yan, Shaosen Yang, Jiabao Hu, Yajun Wang","doi":"10.1016/j.cbd.2025.101598","DOIUrl":"10.1016/j.cbd.2025.101598","url":null,"abstract":"<p><p>Fish are poikilothermic organisms with species-specific optimal temperature ranges for survival. As an economically important marine fish in China, silver pomfret (Pampus argenteus) has overcome artificial breeding bottlenecks. To meet aquaculture requirements in northern regions, we simulated gradual winter cooling from 18 °C to 6 °C using recirculating aquaculture systems with precision temperature control. Through histological sectioning, 16S rRNA gene sequencing, and ecological community assembly modeling, we found that feeding activity in silver pomfret is positively correlated with water temperature, exhibiting a significant decrease with declining thermal conditions. Concurrently, intestinal structural alterations were observed, including diminished collagen staining, enlarged intercellular spaces, and reduced fold height. The microbial diversity initially decreased and subsequently increased during the cooling process. The microbial community was influenced by variable selection and dispersal limitation. At the onset of the cooling period, Vibrio emerged as the dominant genus; however, after prolonged exposure to low-temperature stress, Pseudoalteromonas, Pseudomonas, and Shewanella became predominant genera. Under low temperature conditions, metabolism-related pathways are activated. This study provides new insights into mechanisms underlying low-temperature adaptation and supports silver pomfret breeding at reduced temperatures.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101598"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genome-wide analysis of glutathione S-transferase family and their response to salinity and ammonia stresses in a freshwater shellfish Solenaia oleivora.","authors":"Ting Zhang, Yidong Liang, Junlei Ma, Haibo Wen, Xueyan Ma, Yanfeng Zhou","doi":"10.1016/j.cbd.2025.101651","DOIUrl":"10.1016/j.cbd.2025.101651","url":null,"abstract":"<p><p>Glutathione S-transferases (GSTs) are a class of vital detoxification and antioxidant enzymes and exert crucial functions in the response of organisms to environmental stresses. However, currently, data on the systematic identification of GST families in aquatic animals and their responses to environmental stress are still very limited. In this study, genomic analysis identified 29 GSTs in the freshwater shellfish Solenaia oleivora genome, distributed across 12 chromosomes with six tandem duplication events. The physicochemical properties, such as molecular weight and isoelectric point of GST protein, varied among SoGST proteins. According to the phylogenetic analysis, SoGSTs were classified into 13 classes: Alpha (1), Delta (1), Mu (2), Omega (2), Pi (2), Rho (2), Sigma (7), Theta (2), MAPEG (4), EF1B (1), Metaxin (3), mPGES (1) and GDAP (1). Structural, conserved domain, and syntenic analyses suggested the evolutionary conservation and diversity of SoGSTs. RNA-seq analysis showed that 48 h salinity (2.2 ‰) stress induced significant downregulation of SoGSTS4/5/6, SoGSTA, and SoMGST1B in the gills. Under 48 h ammonia (10 mg/L) stress, the expressions of SoGSTS6, SoGSTO1, SoGSTT2, and SoMGST1A were downregulated in the gills, while SoGSTO2 and SoGSTS7 were upregulated in the hepatopancreas, and SoGSTR2 were downregulated. These findings will enhance our understanding of the GST gene family in mollusks and provide a theoretical basis for the environmental adaptation mechanism of S. oleivora.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101651"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145350386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Divergence and conservation of neuropeptide Y receptors in teleosts with diverse feeding habits.","authors":"Xiao-Zheng Yu, Yi-Yao Lu, Yang Yu, Zi-Yan Liu","doi":"10.1016/j.cbd.2025.101662","DOIUrl":"10.1016/j.cbd.2025.101662","url":null,"abstract":"<p><p>Neuropeptide Y (NPY) is a key regulator of appetite, and its receptor family in teleost fish expanded to seven members (Y1, Y2, Y2-2, Y4, Y7, Y8a, Y8b) through genome duplication. To explore the impact of feeding habits on receptor evolution, we analyzed six representative species: herbivorous (Ctenopharyngodon idella, Megalobrama amblycephala), carnivorous (Takifugu rubripes, Scophthalmus maximus), and omnivorous (Danio rerio, Oreochromis niloticus). Coding sequences, amino acid sequences, tertiary structures, and phylogenetic relationships were compared. Results revealed lineage-specific receptor loss, with O. niloticus lacking Y1, T. rubripes lacking Y1 and Y2-2, and S. maximus lacking Y1, Y4, and Y8a. Structural modeling showed higher conservation in herbivorous fish, moderate divergence in carnivorous fish, and pronounced differences in omnivorous fish. Phylogenetic analysis separated receptors into Y1 and Y2 families and indicated that omnivorous species cluster with herbivorous or carnivorous lineages depending on dietary bias. These findings, including comparative genomic, structural, and phylogenetic analyses, provide insights into the adaptive diversification of appetite-regulating receptors and contribute to understanding the molecular basis of feeding behavior and nutritional adaptation in fish.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101662"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145350371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dynamic expression of the zebrafish (Danio rerio) proteome across early larval development.","authors":"Abigail N Henke, Laura M Langan, Bryan W Brooks","doi":"10.1016/j.cbd.2025.101631","DOIUrl":"10.1016/j.cbd.2025.101631","url":null,"abstract":"<p><p>Zebrafish is one of the most important model organisms across diverse disciplines from developmental biology to environmental science and engineering, and toxicology, substantially contributing to reductions in the use of mammals in disciplines that have previously relied on rodent models. The use of immature zebrafish in particular have arguably contributed to the largest reduction in animal usage, at least during toxicology experimentation, since these ages are not counted as laboratory animals unless they have reached the free-feeding stage (> 5 dpf for zebrafish reared at 28 °C). Despite its use as a developmental and animal alternative model, baseline biomolecule expression dynamics are poorly understood throughout the zebrafish lifecycle. While the adult (> 3 months) and embryonic proteome (2-120 hpf) of this species have been previously characterized, variations in proteome expression across early life stages is limited. Here, we examined proteome expression patterns in larval zebrafish at 4-, 7- and 10 dpf. We specifically identified 11,344 proteins (5 % false discovery rate) using bottom-up shotgun proteomics, with many proteins unique to experimental time points and minimal overlap among age groups (∼ 5-12 %). Longitudinal examination of differentially expressed proteins indicates coordinated expression of the muscular system and contractile proteins with extracellular matrix structure aligning with growth, muscle development, and movement observations in larval fish. Considering the use of early life stage zebrafish as a model organism and an animal alternative vertebrate method, differential expression and enrichment of evolutionarily conserved processes, especially associated with developmental periods of metabolic stress, highlight potential experimental confounders requiring further investigation.</p>","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":"56 ","pages":"101631"},"PeriodicalIF":2.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13527823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145304888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}