Protein Metabolism Research Articles

Colonization profiles of gut microbiota in goat kids from neonatal to weaning period

Understanding the colonization and change patterns of gut microbiota is pivotal for comprehending host health. As a newly cultured breed, the studies on the gut microbiota of Tianfu goats remain limited. This study aimed to address this gap by analyzing the microbial composition and colonization patterns of fecal samples collected from goat kids from birth to weaning. Fecal samples were collected on days 0, 7, 14, 21, 28, 35, 42, 49, 53, 55, 57, and 64, and the changes and colonization patterns of microorganisms were analyzed through high-throughput 16S rRNA sequencing. The results showed that the abundance of fecal microbiota in goat kids gradually increased over time, followed by a decrease after weaning and stabilization, with reduced individual differences. The colonization of fecal microorganisms mainly presented three different stages: days 0–14, days 21–49, and days 53–64. During the suckling period, the relative abundance of Proteobacteria (72.34%) was the highest, followed by Firmicutes (21.66%). From 21 days old, the microbiota in goat kids gradually to be diverse, with Lachnospiraceae and Ruminococcaceae being dominant. During post-weaning, Ruminococcaceae (30.98–33.34%) was becoming prominence which helpful for cellulose decomposition. LEfSe analyzed three important time points (d0 vs. d7, d7 vs. d14, d49 vs. d53, LDA score > 4 and p < 0.05), 53 microbial communities with stage differences were identified. Functional prediction using PICRUSt revealed that differential microbial communities are mainly related to carbohydrate and amino acid metabolism pathways. Overall, this study addresses the intricate relationship between ages, diets, and microbiota compositions in Tianfu goat kids, and also offering insights into microorganisms-host interactions.

An integrated metabolomics and proteomics analysis reveals copper‑zinc alloy surface contact-mediated metabolic disruption, lipid peroxidation, and osmotic imbalance of Cryptocaryon irritans tomonts

Cryptocaryon irritans cause massive losses in the mariculture industry and are among the most threatening pathogens affecting teleost species. Copper‑zinc alloy (CZA) surface contact effectively kills C. irritans within minutes. Thus, this study employed integrated metabolomics and proteomics analysis to investigate the killing mechanism of CZA against C. irritans. Moreover, malondialdehyde contents, CuZn-SOD, and ATPase activities were evaluated. Proteomics analysis identified 142 differentially expressed proteins (DEPs), including 91 (59 upregulated, 32 downregulated), 92 (42 upregulated, 50 downregulated), and 43 (17 upregulated, 26 downregulated) DEPs at 0.5 h, 1 h, and 0.5 h vs 1 h of contact treatment with the CZA surface, respectively. Similarly, the metabolomic analysis identified 377 differentially expressed metabolites (DEMs). There were 237 (94 upregulated, 143 downregulated), 264 (112 upregulated, 152 downregulated), and 193 (101 upregulated, 92 downregulated) DEMs at 0.5 h, 1 h, and 0.5 h vs 1 h of contact treatment with the CZA surface, respectively. KEGG-based integrative analyses revealed that CZA exposure significantly enriched proteins and metabolites involved in oxidative phosphorylation, purine, pyrimidine, cysteine, and methionine metabolism. Notably, CZA exposure inhibited the TCA cycle, disrupting energy metabolism, as evidenced by downregulation of key TCA proteins, including citrate synthase and malate dehydrogenase, and metabolites like succinic and malic acids at both 0.5 h and 1 h of CZA treatment. Prolonged CZA exposure also affected protein metabolism, with significant downregulation of ribosomal protein S3a (RPS3a) and proteasome activity. Additionally, CZA surface contact downregulated key proteins involved in pyrimidine (DHFR-TS), purine (RRM1), and cysteine and methionine metabolism (AHCY), leading to disturbances in the methionine cycle, suppression of glutathione metabolism, and alterations in cellular redox status. Quantitative polymerase chain reaction (qPCR) analysis confirmed the upregulation of citrate synthase, proteasome subunit alpha type, and adenosylhomocysteinase with prolonged CZA exposure. Additionally, extended CZA exposure significantly decreased the MDA content due to the increased CuZn-SOD activity. Moreover, CZA exposure reduced Ca2+/Mg2+-ATPase and Na+/K+-ATPase activities. Altogether, CZA surface contact caused metabolic disruption, lipid peroxidation, and osmotic imbalance of C. irritans tomonts, highlighting the broad molecular impact of CZA on cellular processes.

Overexpression of the key metabolic protein Carnitine Palmitoyl Transferase 1A (CPT1A) in equine sarcoid

The equine sarcoid is the most common skin neoplasia of fibroblastic origin in horses, characterized by an excessive accumulation of extracellular matrix produced by sarcoid fibroblasts under hypoxic condition. Neoplastic cells can adapt to hypoxia by using alternative energy sources, particularly those that arise from fatty acid oxidation (FAO). The Carnitine Palmitoyl Transferase 1A (CPT1A) belongs to Carnitine System (CS) and promotes the entrance of fatty acids into the mitochondria for β-oxidation. In this study, CPT1A expression was comparatively addressed in 25 equine sarcoids and 5 normal skin samples using immunohistochemistry (IHC). Specificity of CPT1A antibody was validated by Western Blotting (WB). In normal skin samples IHC staining was weak and mainly confined to basal epidermis and few dermal fibroblasts. Sarcoid fibroblast exhibited a strong cytoplasmic and nuclear signal in 60% of the tumor samples. Cytoplasmic CPT1A expression in sarcoid fibroblasts indicates that the protein is actively involved in metabolic reprogramming processes. Nuclear CPT1A expression suggests that the protein may also be involved in the regulation of neoplastic proliferation.

Evolution of aromatic amino acid metabolism in plants: a key driving force behind plant chemical diversity in aromatic natural products.

A diverse array of plant aromatic compounds contributes to the tremendous chemical diversity in the plant kingdom that cannot be seen in microbes or animals. Such chemodiversity of aromatic natural products has emerged, occasionally in a lineage-specific manner, to adopt to challenging environmental niches, as various aromatic specialized metabolites play indispensable roles in plant development and stress responses (e.g. lignin, phytohormones, pigments and defence compounds). These aromatic natural products are synthesized from aromatic amino acids (AAAs), l-tyrosine, l-phenylalanine and l-tryptophan. While amino acid metabolism is generally assumed to be conserved between animals, microbes and plants, recent phylogenomic, biochemical and metabolomic studies have revealed the diversity of the AAA metabolism that supports efficient carbon allocation to downstream biosynthetic pathways of AAA-derived metabolites in plants. This review showcases the intra- and inter-kingdom diversification and origin of committed enzymes involved in plant AAA biosynthesis and catabolism and their potential application as genetic tools for plant metabolic engineering. I also discuss evolutionary trends in the diversification of plant AAA metabolism that expands the chemical diversity of AAA-derived aromatic natural products in plants. This article is part of the theme issue 'The evolution of plant metabolism'.

A Single-Cell Atlas of the Substantia Nigra Reveals Therapeutic Effects of Icaritin in a Rat Model of Parkinson’s Disease

Degeneration and death of dopaminergic neurons in the substantia nigra of the midbrain are the main pathological changes in Parkinson’s disease (PD); however, the mechanism underlying the selective vulnerability of specific neuronal populations in PD remains unclear. Here, we used single-cell RNA sequencing to identify seven cell clusters, including oligodendrocytes, neurons, astrocytes, oligodendrocyte progenitor cells, microglia, synapse-rich cells (SRCs), and endothelial cells, in the substantia nigra of a rotenone-induced rat model of PD based on marker genes and functional definitions. We found that SRCs were a previously unidentified cell subtype, and the tight interactions between SRCs and other cell populations can be improved by icaritin, which is a flavonoid extracted from Epimedium sagittatum Maxim. and exerts anti-neuroinflammatory, antioxidant, and immune-improving effects in PD. We also demonstrated that icaritin bound with transcription factors of SRCs, and icaritin application modulated synaptic characterization of SRCs, neuroinflammation, oxidative stress, and survival of dopaminergic neurons, and improved abnormal energy metabolism, amino acid metabolism, and phospholipase D metabolism of astrocytes in the substantia nigra of rats with PD. Moreover, icaritin supplementation also promotes the recovery of the physiological homeostasis of the other cell clusters to delay the pathogenesis of PD. These data uncovered previously unknown cellular diversity in a rat model of Parkinson’s disease and provide insights into the promising therapeutic potential of icaritin in PD.

Integration of bile proteomics and metabolomics analyses reveals novel insights into different types of gallstones in a high-altitude area

BackgroundTo explore the pathogenesis of different subtypes of gallstones in high-altitude populations from a molecular perspective.MethodsWe collected bile samples from 20 cholesterol gallstone disease (CGD) patients and 20 pigment gallstone disease (PGD) patients. Proteomics analysis was performed by LC/MS DIA, while metabolomics analysis was performed by UPLC- Q-TOF/MS.ResultsWe identified 154 up-regulated and 196 down-regulated differentially expressed proteins, which were significantly enriched in neurodegenerative diseases, energy metabolism, amino acid metabolism etc. In metabolomics analysis, 20 up-regulated and 63 down-regulated differentially expressed metabolites were identified, and they were significantly enriched in vitamin B6 metabolism. Three pathways of integrated proteomics and metabolomics were significantly enriched: porphyrin and chlorophyll metabolism, riboflavin metabolism and aminoacyl-tRNA biosynthesis. Remarkably, 7 differentially expressed proteins and metabolites showed excellent predictive performance and were selected as potential biomarkers.ConclusionThe findings of our metabolomics and proteomics analyses help to elucidate the underlying mechanisms of gallstone formation in high-altitude populations.

A Moderate Water Deficit Induces Profound Changes in the Proteome of Developing Maize Ovaries

Water deficit is a major cause of yield loss for maize (Zea mays), leading to ovary abortion when applied at flowering time. To help understand the mechanisms involved in this phenomenon, the proteome response to water deficit has been analysed in developing ovaries at the silk emergence stage and five days later. Differential analysis, abundance pattern clustering and co-expression networks were performed in order to draw a general picture of the proteome changes all along ovary development and under the effect of water deficit. The results show that even mild water deficit has a major impact on ovary proteome, but this impact is very different from a response to stress. A part of the changes can be related to a slowdown of ovary development, while another part cannot. In particular, ovaries submitted to water deficit show an increase in proteins involved in protein biosynthesis and in vesicle transport together with a decrease in proteins involved in amino acid metabolism and proteolysis. According to the functions of increased proteins, the changes may be linked to auxin, brassinosteroids and jasmonate signalling but not abscisic acid.

A Simple Dispersive Liquid-Liquid Microextraction for the Determination of Copper II in the Water Samples of the Halfaya Oil Field in Maysan

Background: Copper, an important trace element for life on Earth, is crucial to many metabolic processes. This includes its role in the production and breakdown of nucleic acids and the metabolism of proteins, lipids, and carbohydrates. Objective: We aim to integrate DLLME with a spectrophotometric method to establish a novel approach for quantifying trace amounts of copper in water samples. Methods: In this study, a new ligand known as a 2-(4 aminophenol) benzimidazole azo derivative was successfully synthesized. This ligand was created by converting 2-(4-aminophenyl) benzimidazole into a diazonium salt and coupling it with 8-hydroxyquinoline in an alkaline environment. The resulting product was a brown azo dye, which served as the ligand for detecting copper (II) in aqueous samples. Results: To analyze copper (II) in both pure and aqueous samples, we developed and validated micro-extraction techniques combined with UV-Vis measurement. Specifically, we used the DLLME (dispersive liquid-liquid microextraction) method to separate, enrich, and assess copper (II) in both its pure form and in aqueous samples. UV-Vis spectroscopy at a wavelength of 503 nm was used for this purpose. We considered several variables during the experiment, including the type and volume of the dispersive solvent, the extraction solvents, the temperature, the reaction duration, and the centrifuging time. By optimizing these conditions, we achieved linear procedures within the concentration range of (1.0–25.0) and (2.0–25.0) μg/mL for spectroscopy and DLLME methods, respectively. For the spectroscopic and DLLME approaches, the coefficient of determination (R2) was found to be 0.9963 and 0.9979 for the spectrophotometric and DLLME methods, respectively. The limit of detection (LOD) for copper (II) was found to be 0.23 and 0.04 μg/mL, respectively. Moreover, the recovery of the target analyte in aqueous samples was found to be between 95.6% and 101% for the spectroscopy method and between 102.4% and 108.2% for the DLLME method. Conclusions: These results demonstrate the effectiveness and accuracy of both methods in analyzing copper (II) in aqueous samples.

Assessments of coagulation profile among good glycemic control and poor glycemic control type 2 diabetic patient attending at Wolkite University specialized hospital, Central Ethiopia: a comparative study

IntroductionDiabetes Mellitus (DM) is a worldwide health issue that is defined by elevated blood glucose levels and impaired metabolism of fat, carbohydrates, and proteins. Atherosthrombotic events are very likely to occur in patients with diabetes mellitus. This results in the development of both microvascular and macrovascular complications.ObjectiveTo compare the coagulation profile parameters between patients with good glycemic control and poor glycemic control and to evaluate the association of coagulation profile and glycemic control in type 2 DM patients.Materials and methodsThis study was conducted in Wolkite university specialized hospital on 90 type 2 Diabetics patients among which 45 were with good glycemic control and 45 were with poor glycemic control. Seven ml blood samples were collected from each study participant and analyzed to assess coagulation profile including Platelet Count, activated Partial Thromboplastin Time (aPTT), and Prothrombin Time (PT). Using SPSS 21.0, an independent sample t-test was used for statistical analysis.ResultsAccording to the current study, when comparing Type 2 Diabetes with poor glycemic control to those with good glycemic control, there was an increase in PT and aPTT concentration (statistically significant, p < 0.05). The platelet counts of the two groups did not differ significantly.ConclusionPeople with Type 2 diabetes have altered coagulation profiles, which have demonstrated that hyperglycemia causes abnormalities in coagulation. Patients with Type 2 diabetes who have poor glycemic control are particularly vulnerable to atherothrombotic and hemorrhagic events. In order to prevent the onset of microvascular and macrovascular illness as soon as possible, physicians may find it helpful to evaluate the coagulation profile of diabetic patients.

Preparation of bee venom-loaded chitosan nanoparticles for treatment of streptozotocin-induced diabetes in male Sprague Dawley rats

BackgroundDiabetes mellitus (DM) can be defined as an increase in the blood sugar level and a disturbance in protein, fat and carbohydrate metabolism. Bee venom (BV) is useful for treating and preventing diabetic rats’ histological and biochemical problems. Although the medical advantages of BV have been identified, its safety has remained a substantial barrier for its application. Consequently, the goal of our work was to prepare bee venom-loaded chitosan (BV-CS) nanoparticles (NPs), which would then be physically characterized. This was followed by examining the effect of the synthetized BV-CS NPs on oxidation, inflammation and coagulation in vitro. In diabetic rats’ model [induced by streptozotocin (STZ)], the produced BV-CS NPs were tested as an anti-diabetic medication.ResultsIn vivo testing on pancreatic tissue homogenates showed that BV-CS NPs have antioxidant and anti-inflammatory properties. The results showed that BV-CS NPs can be used as a safe and efficient therapy for diabetes. Up to a concentration of 250 µg/ml, the generated NPs demonstrated potential antioxidant, membrane stabilizing, and non-cytotoxic capabilities. Our findings indicated that the administration of BV-CS NPs significantly controlled blood glucose levels and metabolic abnormalities that accompanied diabetes induction.ConclusionsBV-CS NPs were successful in treating STZ-induced diabetes in rats, stimulated insulin secretion and were safe to be used in vivo.Graphical abstract

Influences of lactic acid bacteria strains on the flavor profiles, metabolites and quality characteristics of red yeast rice produced by solid-state fermentation

Red yeast rice (RYR) as a traditional fermented food produced by inoculation of the Monascus genus into steamed rice through solid-state fermentation, has been used intensively for thousands of years in China. Herein, we investigated the flavor profiles, metabolites and quality characteristics of RYR produced by mix fermentation with lactic acid bacteria (LAB) using the headspace solid phase microextraction gas chromatography–mass spectrometry (HS–SPME–GCMS) approach integrated with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC–MS). 56 volatile organic compounds (VOCs) and 1287 non-volatile metabolites were identified and classified into eight classes, the inoculation of Lactiplantibacillus plantarum (LP) and Limosilactobacillus fermentum (LF) increased VOCs and enhanced the flavor characteristics of RYR, with LP being the more significant. The KEGG pathway enrichment analysis revealed that most of the differential metabolites were enriched in amino acid metabolism when integrating volatile and non-volatile omics data, meanwhile, the addition of LAB promoted the metabolism of amino acid, alcohols, fatty acid and some flavonoids, in particular, amino acid metabolism was almost upregulated in the LP group. Therefore, this study highlights the tremendous potential of LAB in improving the flavor quality of RYR. This study provides novel insights into RYR fermentation processes and establishes a theoretical foundation for developing and applying new RYR products.

Differential Effects of Sulfur Fertilization on Soil Microbial Communities and Maize Yield Enhancement

Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This study investigates the impact of different S fertilizer types on maize yield and the structure and stability of soil microbial communities, with a particular focus on abundant and rare taxa. S fertilization led to significant increases maize yield on two typical soils (black soil and sandy soil) (5.3–24.3%) and altered soil properties, including reducing pH (0.04–0.20) and increasing the available sulfur (AS) content (3.8–8.0 mg kg−1), with ammonium sulfate having a more pronounced effect than elemental sulfur. Microbial analysis revealed distinct impacts on the diversity and community structure of both abundant and rare taxa. Elemental sulfur reduced the alpha diversity of abundant taxa more than ammonium sulfate, while NMDS indicated significant shifts in community structures, particularly among abundant taxa. Network analysis showed that S fertilization decreased the complexity of microbial interactions among rare taxa, with ammonium sulfate leading to simpler networks and elemental sulfur resulting in higher modularity. SEM highlighted that the diversity of rare taxa played a crucial role in influencing maize yield, alongside direct effects from soil properties such as AS and SAR (aryl sulfatase). Functional predictions demonstrated that amino acid metabolism and xenobiotic biodegradation and metabolism pathways were enriched in rare taxa, suggesting significant implications for soil health and crop productivity. This study provides new insights into the roles of abundant and rare bacterial taxa under S fertilization, emphasizing their importance in optimizing fertilization strategies for enhanced crop yield in specific soil types.

Interactions between Brassinosteroids and Strigolactones in Alleviating Salt Stress in Maize

Exogenous brassinolide (BR) and strigolactones (SLs) play an important role in alleviating salt stress in maize. We studied the morphological and physiological responses of the salt-sensitive genotype PH4CV and salt-tolerant genotype Zheng58 to BR (1.65 nM), SL (1 µM), and BS (1.65 nM BR + 1 µM SL) under salt stress. Phenotypic analysis showed that salt stress significantly inhibited the growth of maize seedlings and significantly increased the content of Na+ in the roots. Exogenous hormones increased oxidase activity and decreased Na+ content in the roots and mitigated salt stress. Transcriptome analysis showed that the interaction of BR and SL is involved in photosynthesis–antenna proteins, the TCA cycle, and plant hormone signal transduction pathways. This interaction influences the expression of chlorophyll a/b-binding protein and glucose-6-phosphate isomerase 1 chloroplastic, and aconitase genes are affected. Furthermore, the application of exogenous hormones regulates the expression of genes associated with the signaling pathways of cytokinin (CK), gibberellins (GA), auxin (IAA), brassinosteroid (BR), abscisic acid (ABA), and jasmonic acid (JA). Additionally, exogenous hormones inhibit the expression of the AKT2/3 genes, which are responsible for regulating ion transduction and potassium ion influx. Four candidate genes that may regulate the seedling length of maize were screened out through WGCNA. Respective KOG notes concerned inorganic ion transport and metabolism, signal transduction mechanisms, energy production and conversion, and amino acid transport and metabolism. The findings of this study provide a foundation for the proposition that BR and SL can be employed to regulate salt stress alleviation in maize.

Transcriptome and Metabolome Analyses Reveal the Molecular Mechanisms of Albizia odoratissima’s Response to Drought Stress

Albizia odoratissima is a deciduous tree species belonging to the family Leguminosae. It is widely distributed in the southern subtropical and tropical areas of China and has important ecological and economic value. The growth and metabolic processes of A. odoratissima are affected by drought stress, but the molecular mechanisms remain unknown. Therefore, this study investigated the physicochemical properties, gene expression, and metabolites of A. odoratissima seedlings under drought stress. The results show that, in leaves of A. odoratissima seedlings, drought stress reduced the moisture content, chlorophyll content, photosynthetic efficiency, superoxide dismutase (SOD) activity, and gibberellin (GA) and indoleacetic acid (IAA) contents while increasing the catalase (CAT) and peroxidase (POD) activities and malondialdehyde (MDA), proline, soluble sugar, and soluble protein contents. Within the CK5 (Day 5 of control group) vs. T5 (Day 5 of drought treatment), CK10 vs. T10, CK15 vs. T15, and CK20 vs. T20 groups (CK: control group; T: drought treatment), a total of 676 differentially expressed genes (DEGs) were upregulated and 518 DEGs were downregulated, and a total of 228 and 143 differential accumulation metabolites (DAMs) were identified in the CK10 vs. T10 and CK20 vs. T20 groups. These were mainly involved in the amino acid and alkaloid metabolism pathways in the leaves of the A. odoratissima seedlings. In the amino acid and alkaloid biosynthesis pathways, the relative expression levels of the AoproA (Aod04G002740, ORTHODONTIC APPLIANCE), AoOAT (Aod07G015970, ORNITHINE-OXO-ACID TRANSAMINASE), and AoAOC3 (Aod12G005010/08G003360/05G023920/08G003000/08G003010, AMINE OXIDASE COPPER CONTAINING 3) genes increased, which concurrently promoted the accumulation of arginine, proline, piperine, cadaverine, and lysine. Furthermore, some key transcription factors in the response to drought were identified in the leaves using the weighted gene co-expression network analyses (WGCNA) method. These findings reveal that A. odoratissima seedlings respond to drought stress by improving the capacities of the antioxidant system and secondary metabolism.

Dysregulation of lipid metabolism in the liver of Tspo knockout mice

The translocator protein, TSPO, has been implicated in a wide range of cellular processes exerted from its position in the outer mitochondrial membrane from where it influences lipid metabolism and mitochondrial oxidative activity. Understanding how this protein regulates a profusion of processes requires further elucidation and to that end we have examined lipid metabolism and used an RNAseq strategy to compare transcript abundance in wildtype and Tspo knockout (KO) mouse liver. The levels of cholesterol, triglyceride and phospholipid were significantly elevated in the KO mouse liver. The expression of cholesterol homeostasis genes was markedly downregulated. Determination of the differential expression revealed that many genes were either up- or downregulated in the KO animals. However, a striking observation within the results was a decrease of transcripts for protein degradation proteins in KO animals while protease inhibitors were enriched. When the entire abundance data-set was analysed with CEMiTool, and revealed a module of proteins that were under-represented in the KO animals. These could subsequently be formed into a network comprising three interlinked clusters at the centre of which were proteins of cytoplasmic ribosomes with gene ontology terms suggesting impairment to translation. The largest cluster was dominated by proteins of lipid metabolism but also contained disparate systems of iron metabolism and behaviour. The third cluster was dominated by proteins of the electron transport chain and oxidative phosphorylation. These findings suggest that TSPO contributes to lipid metabolism, detoxification of active oxygen species and oxidative phosphorylation, and regulates mitochondrial retrograde signalling.

A study on the hepatic response to heat stress in Gymnocypris eckloni through an approach combining metabolomic and transcriptomic profiling

Gymnocypris eckloni, an economically important cold-water fish widely cultivated in southwest China, is at increased risk of prolonged exposure to heat stress owing to persistent high temperatures in summer, extreme climate changes, and expansion of factory farming. In this study, G. eckloni was subjected to both chronic and acute heat stress, with subsequent analysis focusing on changes in the pathological and physiological characteristics and transcriptomic and metabolic responses of the liver to high temperature. The results revealed heat stress-induced damage to liver tissues, lipid accumulation and mitochondrial abnormalities in hepatocytes, and an increased number of apoptotic cells, with the damage being more severe under acute heat stress conditions. Assessment of biochemical indices showed that the antioxidant enzyme catalase (CAT) was activated in response to oxidative stress and energy demands increased following heat stress. Transcriptomic analysis showed significant enrichment in the protein processing in the endoplasmic reticulum pathway, along with upregulation of key genes associated with protein degradation (hsp40, hsp70, hsp90, ero1l, and pdia4) and activation of the unfolded protein response (UPR), which effectively reduces or clears the accumulation of misfolded proteins to combat stress. Most identified differential metabolites were associated with amino acid and lipid metabolism under heat stress. Notably, integrated transcriptomic and metabolomic analysis suggested that tryptophan metabolism played an important role in the adaptation of G. eckloni to chronic heat stress. These findings improve the understanding of the mechanisms through which G. eckloni adapts to high temperatures, providing a valuable foundation and novel avenues for developing strategies to alleviate the effects of heat stress and improve the outcomes of aquaculture.

Brain gene expression reveals pathways underlying nocturnal migratory restlessness

Migration is one of the most extreme and energy demanding life history strategies to have evolved in the animal kingdom. In birds, champions of long-distance migrations, the seasonal emergence of the migratory phenotype is characterised by rapid physiological and metabolic remodelling, including substantial accumulation of fat stores and increases in nocturnality. The molecular underpinnings and brain adaptations to seasonal migrations remain poorly understood. Here, we exposed Common quails (Coturnix coturnix) to controlled changes in day length to simulate southward autumn migration, and then blocked the photoperiod until birds entered the non-migratory wintering phase. We first performed de novo RNA-Sequencing from selected brain samples (hypothalamus) collected from birds at a standardised time at night, either in a migratory state (when restlessness was highest and at their body mass peak), or in a non-migratory state and conducted differential gene expression and functional pathways analyses. We found that the migratory state was associated with up-regulation of a few, yet functionally well defined, gene expression networks implicated in fat trafficking, protein and carbohydrate metabolism. Further analyses that focused on candidate genes (apolipoprotein H or APOH, lysosomal associated membrane protein-2 or LAMP2) from samples collected during the day or night across the entire study population suggested differences in the expression of these genes depending on the time of the day with the largest expression levels being found in the migratory birds sampled at night. We also found that expression of APOH was positively associated with levels of nocturnal activity in the migratory birds; such an association was absent within the non-migratory birds. Our results provide novel experimental evidence revealing that hypothalamic changes in expression of apolipoprotein pathways, which regulate the circulatory transport of lipids, are likely key regulatory activators of nocturnal migratory movements. Our study paves the way for performing deeper functional investigations on seasonal molecular remodelling underlying the development of the migratory phenotype.

Physiological and proteomic responses of Posidonia oceanica to phytotoxins of invasive Caulerpa species

The invasive green algae Caulerpa taxifolia (M. Vahl) C. Agardh, 1817 and Caulerpa cylindracea Sonder, 1845 are widely diffused in the Mediterranean Sea, where they compete for space with the endemic seagrass Posidonia oceanica (Linnaeus) Delile, 1813, a keystone species in Mediterranean marine biodiversity. The present study aims to explore the possible effects of bioactive metabolites from the invasive algae on the seagrass, which may imply an allelopathic action. In particular, the study focuses on the effects of the algal alkaloid caulerpin and the sesquiterpene caulerpenyne. Changes in leaf growth, chlorophyll content, and leaf protein expression of P. oceanica genets under treatments were evaluated after 28 days of cultivation in mesocosms. Caulerpenyne strongly inhibited the growth of adult leaves and the formation of new ones, while inducing the elongation of the intermediate leaves and increased total chlorophyll content; on the contrary, caulerpin did not significantly influence leaf growth and the formation of new ones. A total of 107 differentially accumulated proteins common to the two treatments were also identified using the proteomic approach. Both molecules induced cells to maintain homeostasis, enhancing the amino acid metabolism or fatty acid biosynthesis. Despite these disruptions, P. oceanica demonstrated a more efficient response to stress induced by caulerpin, stimulating the biosynthesis of essential amino acids to maintain cellular homeostasis and mitigate damage caused by reactive oxygen species (ROS). Overall, obtained results supports the possible role of caulerpenyne, and not caulerpin, as an effector in allelopathic interactions among invasive Caulerpa species and P. oceanica in the Mediterranean.

Transcriptomic and protein analysis of Trametes versicolor interacting with a Hypholoma fasciculare mycelium foraging in soil

The decomposition of large woody material is an important process in forest carbon cycling and nutrient release. Cord-forming saprotrophic basidiomycete fungi create non-resource limited mycelial networks between decomposing branches, logs and tree stumps on the forest floor where colonisation of new resources is often associated with the replacement of incumbent decay communities. To date, antagonism experiments have mostly placed competing fungi in direct contact, while in nature cord-forming saprobes encounter colonised wood as mycelia in a network. Transcriptomic and peptide analyses were conducted on soil-based microcosms were foraging cord-forming Hypholoma fasciculare encountered a wood block colonised by Trametes versicolor. Protein turnover featured strongly for both species and genes putatively involved in secondary metabolite production were identified. H. fasciculare demonstrated an exploitative profile with increased transcription of genes associated with carbohydrate metabolism and RNA and ribosome processing. T. versicolor showed a shift in signalling, energy generation and amino acid metabolism. By identifying genes and proteins putatively involved in this fungal interaction, this work may help guide the discovery of bioactive molecules and mechanisms underpinning community succession.

Phosphoproteomics-directed manipulation reveals SEC22B as a hepatocellular signaling node governing metabolic actions of glucagon

The peptide hormone glucagon is a fundamental metabolic regulator that is also being considered as a pharmacotherapeutic option for obesity and type 2 diabetes. Despite this, we know very little regarding how glucagon exerts its pleiotropic metabolic actions. Given that the liver is a chief site of action, we performed in situ time-resolved liver phosphoproteomics to reveal glucagon signaling nodes. Through pathway analysis of the thousands of phosphopeptides identified, we reveal “membrane trafficking” as a dominant signature with the vesicle trafficking protein SEC22 Homolog B (SEC22B) S137 phosphorylation being a top hit. Hepatocyte-specific loss- and gain-of-function experiments reveal that SEC22B was a key regulator of glycogen, lipid and amino acid metabolism, with SEC22B-S137 phosphorylation playing a major role in glucagon action. Mechanistically, we identify several protein binding partners of SEC22B affected by glucagon, some of which were differentially enriched with SEC22B-S137 phosphorylation. In summary, we demonstrate that phosphorylation of SEC22B is a hepatocellular signaling node mediating the metabolic actions of glucagon and provide a rich resource for future investigations on the biology of glucagon action.