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

Scalloped spiny lobster (Panulirus homarus) aquaculture is the preferred strategy to resolve the conflict between supply and demand for lobster. Environmental conditions, such as salinity, are key to the success of lobster aquaculture. However, physiological responses of P. homarus to salinity stress have not been well studied. This study investigated the gill histology, osmoregulation and gill transcriptome of the early juvenile P. homarus (weight 19.04 ± 3.95 g) cultured at salinity 28 (control), 18, and 38 for 6 weeks. The results showed that the gill filaments of P. homarus exposed to low salinity showed severe separation of the cuticle and epithelial cells due to water absorption and swelling, as well as the dissolution and thinning of the cuticle and the rupture of the septum that separates the afferent and efferent channels. The serum osmolarity of P. homarus varied proportionately with external medium salinity and remained consistently above ambient osmolarity. The serum Na⁺, Cl⁻, K⁺, and Mg²⁺ concentrations P. homarus exhibited a pattern similar to that of serum osmolality, while the concentration of Ca²⁺ remained unaffected at salinity 18 but significantly increased at salinity 38. Gill Na⁺/K⁺-ATPase activity of P. homarus increased (p < 0.05) under the both salinity stress. Salinity 18 significantly increased Glutamate dehydrogenase (GDH) and Glutamicpyruvic transaminase (GPT) activity in the hepatopancreas of P. homarus (p < 0.05). According to transcriptome analysis, versus control group (salinity 28), 929 and 1095 differentially expressed genes (DEGs) were obtained in the gills of P. homarus at salinity 18 and 38, respectively, with these DEGs were mainly involved in energy metabolism, transmembrane transport and oxidative stress and substance metabolism. In addition, the expression patterns of 8 key DEGs mainly related to amino acid metabolism, transmembrane transport and oxidative stress were verified by quantitative real-time PCR (RT-qPCR). The present study suggests that salinity 18 has a greater impact on P. homarus than salinity 38, and P. homarus demonstrates effective osmoregulation and handle with salinity fluctuations (18 to 38) through physiological and functional adaptations. This study provides an improved understanding of the physiological response strategies of P. homarus facing salinity stress, which is crucial for optimizing aquaculture practices for this species.

Mandarin fish (Siniperca chuatsi) represents a typical carnivorous freshwater economic fish in China. Recently, the study of their feeding behavior to acclimate formulated diets has become a research focus. This study evaluated the effects of various diets on the body composition, nutritional content, digestive enzyme activity, gene expression, and gut microbiota of mandarin fish. Firstly, no significant differences were found in the muscle's basic nutritional components (moisture, crude protein, crude fat, and crude ash), as well as in the fatty acid and amino acid content, between the live feed group (LFSC) and the compound feed group (CFSC). However, mandarin fish in the LFSC group exhibited significantly higher lipase activity in the liver and intestine compared to the CFSC group, while amylase activity in the intestine showed an opposite pattern. Additionally, intestinal transcriptome analysis revealed 6238 differentially expressed genes and identified several differentially expressed clock genes associated with diet type. Furthermore, gut microbiota analysis indicated that different feeding regimens influenced microbial composition, revealing correlations between bacterial genera and intestinal gene expression levels. These findings provided novel insights into the gut microbiota and transcriptomic responses of mandarin fish to different dietary types.

N6-methyladenosine (m⁶A) methylation is the most prevalent post-transcriptional RNA modification in eukaryotic organisms, but its roles in the regulation of physiological resistance of marine crustaceans to heavy metal pollutants are poorly understood. In this study, the transcriptome-wide m⁶A RNA methylation profiles and dynamic m⁶A changes induced by acute Cd²⁺ exposure in the the pacific whiteleg shrimp Litopenaeus vannamei were comprehensively analyzed. Cd²⁺ toxicity caused a significant reduction in global RNA m⁶A methylation level, with major m⁶A regulators including the m⁶A methyltransferase METTL3 and the m⁶A binding protein YTHDF2 showing declined expression. Totally, 11,467 m⁶A methylation peaks from 6415 genes and 17,291 peaks within 7855 genes were identified from the Cd²⁺ exposure group and the control group, respectively. These m⁶A peaks were predominantly enriched in the 3′ untranslated region (UTR) and around the start codon region of the transcripts. 7132 differentially expressed genes (DEGs) and 7382 differentially m⁶A-methylated genes (DMGs) were identified. 3186 genes showed significant changes in both gene expression and m⁶A methylation levels upon cadmium exposure, and they were related to a variety of biological processes and gene pathways. Notably, an array of genes associated with antioxidation homeostasis, transmembrane transporter activity and intracellular detoxification processes were significantly enriched, demonstrating that m⁶A modification may mediate the physiological responses of shrimp to cadmium toxicity via regulating ROS balance, Cd²⁺ transport and toxicity mitigation. The study would contribute to a deeper understanding of the evolutionary and functional significance of m⁶A methylation to the physiological resilience of decapod crustaceans to heavy metal toxicants.

The skin mucus of fish is equipped with immunological and antimicrobial peptides that confer protection against invading pathogens. The skin mucus has been studied in fish however information regarding its immunological roles in bacterial infection is rare. This study highlighted the proteins and peptides in the skin mucus of Obscure puffer Takifugu obscurus that quantitatively altered against Aeromonas hydrophila infection. We infected the fish through bath immersion, intraperitonially, and treated with PBS (control) then compared the level of proteins in the skin mucus among the groups using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The Tandem Mass Tag (TMT) based quantification showed that 4896 proteins were Deferentially Quantified Proteins (DQPs), based on 19,751 unique peptides. Of which 170 were depleted (decreased in abundance) and 69 were abundant in comparison of Bath Treated (BT) vs Control (C) groups. Similarly, 76 DQPs were depleted and 70 were abundant in comparison of Treated (T) vs BT groups. Further, 126 DQPs were depleted, and 34 were abundant in comparison to T vs C groups. The DQPs we report were mostly immunological and were involved in unique biological functions and pathways. The interesting protein we report, where some of the proteins are for the first time in fish, shows the protein-rich structure of the mucus of fish, which may act as a biomarker to be targeted for bacterial disease therapy in fish and ultimately hint to the way of making resistance in fish against bacterial pathogens.

Maconellicoccus hirsutus is a highly polyphagous insect pest, posing a substantial threat to various crop sp., especially in the tropical and sub-tropical regions of the world. While extensive physiological and biological studies have been conducted on this pest, the lack of genetic information has hindered our understanding of the molecular mechanisms underlying its growth, development, and xenobiotic metabolism. The Cytochrome P450 gene, a member of the CYP gene superfamily ubiquitous in living organisms is associated with growth, development, and the metabolism of both endogenous and exogenous substances, contributing to the insect's adaptability in diverse environments. To elucidate the specific role of the CYP450 gene family in M. hirsutus which has remained largely unexplored, a de novo transcriptome assembly of the pink mealybug was constructed. A total of 120 proteins were annotated as CYP450 genes through homology search of the predicted protein sequences across different databases. Phylogenetic studies resulted in categorizing 120 CYP450 genes into four CYP clans. A total of 22 CYP450 families and 30 subfamilies were categorized, with CYP6 forming the dominant family. The study also revealed five genes (Halloween genes) associated with the insect hormone biosynthesis pathway. Further, the expression of ten selected CYP450 genes was studied using qRT-PCR across crawler, nymph, and adult stages, and identified genes that were expressed at specific stages of the insects. Thus, the findings of this study reveal the expression dynamics and possible function of the CYP450 gene family in the growth, development, and adaptive strategies of M. hirsutus which can be further functionally validated.

Pinctada fucata martensii is an economically important bivalve mollusk, as this species makes a major contribution to seawater pearl production. Pearl production efficiency varies between the sexes of P. f. martensii, but many aspects of the molecular mechanisms underlying sex determination and sex differentiation in P. f. martensii remain unclear. Here, transcriptomic and metabonomic analyses were conducted to identify the major genes and metabolic changes associated with sex determination and gametogenesis. We identified a total of 3426 differentially expressed genes (DEGs) between females and males. These included Fem-1c and Foxl2, which are involved in sex determination and sex differentiation, and SOHLH2, Nanos1 and TSSK4, which are involved in gametogenesis. We also identified a total of 5231 significant differential metabolites (SDMs) between females and males. These DEGs were enriched in 47 metabolic pathways, including “ABC transporters,” “purine metabolism,” and “glycerophospholipid metabolism.” Our findings provide new insights into the molecular mechanisms underlying sex determination, sex differentiation, and gametogenesis and will aid future studies of P. f. martensii.

Spider venom is a natural source of diverse biomolecules, but due to technical limitations, only a small fraction has been studied. With the advancement of omics technologies, research on spider venom has broadened, greatly promoting systematic studies of spider venom. Agelena limbata is a common spider found in vegetation, known for constructing funnel-shaped webs, and feeding on insects such as Diptera and Homoptera. However, due to its small size and the difficulty in obtaining venom, the composition of Agelena limbata venom has never been studied. In this study, a transcriptomics approach was used to analyze the toxin components in the venom of Agelena limbata, resulting in the identification of 28 novel toxin-like sequences and 24 peptidases. Based on sequence similarity and differences in cysteine motifs, the 28-novel toxin-like sequences were classified into 10 superfamilies. According to the results annotated in the database, the 24 peptidases were divided into six distinct families, with the serine protease family being the most common. A phylogenetic tree was constructed using the toxin-like sequences of Agelena limbata along with Psechrus triangulus and Hippasa lycosina. An analysis of the structural domains and motifs of Agelena limbata was also conducted. The results indicated that Agelena limbata is more distantly related to the other two species of funnel-web spiders, and that the toxin superfamily IX has a unique function compared to the other superfamilies. This study reveals the components of the Agelena limbata venom, deepening our understanding of it, and through bioinformatics analysis, has identified unique functions of the toxin superfamilies, providing a scientific basis for the development of bioactive drugs in the future.

The Alexandrine parakeet (Palaeornis eupatria), also known as the Alexandrine parrot, is a critically endangered species in the world and a national second class protected animal. Current knowledge on gut microbiome and metabolome of captive Alexandrine parrots is limited. In the current study, we characterized the effect of dietary change with pellet feeding on the gut microbiome and metaboliome in Alexandrine parrots using 16S gene sequencing and liquid chromatography with tandem mass spectrometry (LC-MS/MS). Total of 12 Alexandrine parrots were used in a cross-over study with each period for 10 days. The results showed that dietary change with pellet feeding did not affect alpha indices of gut microbiota. Cyanobacteria, Firmicutes and Proteobacteria were the predominant bacterial phyla in the gut of Alexandrine parrot with Cynobacteria being the highest. Change of diet significantly increased the relative abundance of Actinobacteria and decreased Spirochaetota. The relative abundance of Fusobacteriota tended to increase with pellet feeding. No treatment effects were observed between the control and pellet feeding groups at the genus level. Based on the annotation results from Clusters of Orthologous Genes (COG) database, dietary change with pellet feeding significantly increased the relative abundance of genes coding for extracellular structures and lipid transport and metabolism. Metabolomics analysis combined with enrichment analysis revealed that dietary change altered the concentrations of gut metabolites as well as the metabolic pattern, and significantly affected the concentrations of fecal metabolites involved in isoflavonoid biosynthesis, flavonoid biosynthesis, nucleotide metabolism etc. In summary, dietary changes with pellet feeding affected the gut microbial composition and metabolites to some extent. The relevance of current findings to Alexandrine parrots' health and potential zoonosis need further exploring.

Plutella xylostella is one of the most destructive pests for cruciferous vegetables, and is adaptability to different environmental stressors. However, we still know little about the molecular mechanisms of how P. xylostella adapt to thermal stress. Here, the comparative transcriptome analysis was conducted from the samples of control (27 °C, CK) and heat treatment (40 °C, 40 T) P. xylostella. The results showed 1253 genes were differentially expressed, with 624 and 629 genes up- and down-regulated respectively. The annotation analysis demonstrated that “Energy production and conversion”, “Protein processing in endoplasmic reticulum”, “Peroxisome” and “Tyrosine metabolism” pathways were significantly enriched. Additionally, we found the expression levels of heat shock protein genes (Hsps), cuticle related genes and mitochondrial genes were significantly up-regulated in 40 T insects, suggesting their vital roles in improving adaption to heat stress. Importantly, the SOD activity and MDA content of P. xylostella were both identified to be increased under high temperature stress, indicating the elevated antioxidant reactions might be involved in response to heat stress. In conclusion, the present study offered us an overview of gene expression changes after 40 °C treatments, and found some critical pathways and genes of P. xylostella might play the critical roles in resisting heat stress.

The olfactory gene families include odorant binding proteins (OBPs), chemosensory proteins (CSPs), olfactory receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). To investigate the molecular function of olfactory perception in Macrobrachium rosenbergii, we integrated the full-length transcripts and whole-genome sequences to identify the olfactory gene families. In this study, a total of 38,955 full-length transcripts with an N50 length of 3383 bp were obtained through PacBio SMRT sequencing. Through the annotation of full-length transcripts and whole-genome sequences, several olfactory gene families were identified, including 18 MrORs, 16 MrIRs, 151 MrIGluRs (ionotropic glutamate receptors), 2 MrVIGluRs (variant ionotropic glutamate receptors) and 3 MrCRs (chemosensory receptors). Notably, the CRs were first identified in prawns and shrimps. Additionally, the olfactory gene families in M. nipponense were identified, comprising 4 MnORs, 21 MnIRs, 79 MnIGluRs, 5 MnVIGluRs, 1 MnGR and 1 MnOBP, using the available whole-genome sequences. Meanwhile, the external morphology of the chemical sensory organs of M. rosenbergii was explored, and the presence of plumose setae (PS), hard thorn setae (HTS), bamboo shoot setae (BSS), soft thorn setae (STS) and aesthetascs (AE) on the antennules, HTS and BSS on the second antennae, and PS on the pereiopods were observed by scanning electron microscope. This study provides valuable insights for future functional studies into the olfactory perception of crustaceans and establishes a theoretical basis for molecular design breeding in M. rosenbergii.