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

The Amur sleeper (Perccottus glenii) exhibits remarkable tolerance to freezing conditions, yet the molecular and physiological mechanisms underlying its recovery from cold stress remain poorly understood. This study investigated the recovery process in P. glenii following freezing by integrating transcriptomic, histological, and biochemical analyses. Fish were subjected to a freezing experiment at -2 °C for 24 h, followed by a recovery phase at 4 °C. Liver transcriptome sequencing revealed 5622 differentially expressed genes (DEGs) across comparison groups (DEA vs. CK, SUR vs. CK, and DEA vs. SUR). KEGG enrichment analysis highlighted the significant upregulation of genes involved in the pancreatic secretion pathway and in the metabolism of xenobiotics by cytochrome P450 and steroid biosynthesis pathways in successfully resuscitated individuals. Histological examination showed restored liver architecture in the successful recovery group, contrasting with vacuolation and structural disorganization in the death group. Biochemically, successful recovery was associated with significantly elevated activities of antioxidant enzymes and digestive enzymes (lipase), alongside increased triglyceride (TG) content. These findings demonstrate that the successful post-freezing recovery in P. glenii is underpinned by the coordinated upregulation of genes facilitating the restoration of digestive function, enhancement of detoxification capacity, regulation of steroid biosynthesis, and mitigation of oxidative stress. This study provides comprehensive insights into the adaptive molecular mechanisms that confer exceptional freezing tolerance and recovery capability in this vertebrate model.

The spruce cone worm, Dioryctria abietella (Lepidoptera: Pyralidae), is a major conifer pest that threatens forest regeneration and seed production. To investigate the molecular basis of sex pheromone perception, we performed antennal transcriptome analysis and molecular investigation of candidate pheromone-binding proteins (PBPs). Transcriptome profiling identified diverse olfactory-related genes, including five candidate PBPs, some of which showed high sequence similarity to previously reported Lepidopteran PBPs. Phylogenetic analysis revealed distinct evolutionary relationships among these proteins, with several clustering with known PBPs while others formed separate lineages within the OBP/PBP family. Structural modeling combined with molecular docking suggested differential binding potentials of selected PBPs to two sex pheromone components of D. abietella. Quantitative RT-PCR analysis showed that three PBPs exhibited male head-enriched expression patterns consistent with roles in male pheromone detection, whereas one candidate displayed comparable expression in both sexes, suggesting possible involvement in female olfactory perception. Together, these findings provide integrative molecular evidence linking predicted pheromone interactions with expression patterns, contributing to our understanding of olfactory mechanisms in D. abietella and providing a basis for future functional validation and species-specific pheromone-based pest management strategies.

Aging is accompanied by progressive physiological declines in body functions. However, the molecular mechanisms of aging remain poorly understood in decapod crustaceans, a diverse group of invertebrates. We investigated age-related differences in the hemolymph proteomes of marbled crayfish using label-free protein quantification (LC-MS/MS), applying a significance threshold of p < 0.05 and a fold change >2 to elucidate molecular mechanisms underpinning aging. Two groups including young (n = 6) and old (n = 7) crayfish were used. Results showed a downregulation of superoxide dismutase in the hemolymph of older individuals. At the same time, glutathione peroxidase and transketolase were upregulated, which may reflect age-dependent changes in oxidative stress regulation and potential compensatory responses. Aging crayfish exhibited changes in levels of the ProPO system and phagocytosis-related proteins that suggest a possible shift from melanization to phagocytosis in the aging immune system. Additionally, the lower levels of some other immune-related proteins in the old individuals may be consistent with a decline in the crayfish immune system with age. Proteins associated with wound healing and regeneration were higher in young individuals, which may suggest an age-based decline in regenerative capacity. Cytoskeletal and extracellular matrix proteins were upregulated in older crayfish, which could potentially influence immune cell functions. Age-related alterations in the quantities of vitellogenins, hemocyanins, and metabolic enzymes maybe associated with changes in reproductive investment, respiratory capacity, and energy metabolism. Together, these findings highlight the complex molecular basis by which aging reshapes the hemolymph composition and alters immune system characteristics in an invertebrate, revealing molecular signatures that may represent aging mechanisms. Data are available via ProteomeXchange with identifier PXD065434.

Heat stress impairs intestinal barrier function and microbial balance in cold-water fish like Siberian sturgeon. Resveratrol improves aquatic animal growth and intestinal homeostasis, but its protective mechanism in heat-stressed Siberian sturgeon remains unclear. This study found resveratrol maintains intestinal integrity, enhances antioxidant capacity, and regulates gut microbiota in heat-stressed Siberian sturgeon: the HRH group showed higher Cetobacterium and lower pathogenic Rhodococcus, Acinetobacter, and Pseudomonas than the HC group. Transcriptomic analysis suggested that heat stress might induce uncoupling protein 1 (UCP1)-mediated uncoupling of ATP synthesis from oxidative phosphorylation, which could in turn reduce mitochondrial energy production and cause intestinal villus damage. Resveratrol regulates duodenal lipid metabolism via the PPAR pathway to boost energy supply, and modulates valvular intestinal immune response through the NF-κB pathway. Meanwhile, the protective effect of the resveratrol-supplemented group remained significantly superior to that of the control group. These findings indicate resveratrol mitigates heat stress by preserving villi integrity, alleviating oxidative stress and pathogenic proliferation, and regulating lipid metabolism/immunity via PPAR/NF-κB, clarifying its protective mechanism for Siberian sturgeon intestinal homeostasis and providing a theoretical basis for heat stress mitigation in aquatic animals.

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.