Metabolic Pathways Research Articles

The impact of genetic variants related to the fatty acid metabolic process pathway on milk production traits in Jersey cows

The synthesis of fatty acids plays a critical role in shaping milk production characteristics in dairy cattle. Thus, identifying effective haplotypes within the fatty acid metabolism pathway will provide novel and robust insights into the genetics of dairy cattle. This study aimed to comprehensively examine the individual and combined impacts of fundamental genes within the fatty acid metabolic process pathway in Jersey cows. A comprehensive phenotypic dataset was compiled, considering milk production traits, to summarize a cow’s productivity across three lactations. Genotyping was conducted through PCR-RFLP and Sanger sequencing, while the association between genotype and phenotype was quantified using linear mixed models. Moderate biodiversity and abundant variation suitable for haplotype analysis were observed across all examined markers. The individual effects of the FABP3, LTF and ANXA9 genes significantly influenced both milk yield and milk fat production. Additionally, this study reveals novel two-way interactions between genes in the fatty acid metabolism pathway that directly affect milk fat properties. Notably, we identified that the GGAAGG haplotype in FABP3×LTF×ANXA9 interaction may be a robust genetic marker concerning both milk fat yield and percentage. Consequently, the genotype combinations highlighted in this study serve as novel and efficient markers for assessing the fat content in cow’s milk.

Characteristics of airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma

Objective: To study the characteristics of the airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma. Methods: In a prospective study based on a cohort of asthma patients, respiratory induced sputum samples were collected from 55 asthma patients [25 males and 30 females, with a median age of 47.7 years (age range 34.3-63.0 years)] admitted to the Department of Respiratory and Critical Care, Beijing Chaoyang Hospital, Capital Medical University and 12 healthy controls from the Physical Examination Centre of Beijing Chaoyang Hospital, Capital Medical University, from May 2021 to May 2022. According to the level of exhaled breath nitric oxide (FeNO), the asthma patients were divided into 22 cases in the high FeNO group (FeNO≥40 ppb, i.e., type 2 asthma group) and 33 cases in the low FeNO group (FeNO<40 ppb, i.e., non-type 2 asthma group). All induced sputum samples were subjected to second-generation macrogenomic sequencing and bioinformatic analyses of microbial community diversity, compositional characteristics, symbiotic network characteristics and metabolic function prediction. The Kruskal-Wallis rank sum test was used for between-group comparisons, and the linear discriminant analysis (LEfSe) method was used to compare the differences in flora composition between groups. The R language was used for microbial network analysis. In addition, PICRUSt was used to predict the metabolic-functional characteristics of the microbial communities. Results: The microbial communities in the healthy control group had a lower proportion of p_Firmicutes and p_Proteobacteria than asthma patients, 29% and 21%, respectively; 37% and 33% in the low FeNO group and 42% and 26% in the high FeNO group. The microbial network in the low FeNO group had 64 pairs of edges forming 16 communities, and about 75% of the nodes had eigenvector centrality values between 0 and 0.05, and 25% of the nodes had eigenvector centrality values between 0.10 and 0.45. There were four layers of κ-nucleosynthesis, and about 42% of the vertices were in the centre of the two layers. The microbial network of the high-FeNO group had 80 pairs of edges forming 18 clusters, and 81% of the nodes had eigenvector centrality values between 0 and 0.05, and 19% of the nodes had eigenvector centrality values between 0.10 and 0.35. The κ-nucleus decomposition had eight layers, and 21% of the vertices were located in the centre's two layers. The main functional differences between the low and high FeNO groups were shown in metabolic pathways (including sugar, lipid, amino acid, and energy metabolism), drug resistance, biofilm transport, signalling, intercellular communication, and cellular repair. Conclusions: Compared with non-type 2 asthmatics, type 2 asthmatics had a higher alpha diversity of respiratory microbiota, lower levels of microorganisms in the p_Proteobacteria, and a more aggregated microbial network. There was a significant difference in the predicted metabolic function of the two endotypes of asthmatics.

Regulatory dynamics of arginine metabolism in Staphylococcus aureus.

Staphylococcus aureus is a highly significant pathogen with several well studied and defined virulence factors. However, the metabolic pathways that are required to facilitate infection are not well described. Previous data have documented that S. aureus requires glucose catabolism during initial stages of infection. Therefore, certain nutrients whose biosynthetic pathway is under carbon catabolite repression and CcpA, including arginine, must be acquired from the host. However, even though S. aureus encodes pathways to synthesize arginine, biosynthesis of arginine is repressed even in the absence of glucose. Why is S. aureus a functional arginine auxotroph? This review discusses recently described regulatory mechanisms that are linked to repression of arginine biosynthesis using either proline or glutamate as substrates. In addition, recent studies are discussed that shed insight into the ultimate mechanisms linking arginine auxotrophy and infection persistence.

Circulating small extracellular vesicles as blood-based biomarkers of muscle health in aging nonhuman primates.

Age-associated loss of muscle mass and function and subsequent mobility decline define poor health outcomes, reduced quality of life, and mortality risk. The rate and extent of aging-related muscle loss varies across older adults. It is challenging to understand the molecular pathogenesis of mobility decline, as anthropometric and imaging techniques, primarily used in muscle function assessment, do not offer much molecular information. Small extracellular vesicles (sEV) are lipid membrane-bound, nano-sized (≤ 200nm) vesicles which carry a wide array of biomolecules as their cargo. sEV contain cell/tissue-specific signatures on their surface and can be isolated from biofluids. These properties pose sEV as a minimally invasive means to monitor the functional and biological health of difficult-to-access tissues, establishing them as a promising liquid biopsy tool. Here, we first isolated skeletal muscle-derived sEV (sEVSKM) from the serum of vervet monkeys (16 to < 25years old) using alpha sarcoglycan (SGCA) as a muscle-specific sEV surface marker. sEVSKM were extensively characterized for size, concentration, purity, and specificity. Further, sEVSKM isolated from young (11-15years) and old (25-29years) monkeys' serum were characterized for oxidized proteins by mass spectrometry and miRNAs by small-RNAseq. Notably, the analysis of oxidized proteins indicated perturbation of metabolic pathways, actin cytoskeleton, muscle cytoskeleton regulation, and HIF-1 signaling in older monkeys. Furthermore, small-RNAseq analysis identified differential expression of several miRNAs regulating metabolic pathways, inflammation, and stress signaling. Altogether, these results suggest that it is feasible to isolate sEVSKM and use them to identify molecular biomarkers that reflect the physiological state of muscle tissue.

Gut microbiota may mediate the causality of statins on diabetic nephropathy: a mediation Mendelian randomization study.

Increasing evidence indicates that statins may increase the risk of developing diabetic nephropathy (DN). As the gut-kidney axis concept gains traction, it remains unclear whether statins contribute to the onset and progression of DN by modulating gut microbiota. To investigate the association between statins and DN and the proportion of this association mediated through gut microbiota. This study utilized a two-sample Mendelian randomization (MR) approach and a cross-sectional observational design to investigate the causal relationships among statins, 473 gut microbiota, and DN. Furthermore, mediation MR analysis was employed to explore the potential mediating effects of gut microbiota in the statins-DN relationship. HMGCR inhibitors were causally linked to the increased incidence of DN (odds ratio [OR]: 0.732, 95% confidence interval [CI] 0.647, 0.828, PFDR = 0.000004). Supporting results from a cross-sectional study based on the Medical Information Marketplace in Intensive Care (MIMIC-IV) database also indicated this association (OR: 0.74, 95% CI: 0.61, 0.91, P = 0.004). Among the 473 identified gut microbiota species, 13 (PFDR < 0.05) were causally associated with DN. The mediation MR analysis revealed that 10 gut microbiota mediated the relationship between statins and DN, acting as either protective or risk factors (P < 0.05). In addition, HMGCR and related proteins may be involved in lipid metabolism, insulin resistance, and AMPK signaling pathway. Statins may become a risk factor for DN by increasing or decreasing the abundance of specific gut microbiota. These specific gut bacteria have the potential to become a new indicator for guiding the clinical use of statins in diabetic patients.

Inflammation-driven NFκB signaling represses Ferroportin transcription in macrophages via HDAC 1 and 3.

Anemia of Inflammation is a prevalent co-morbidity in patients with chronic inflammatory disorders. Inflammation causes hypoferremia and iron-restricted erythropoiesis by limiting Ferroportin (FPN)-mediated iron export from macrophages that recycle senescent erythrocytes. Macrophage cell surface expression of FPN is reduced by hepcidin-induced degradation and/or by repression of FPN (Slc40a1) transcription via cytokine and Toll-like receptor (TLR) stimulation. While the mechanisms underlying hepcidin-mediated control of FPN have been extensively studied, those inhibiting Slc40a1 mRNA expression remain unknown. We applied targeted RNA interference and pharmacological screens in macrophages stimulated with the TLR2/6 ligand FSL1 and identified critical signalling regulators of Slc40a1 mRNA repression downstream of TLRs and NFкB signaling. Interestingly, the NFкB regulatory hub is equally relevant for Slc40a1 mRNA repression driven by the TLR4 ligand LPS, the cytokine TNFβ/LTA and heat-killed bacteria. Mechanistically, macrophage stimulation with heat-killed Staphylococcus aureus recruits the Histone deacetylases (HDAC) 1 and 3 to the antioxidant response element (ARE) located in the Slc40a1 promoter. Accordingly, pre-treatment with a pan-HDAC inhibitor abrogates Slc40a1 mRNA repression in response to inflammatory cues, suggesting that HDACs act downstream of NFкB to repress Slc40a1 transcription. Consistently, recruitment of HDAC 1 and 3 to the Slc40a1 ARE following stimulation with heat-killed Staphylococcus aureus is dependent on NFκB signaling. These results support a model in which the ARE integrates the transcriptional responses of Slc40a1 triggered by signals from redox, metabolic and inflammatory pathways. This work identifies the long-sought mechanism of Slc40a1 transcriptional downregulation upon inflammation, paving the way for therapeutic interventions at this critical juncture.

Transcriptome Analysis Reveals Sertoli Cells Adapting Through Redox and Metabolic Pathways Under Heat Stress in Goats

Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. Methods: SCs were isolated from testes of 4-month-old black goats and exposed to heat stress (44 °C for 2.5 h). We employed transcriptome sequencing, CCK-8 assay, electron microscopy, ROS measurement, autophagy detection, Western blot analysis, and lactate concentration measurement. Bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction network analyses were performed on the transcriptome data. Results: Heat stress significantly reduced SC viability, induced oxidative stress and autophagy, and altered gene expression profiles. We identified 1231 significantly differentially expressed genes, with significant enrichment in membrane-related processes and metabolic pathways. Metabolism-related genes, including PKLR, ACOT11, and LPCT12, were significantly downregulated. Protein–protein interaction network analysis revealed ten hub genes potentially crucial in the heat-stress response: HSP90AA1, HSPA5, BAG3, IGF1, HSPH1, IL1A, CCL2, CXCL10, ALB, and CALML4. Conclusions: This study provides comprehensive insights into the molecular mechanisms underlying goat SC response to heat stress. The identified genes and pathways, particularly those related to metabolism and stress response, offer potential targets for developing strategies to mitigate heat-stress effects on livestock reproduction. These findings contribute to our understanding of climate change impacts on animal husbandry and may inform the development of heat-stress resistant livestock lines.

Physiological characteristics and transcriptomic analyses of alfalfa root crown in wintering

BackgroundAlfalfa, scientifically identified as Medicago sativa, is repeatedly referred to as the “king of forages”. Because of its tight relationship to winter hardiness, the alfalfa’s root crown plays a significant role as a storage organ over the winter. At present, it is still unknown what molecular process makes the alfalfa root crown resistant to cold. This study was aimed to study these knowledge gaps. Using RNA sequencing (RNA-Seq) technology, significant genes associated with cold hardiness were found.MethodsAccording to the random block design, Longmu 806 alfalfa and Sardi alfalfa were planted in regional experiments. Under the condition of low-temperature treatment in winter, the differentially expressed genes (DEGs), winter survival rate (WSR), and physiological characteristics were, in turn, calculated by RNA-Seq, chemical analysis, and field investigation.ResultsThe WSR of the Longmu 806 alfalfa was 3.68-fold greater than that of the Sardi alfalfa. The jasmonic acid (JA), soluble sugar (SS), proline (Pro), and glutathione (GSH) concentration in the roots of Longmu 806 alfalfa was more than the same amount in Sardi alfalfa in other words P is less than 0.05. An entire set of 878 DEGs related to winter hardiness was found by statistical analysis. Among them, 463 DEGs showed an increase in expression, whereas 415 DEGs showed a decrease in expression. The metabolic pathways’ examination presented that the DEGs (MsERF1, MsCHIB, MsJAZ, MsAOC, MsGST, MsINV, MsTPS, and MsOAT) were linked to the pathways of “plant hormone signaling transduction”, “Amino sugar and nucleotide sugar metabolism”, and “glutathione metabolism”. Furthermore, the physiological changes in JA, SS, Pro content, and GSH were influenced by the dynamic transcription profile of LT (low- temperature) resistance-related genes.

Non-Targeted Metabolomics Analysis Reveals Metabolite Profiles Change During Whey Fermentation with Kluyveromyces marxianus

Background: Whey fermentation could produce bioactive substances with immunomodulatory effects, metabolic syndrome modulation, and antioxidant properties, thereby imparting functional characteristics to products and facilitating the development of novel foods with health-promoting potential. Methods: A non-targeted metabolomics approach using liquid chromatography–mass spectrometry (LC-MS) was employed to investigate changes in the metabolite profiles of whey fermented by Kluyveromyces marxianus strain KM812 over varying fermentation durations. Results: The findings demonstrated a progressive enrichment of metabolites over time. A total of 151 differential metabolites were identified and categorized primarily into amino acids, peptides, and analogues, fatty acids and conjugates, and carbohydrates and conjugates, as well as benzoic acids and derivatives. The highest relative content of whey metabolites was observed at 48 h of fermentation, with a cumulative increase of 1.45-fold, 1.49-fold, 3.39-fold, and 1.24-fold for peptides and amino acids, peptides, and analogues, fatty acids and conjugates, and carbohydrates and conjugates, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed associations with 23 specific metabolites and delineated 9 metabolic pathways, predominantly involved in amino acid and lipid metabolism. Conclusions: Based on the above, KM812 could effectively degrade macromolecular substances in whey into small molecules such as L-isoleucine, ornithine, betaine, α-linolenic acid, and palmitoleic acid, thereby influencing the nutritional and functional properties of whey. In-depth analysis of the metabolic products in KM812-fermented whey could provide a theoretical basis for the development of functional foods derived from small molecules in the future.

Bibliometric and visual analysis of human microbiome—breast cancer interactions: current insights and future directions

The composition of the gut microbiome differs from that of healthy individuals and is closely linked to the progression and development of breast cancer. Recent studies have increasingly examined the relationship between microbial communities and breast cancer. This study analyzed the research landscape of microbiome and breast cancer, focusing on 736 qualified publications from the Web of Science Core Collection (WoSCC). Publications in this field are on the rise, with the United States leading in contributions, followed by China and Italy. Despite this strong output, the centrality value of China in this field is comparatively low at ninth, highlighting a gap between the quantity of research and its global impact. This pattern is repetitively observed in institutional contributions, with a predominance of Western institutes among the top contributors, underscoring a potential research quality gap in China. Keyword analysis reveals that research hotspots are focused on the effect of microbiome on breast cancer pathogenesis and tumor metabolism, with risk factors and metabolic pathways being the most interesting areas. Publications point to a shift toward anti-tumor therapies and personalized medicine, with clusters such as “anti-tumor” and “potential regulatory agent” gaining prominence. Additionally, intratumor bacteria studies have emerged as a new area of significant interest, reflecting a new direction in research. The University of Helsinki and Adlercreutz H are influential institutions and researchers in this field. Current trends in microbiome and breast cancer research indicate a significant shift toward therapeutic applications and personalized medicine. Strengthening international collaborations and focusing on research quality is crucial for advancing microbiome and breast cancer research.

Review of Alzheimer's disease and treatments

Alzheimer's disease (AD) is a neurodegenerative disease that primarily affects older adults and is characterized by progressive memory loss and cognitive dysfunction. The disease is the most common type of dementia worldwide and imposes a significant burden on patients, families and society. More than 50 million people worldwide are affected by Alzheimer's disease, placing enormous financial strain on healthcare systems and families. The main molecular metabolic pathways of Alzheimer's disease include amyloid beta protein metabolic pathway and tau protein phosphorylation pathway. Abnormal accumulation of amyloid beta protein in the brain to form plaques, and excessive phosphorylation of tau protein to form neurofibrillary tangles, these pathological changes lead to nerve cell damage and death, resulting in the gradual loss of cognitive function. Current treatments can only slow the progression of the disease or alleviate symptoms and cannot completely cure AD. Finding effective treatment and intervention strategies can not only significantly improve the quality of life of Alzheimer's patients, but also reduce the burden of the disease on society and families. This article will review the background and epidemiology of Alzheimer's disease, discuss its main molecular metabolic pathways in detail, and review the current status of treatment, with a view to providing references for future research and treatment strategies.

Transcriptome Sequencing of Bacillus sp. TTMP20 and Analysis of the Effect of BDH Gene on Tetramethylpyrazine Synthesis.

Bacillus sp. TTMP20 has high tetramethylpyrazine (TTMP) yield. However, the mechanism of TTMP production in this strain is unclear at present, which limits the modification for strain TTMP20. In this study, key metabolic pathways related to TTMP synthesis were identified, which included glycolytic pathway, tricarboxylic acid cycle and nitrogen metabolism pathway. Moreover, transgenic Bacillus sp. TTMP20 with recombinant vector PHY-300PLK-BDH was constructed. 2,3-butanediol dehydrogenase gene (BDH) overexpression considerably reduced TTMP biosynthesis. This study will supply new insight into the regulation of TTMP biosynthesis at key enzyme gene level.

Cytochrome P450-derived Epoxyeicosatrienoic Acid, the Regulation of Cardiovascular-related Diseases, and the Implication for Pulmonary Hypertension.

Cytochrome P450 (CYP) epoxygenases metabolize arachidonic acid (AA) into biologically active epoxyeicosatrienoic acids (EETs), forming a pivotal metabolic pathway (AA-CYP-EETs-soluble epoxide hydrolase-dihydroxyeicosatrienoic acids) implicated in the progression of various disorders. Inflammation is a key contributor to the onset and progression of numerous systemic diseases, and EETs play a significant role in mitigating inflammation. Extensive research highlights the cardiovascular protective effects of EETs, which include vasodilation, anti-hypertensive, and anti-atherosclerotic properties. Interestingly, the relatively less-explored third metabolic pathway of AA exhibits both pro-proliferative and anti-apoptotic effects in endothelial cells and smooth muscle cells. Recent studies have shown elevated levels of EETs catalyzed by CYP epoxygenases in human tumors, promoting tumor progression and metastasis-phenomena closely related to the disease progression in pulmonary hypertension (PH). This review explores the current understanding of the regulatory functions of CYP-derived EETs in cardiovascular diseases and seeks to elucidate their potential implications in PH. Ultimately, understanding the multifaceted roles of EETs may help identify novel therapeutic targets for both cardiovascular diseases and PH.

Fishmeal intervention after short-term novel proteins stimulates compensatory growth and affects intestinal health in largemouth bass (Micropterus salmoides).

This research utilized a compensatory growth phenomenon aimed at reducing the use of fishmeal in aquatic animal feed. However, the compensatory growth triggered by fishmeal restriction with novel protein replacement has yet to be understood. Five isonitrogenous and isolipidic diets containing different proteins were manufactured, with fishmeal serving as the control and diets containing novel proteins, i.e., Chlorella (Chlorella vulgaris), cottonseed protein concentrate, Clostridium autoethanogenum, and yellow mealworm (Tenebrio molitor), serving as the experimental diets. Largemouth bass (Micropterus salmoides) with a starting body weight of 4.73 ± 0.04g were respectively fed these five diets for the first 29days (first stage), followed by a fishmeal diet for the remaining 29days (second stage). The diet of fishmeal, Chlorella vulgaris, cottonseed protein concentrate, Clostridium autoethanogenum, and Tenebrio molitor was referred to as FM, ChM, CSM, CAP, and TM, respectively. All novel protein groups showed a 60-73% higher weight gain compared to the fishmeal group during the second phase; however, they did not reach the weight level seen in the control group. In addition, the second stage of fishmeal intervention resulted in a reduction of approximately 35% in the area of positive Alcian blue (AB) staining of intestinal tissues in the CSM group, and about 40% in the CAP group, compared to the first stage. Furthermore, the area of intestinal apoptosis in TM was enlarged after fishmeal intervention while it was decreased in other experimental groups. At day 58, gene expression analysis of the CAP group fish at the end of the trial revealed increased levels of the anti-apoptotic gene bcl-2, as well as higher expression of intestinal inflammatory cytokines il-1β, tnf-α, nf-κb p65, and il-10, compared to the FM group. In terms of the biochemical indices, the levels of catalase (CAT) and glutathione peroxidase (GSH-Px) were reduced in CSM on day 58. An assessment of potential microbial function at end of trial demonstrated that CAP could reduce the lipid metabolism and amino acid metabolism, and increased carbohydrate metabolism pathways in the largemouth bass intestine. In conclusion, both CAP and ChM groups showed promise to reduce fishmeal with respect to intestinal health rather than growth. This study should be of value to practitioners wishing to use novel proteins to reduce fishmeal via the utilization of the compensatory growth phenomenon.

Metabolomics profiles of the liquid co-culture of Sanghuangporus vaninii and Pleurotus sapidus

IntroductionFungal secondary metabolites (SMs) have broad application prospects in the food and medicine industries. Co-culturing strategies that simulate natural symbiotic relationships among microorganisms are used to discover and enhance the production of new SMs. We aimed to use the abundant resources of large edible and medicinal fungi to enhance the yield of desired metabolites through co-culture and potentially produce metabolites that cannot be generated in pure cultures.MethodsWe assessed the biomass and intracellular polysaccharide (IPS) content of liquid co-cultures of Sanghuangporus vaninii and Pleurotus sapidus. Subsequently, the effect of the liquid co-culture on fungal intracellular metabolites was studied using UPLC-QTOF.ResultsCo-culturing of S. vaninii with P. sapidus resulted in significantly increased biomass and IPS content; however, P. sapidus had a significant inhibitory effect on the growth of S. vaninii. Metabolomic data further indicated that amino acid, nucleotide, and glycerophospholipid metabolisms were the primary metabolic pathways affected by symbiosis.DiscussionThis study provides insights into fungal interactions and cellular metabolic mechanisms, contributing to the understanding and enhancement of the fungal fermentation potential.

Genomic landscape of circulating tumor DNA in HER2-low metastatic breast cancer

The large population of HER2-low breast cancer patients necessitates further research to provide enhanced clinical guidance. In this study, we retrospectively analyzed 1071 metastatic breast cancer (MBC) patients and the circulating tumor DNA (ctDNA) to investigate clinicopathological and genetic alterations of HER2-low MBC patients. The effect of HER2-low status on different treatment modalities was explored in two prospective clinical trials (NCT03412383, NCT01917279) and a retrospective study. Our findings suggest TP53, PIK3CA, and ESR1 are frequently mutated genes in HER2-low MBC. Compared to the HER2-0 group, mutations observed in the HER2-low group are more closely associated with metabolic pathway alterations. Additionally, among patients with ERBB2 mutations and treated with pyrotinib, the HER2-low group may experience superior prognosis when compared to the HER2-0 group. Notably, we did not find any statistically significant disparity in the response to chemotherapy, endocrine therapy, or CDK4/6 inhibitor therapy between HER2-0 and HER2-low breast cancer patients. Interestingly, within the subgroup of individuals with metabolic pathway-related gene mutations, we found that HER2-low group exhibited a more favorable response to these treatments compared to HER2-0 group. Additionally, dynamic analysis showed the HER2-low MBC patients whose molecular tumor burden index decreased or achieved early clearance of ctDNA after the initial two treatment cycles, exhibited prolonged survival. Moreover, we classified HER2-low MBC into three clusters, providing a reference for subsequent treatment with enhanced precision. Our study offers valuable insights into the biology of HER2-low MBC and may provide reference for personalized treatment strategies.

Identification of crucial drought-tolerant genes of barley through comparative transcriptomic analysis and yeast-based stress assay

Drought is a persistent and serious threat to crop yield and quality. The identification and functional characterization of drought tolerance-related genes is thus vital for efforts to support the genetic improvement of drought-tolerant crops. Barley is highly adaptable and renowned for its robust stress resistance, making it an ideal subject for efforts to explore genes related to drought tolerance. In this study, two barley materials with different drought tolerance were subjected to soil drought treatment, including a variety with strong drought tolerance (Hindmarsh) and a genotype with weaker drought tolerance (XZ5). Transcriptomic sequencing data from the aboveground parts of these plants led to the identification of 1,206 differentially expressed genes associated with drought tolerance. These genes were upregulated in Hindmarsh following drought stress exposure but downregulated or unchanged in XZ5 under these same conditions, or were unchanged in Hindmarsh but downregulated in XZ5. Pathway enrichment analyses suggested that these genes are most closely associated with defense responses, signal recognition, photosynthesis, and the biosynthesis of various secondary metabolites. Using protein-protein interaction networks, the ankyrin repeat domain-containing protein 17-like isoform X2 was predicted to impact other drought tolerance-related protein targets in Hindmarsh. In MapMan metabolic pathway analyses, genes found to be associated with the maintenance of drought tolerance in Hindmarsh under adverse conditions were predicted to include genes involved in the abscisic acid, cytokinin, and gibberellin phytohormone signaling pathways, genes associated with redox homeostasis related to ascorbate and glutathione S-transferase, transporters including ABC and AAAP, transcription factors such as AP2/ERF and bHLH, the heat shock proteins HSP60 and HSP70, and the sucrose non-fermenting-1-related protein kinase. Heterologous HvSnRK2 (one of the identified genes, which encodes the sucrose non-fermenting-1-related protein kinase) gene expression in yeast conferred significant drought tolerance, highlighting the functional importance of this gene as one linked with drought tolerance. This study revealed the drought tolerance mechanism of Hindmarsh by comparing transcriptomes while also providing a set of candidate genes for genetic efforts to improve drought tolerance in this and other crop species.

Analyzing sorbitol biosynthesis using a metabolic network flux model of a lichenized strain of the green microalga Diplosphaera chodatii.

Diplosphaera chodatii, a unicellular terrestrial microalga found either free-living or in association with lichenized fungi, protects itself from desiccation by synthesizing and accumulating low-molecular-weight carbohydrates such as sorbitol. The metabolism of this algal species and the interplay of sorbitol biosynthesis with its growth, light absorption, and carbon dioxide fixation are poorly understood. Here, we used a recently available genome assembly for D. chodatii to develop a metabolic flux model and analyze the alga's metabolic capabilities, particularly, for sorbitol biosynthesis. The model contains 151 genes, 155 metabolites, and 194 unique metabolic reactions participating in 12 core metabolic pathways and five compartments. Both photoautotrophic and mixotrophic growths of D. chodatii were supported by the metabolic model. In the presence of glucose, mixotrophy led to higher biomass and sorbitol yields. Additionally, the model predicted increased starch biosynthesis at high light intensities during photoautotrophic growth, an indication that the "overflow hypothesis-stress-driven metabolic flux redistribution" could be applied to D. chodatii. Furthermore, the newly developed metabolic model of D. chodatii, iDco_core, captures both linear and cyclic electron flow schemes characterized in photosynthetic microorganisms and suggests a possible adaptation to fluctuating water availability during periods of desiccation. This work provides important new insights into the predicted metabolic capabilities of D. chodatii, including a potential biotechnological opportunity for industrial sorbitol biosynthesis.IMPORTANCELichenized green microalgae are vital components for the survival and growth of lichens in extreme environmental conditions. However, little is known about the metabolism and growth characteristics of these algae as individual microbes. This study aims to provide insights into some of the metabolic capabilities of Diplosphaera chodatii, a lichenized green microalgae, using a recently assembled and annotated genome of the alga. For that, a metabolic flux model was developed simulating the metabolism of this algal species and allowing for studying the algal growth, light absorption, and carbon dioxide fixation during both photoautotrophic and mixotrophic growth, in silico. An important capability of the new metabolic model of D. chodatii is capturing both linear and cyclic electron flow mechanisms characterized in several other microalgae. Moreover, the model predicts limits of the metabolic interplay between sorbitol biosynthesis and algal growth, which has potential applications in assisting the design of bio-based sorbitol production processes.

Sugar Transport and Signaling in Shoot Branching

The source–sink relationship is critical for proper plant growth and development, particularly for vegetative axillary buds, whose activity shapes the branching pattern and ultimately the plant architecture. Once formed from axillary meristems, axillary buds remain dormant or become active to grow into new branches. This transition is notably driven by the regulation of the bud sink strength, which is reflected in the ability to unload, metabolize and store photoassimilates. Plants have so far developed two main mechanisms for unloading sugars (sucrose) towards sink organs, a symplasmic pathway and an apoplasmic pathway, but so far limited investigations have been reported about the modes of sugar uptake during the transition from the dormant to the active outgrowth state of the bud. The available data indicate that the switch from dormant bud to active outgrowing state, requires sugar and is shortly preceded by an increase in bud metabolic activity and a remobilization of the stem starch reserves in favor of growing buds. This activation of the bud sink strength is accompanied by an up-regulation of the main markers of apoplasmic unloading, such as sugar transporters (sucrose transporters—SUTs; sugar will eventually be exported transporters—SWEETs), sucrose hydrolyzing enzymes (cell wall invertase—CWINV) and sugar metabolic pathways (glycolysis/tricarboxylic cycle—TCA; oxidative pentose phosphate pathway—OPPP). As these results are limited to a few species, they are not sufficient to provide a complete and accurate picture of the mode(s) of sugar unloading toward axillary buds and deserve to be complemented by additional studies in a wide variety of plants using systems integration, combining genetic, molecular and immunolocalization approaches. Altogether, we discuss here how sugar is a systemic regulator of shoot branching, acting both as an energy-rich molecule and a signaling entity in the establishment of the bud sink strength.

Methods to characterize type, relevance, and interactions of organic matter and microorganisms in fluids along the flow path of a geothermal facility

Abstract. Dissolved organic matter (DOM) and microorganisms were characterized along the flow path of a geothermal facility that produces water from a deep (2800 m) carbonate rock reservoir for energy provision. A variety of analytical techniques were employed to distinguish between natural and synthetic organic matter, determine the composition of the microbial community, and evaluate the role of microorganisms in the operation of the geothermal site in Bad Blumau, Austria. Ion chromatography (IC), liquid chromatography with organic carbon detection (LC-OCD), and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in negative electrospray ionization (ESI(−)) and positive atmospheric pressure photoionization (APPI(+)) mode were applied to the fluid samples for the purpose of characterizing the composition of DOM and distinguishing natural DOM from a chemical inhibitor used to prevent scaling. The concentrations of dissolved organic carbon (DOC) ranged from 8.5 to 10.4 mg C L−1. The chemical scaling inhibitor contributes approximately 1 mg C L−1 of DOC to the produced fluids. Depending on the applied ionization mode, the FT-ICR-MS results show that between 31 % and 65 % of the macromolecular formulas (150–1000 Da) detected in the fluid samples appear to originate from the inhibitor. However, the DOM is primarily composed of low-molecular-weight acids (LMWA), with acetate being the most prevalent, reaching up to 7.4 mg C L−1. To assess the diversity of the bacterial communities, targeted amplification of the 16S rRNA gene was conducted. The composition of the microbial community exhibited variation along the flow path, with Firmicutes, Proteobacteria, and Thermotogae representing the dominant bacterial phyla. Based on the community composition, metabolic pathways associated with the presence of acetate in the samples were predicted. Microorganisms may produce acetate through diverse fermentation processes, including those involving lysine, pyruvate, and hexitol. Assessing the presence and interaction of organic compounds and microorganisms in geothermal fluids can provide a broader understanding of processes within the geothermal facility. This understanding could be beneficial for efficient operation of a geothermal power plant.