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

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.

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.

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.

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.