Comparative biochemistry and physiology. Part D, Genomics & proteomics最新文献

Ghrelin functions to stimulate appetite, promote the release of growth hormone, and regulate energy balance. Currently, research on the ghrelin is primarily focused on a single species, and there have been no systematic studies on the evolution of the ghrelin in fish. Therefore, this thesis conducts a comprehensive analysis of the ghrelin gene in 151 species of ray-finned bony fishes to reveal the universality and specificity of the ghrelin gene in the evolutionary history of fish, supplementing and perfecting the information on the ghrelin gene in Actinopterygii. The gene identification results show that the number of ghrelin genes varies among different fish species, 41 fish have lost the ghrelin gene, 98 fish having one ghrelin gene, and 12 fish having two ghrelin genes. Among the 110 fish species with the ghrelin gene, a total of 182 ghrelin gene sequences were identified, with transcript variant numbers ranging from 1 to 6, encoding 1 to 3 types of isoform proteins, and their mature peptides show a certain degree of similarity across different species. Phylogenetic analysis revealed that teleost ghrelin proteins segregate into three major evolutionary clades, with Salmoniformes orthologs comprising a distinct monophyletic cluster. The Cladistic and Chondrostei are clustered separately and then grouped with the more ancient Cypriniformes and Siluriformes species from the Neopterygii into a large group, while the other fish species from the Neopterygii form another large group. The Synteny analysis results indicate that the upstream gene of the ghrelin is CCDC174, and the downstream gene is TATDN2. The selection pressure analysis results show that there are no positive selection sites in the ghrelin gene, indicating that the ghrelin has been under strong functional constraint during the evolutionary process of fish. This study systematically investigates the evolutionary history of fish ghrelin, providing a theoretical basis for understanding the function and status of ghrelin in the feeding regulation system of fish, and deepening the recognition of its structural and functional evolution in the process of energy metabolism evolution.

The largefin longbarbel catfish (Hemibagrus macropterus) is an important commercially cultured fish in southwestern China, whose regulatory mechanism of gonad development remains unknown. In this study, the first gonadal transcriptome sequencing of immature male, female, and intersexual individuals were performed. A total of 28,543 genes was annotated, of which 12,028, 6283 and 8019 differentially expressed genes (DEGs) were detected by pairwise comparisons of ovary versus (vs.) testis, ovary vs. intersex, and testis vs. intersex. Besides, 26 male-biased, 24 female-biased, and 7 intersex-biased DEGs were screened. Representative pathways related to gonadal development and sex reversal were further enriched. Interestingly, apart from the reproduction-related genes and pathways, apoptosis-related DEGs (bcl2, myc, caspase3 and tp53) and pathways such as JAK-STAT signaling pathway and P53 signaling pathway, were suggested to be involved in the sexual reversal process. The intersexual gonad might be developed by the sex change from ovary to testis, with transcriptions of female-biased genes reduced and male-biased genes increased. Relative real time PCR results of 14 DEGs verified the reliability of transcriptome data. These results will benefit our understanding of gonad development regulations, and further be useful for the achievement of improved artificial propagation of largefin longbarbel catfish.

Salinity changes significantly impact fish physiology, requiring efficient osmoregulation for survival. The kidney is vital for maintaining ion and water balance, crucial for internal stability in varying salinity. This study used transcriptomic analysis to examine molecular responses in the kidneys of Takifugu obscurus, T. rubripes, and their hybrids (Tor1 and Tor2) in freshwater (0 ppt) and seawater (32 ppt). Following the transfer from seawater to freshwater, all four fish groups showed consistent expression trends of three genes in their kidneys-one downregulated gene (ca7) and two upregulated genes (MAP1B and MUC4)-indicating their pivotal roles in renal osmoregulation. Additionally, RNA sequencing unveiled distinct transcriptional profiles specific to each species T. obscurus displayed a limited number of DEGs (14 upregulated and 4 downregulated) in freshwater, suggesting streamlined regulatory mechanisms consistent with its broad salinity tolerance. In contrast, T. rubripes exhibited more extensive transcriptional adjustments (449 upregulated and 139 downregulated), involving ion transport genes and metabolic pathways. Moreover, we observed significant changes in the expression of immune-related genes, indicating that variations in ambient salinity affect the immune responses of the four fish species. Genetic correlation analysis indicated that Tor1 clustered with T. rubripes, while Tor2 grouped with T. obscurus, implying that hybrid offspring inherit adaptive strategies from both parental lineages. These findings shed light on the molecular mechanisms governing kidney function in euryhaline fish and provide a theoretical foundation for breeding aquaculture species with enhanced stress tolerance.

Cirrhina molitorella is an important economic fish species in southern China, and it holds a significant position among the highest-yielding fish species in this region. However, studies on the identification of sex-related genes and gonadal development in C. molitorella remain scarce, which has severely hindered the development of its aquaculture industry. In the present study, transcriptome sequencing data from the female and male gonads of C. molitorella were analyzed and compared for the first time, leading to the successful assembly of 64,954 unigenes. Through comparative transcriptomic analysis, a total of 20,310 differentially expressed genes were identified, among which 16,003 were significantly upregulated in testis and 4307 were highly expressed in ovaries. Furthermore, real-time quantitative PCR was also employed to validate the differential expression profiles of some genes, and the results were in agreement with the transcriptome data. These findings of this study can provide fundamental data for in-depth investigations into the functions of genes and signaling pathways associated with gender determination and gonadal formation in C. molitorella.

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.

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.

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.

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.

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.

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⁺/K⁺-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.