Fatty Acid Degradation Pathway Research Articles

Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin

Silymarin has been used for improving hepatic damage and lipid disorders, but its action mechanism remains to be clarified. Here, we investigate the contributions of the gut microbiota to the improvement of liver lipid metabolism by silymarin. We find i) strong and significant microbial shifts upon silymarin but not silibinin treatment; ii) over 60% variations of liver fat are explained by silymarin-induced bacterial B12 production in male rats but not in male germ-free mice; iii) fecal microbiota transplantation confirms their protective roles against liver fat accumulation; iv) upregulation of one-carbon metabolism and fatty acid degradation pathways are observed based on the liver transcriptome analyses; and v) in humans the delta changes of serum B12 associate negatively with the fluctuations of serum triglycerides. Overall, we reveal a mechanism of action underpinning the lipid-lowering effect of silymarin via the gut microbiota and its vitamin B12 producing capabilities.

Treatment of nitrogen and phosphorus in wastewater by heterotrophic N- and P-starved microalgal cell.

Nitrogen (N) and phosphorus (P) are two major pollutants present in aquaculture wastewater, and their concentrations often do not meet discharge standards. In the present study, the N and P removal efficiency of nutrient-deficient cells (S group) was significantly higher than that of photoautotrophic cells (P group) and heterotrophic cells (H group). After incubation with wastewater, the N and P content of S group cells was significantly increased and reached a level similar to that of the P group and H group cells after 6 days of treatment. Additionally, in the S group cells, the content of total fatty acids (TFAs), which can be used to supply energy and organic carbon for N and P absorption, significantly decreased. In addition, the protein and nucleic acid contents of the S group cells also significantly increased, which revealed the biosynthetic flow of assimilated N and P. Comparative transcriptome analysis showed that compared with the P group and H group, the N metabolism, ribosome, RNA polymerase, and fatty acid degradation pathways were significantly upregulated in the S group cells, and the fatty acid biosynthesis pathway was significantly downregulated, which was in agreement with the biochemical results. In summary, our study showed that N- and P-starved heterotrophic cells are ideal for use in wastewater N and P removal processes. Keypoints • The N and P removal efficiencies of the S group were higher than P and H groups • Fatty acids were degraded to supply energy and carbon for N and P absorption • N metabolism and fatty acid degradation pathways were upregulated in the S group.

Serum metabolomic analysis in patients with Hashimoto's thyroiditis.

Hashimoto's thyroiditis, an autoimmune thyroid disease, shows high morbidity worldwide, particularly in female. Patients with Hashimoto's thyroiditis have an increasing risk of hypothyroidism during the occurrence and progression of Hashimoto's thyroiditis. In recent years, metabolomics has been widely applied in autoimmune diseases, especially thyroid disorders. However, metabolites analysis in Hashimoto's thyroiditis is still absent. A total of 92 samples were collected, including 35 cases in the control group, 30 cases in the Hashimoto's thyroiditis with euthyroidism group, and 27 cases in the Hashimoto's thyroiditis with subclinical hypothyroidism group. SPSS 25.0 for statistical analysis and ROC curve, SIMCA 14.0, Metaboanalysis for multifactor analysis, and Origin 2021 for correlation analysis. 21 metabolites were identified. 10 metabolites were obtained from control group versus HTE group, 8 serum metabolites were abnormal between control group and HTS group, 3 metabolites were derived from HTE group versus HTS. Kyoto Encyclopedia of Genes and Genomes Enrichment analysis showed that fatty acid degradation, Arginine, and proline metabolism have a significant impact on HTE, while lysine degradation, tyrosine metabolism play an important role HTS group, compared to control group. In the comparison between the HTE and HTS group, Valine, leucine, and isoleucine degradation and Valine, leucine, and isoleucine biosynthesis exists a key role. Correlation analysis shows clinical are not related to metabolites. ROC curve indicates SM, LPC, PC can efficiency in identification patients with HT in different clinical stage from healthy individuals. Serum metabolites were changed in HT. Phospholipids such as SM, LPC, PC influence the pathogenesis of Hashimoto's thyroiditis. Fatty acid degradation and lysine degradation pathways have an impact on different clinical stage of HT.

Transcriptome Analysis Reveals the Involvement of Alternative Splicing in the Nitrogen Starvation Response of Chlamydomonas reinhardtii

Alternative splicing (AS) is a regulatory mechanism of post-transcriptional regulation that plays an important role in plant response to abiotic stresses. However, corresponding research involving the mechanism of AS in the nitrogen starvation response of C. reinhardtii is rare. This study performed a comprehensive and systematic analysis of AS events in C. reinhardtii at nine time points (0 h, 10 m, 30 m, 1 h, 6 h, 8 h, 24 h, and 48 h) under nitrogen starvation. It used STAR and rMATS tools to identify and quantify the probability of the AS event happening through the transcriptome high-throughput sequencing data. A total of 5806 AS events in 3500 genes were identified, and the retained intron and skipped exon were considered the main AS types. The genes related to the AS event in nitrogen starvation were mainly involved in spliceosome and transporter and enriched in the citrate cycle and fatty acid degradation pathways. These results suggested that AS may play an important role in the nitrogen starvation response in C. reinhardtii, and provided insights into post-transcriptional regulation under nitrogen starvation.

Biodegradation of MC-LR and its key bioactive moiety Adda by Sphingopyxis sp. YF1: Comprehensive elucidation of the mechanisms and pathways

Microcystins (MCs) are harmful to the ecology and public health. Some bacteria can degrade MCs into Adda, but few can destroy Adda. Adda is the key bioactive moiety of MCs and mainly contributes to hepatotoxicity. We had previously isolated an indigenous novel bacterial strain named Sphingopyxis sp. YF1 that can efficiently degrade MCs and its key bioactive moiety Adda, but the mechanisms remained unknown. Here, the biodegradation mechanisms and pathways of Adda were systematically investigated using multi-omics analysis, mass spectrometry and heterologous expression. The transcriptomic and metabolomic profiles of strain YF1 during Adda degradation were revealed for the first time. Multi-omics analyses suggested that the fatty acid degradation pathway was enriched. Specifically, the expression of genes encoding aminotransferase, beta oxidation (β-oxidation) enzymes and phenylacetic acid (PAA) degradation enzymes were significantly up-regulated during Adda degradation. These enzymes were further proven to play important roles in the biodegradation of Adda. Simultaneously, some novel potential degradation products of Adda were identified successfully, including 7‑methoxy-4,6-dimethyl-8-phenyloca-2,4-dienoic acid (C17H22O3), 2-methyl-3‑methoxy-4-phenylbutyric acid (C12H16O3) and phenylacetic acid (PAA, C8H8O2). In summary, the Adda was converted into PAA through aminotransferase and β-oxidation enzymes, then the PAA was further degraded by PAA degradation enzymes, and finally to CO2 via the tricarboxylic acid cycle. This study comprehensively elucidated the novel MC-LR biodegradation mechanisms, especially the new enzymatic pathway of Adda degradation. These findings provide a new perspective on the applications of microbes in the MCs polluted environment.

Enhancement of fatty acid degradation pathway promoted glucoamylase synthesis in Aspergillus niger

BackgroundOur recent multi-omics analyses of glucoamylase biosynthesis in Aspergillus niger (A. niger) suggested that lipid catabolism was significantly up-regulated during high-yield period under oxygen limitation. Since the catabolism of fatty acids can provide energy compounds such as ATP and important precursors such as acetyl-CoA, we speculated that enhancement of this pathway might be beneficial to glucoamylase overproduction.ResultsBased on previous transcriptome data, we selected and individually overexpressed five candidate genes involved in fatty acid degradation under the control of the Tet-on gene switch in A. niger. Overexpression of the fadE, fadA and cyp genes increased the final specific enzyme activity and total secreted protein on shake flask by 21.3 ~ 31.3% and 16.0 ~ 24.2%, respectively. And a better inducible effect by doxycycline was obtained from early logarithmic growth phase (18 h) than stationary phase (42 h). Similar with flask-level results, the glucoamylase content and total extracellular protein in engineered strains OE-fadE (overexpressing fadE) and OE-fadA (overexpressing fadA) on maltose-limited chemostat cultivation were improved by 31.2 ~ 34.1% and 35.1 ~ 38.8% compared to parental strain B36. Meanwhile, intracellular free fatty acids were correspondingly decreased by 41.6 ~ 44.6%. The metabolomic analysis demonstrated intracellular amino acids pools increased 24.86% and 18.49% in two engineered strains OE-fadE and OE-fadA compared to B36. Flux simulation revealed that increased ATP, acetyl-CoA and NADH was supplied into TCA cycle to improve amino acids synthesis for glucoamylase overproduction.ConclusionThis study suggested for the first time that glucoamylase production was significantly improved in A. niger by overexpression of genes fadE and fadA involved in fatty acids degradation pathway. Harnessing the intracellular fatty acids could be a strategy to improve enzyme production in Aspergillus niger cell factory.

Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei.

Syntrophomonas wolfei is an anaerobic syntrophic microbe that degrades short-chain fatty acids to acetate, hydrogen, and/or formate. This thermodynamically unfavorable process proceeds through a series of reactive acyl-Coenzyme A species (RACS). In other prokaryotic and eukaryotic systems, the production of intrinsically reactive metabolites correlates with acyl-lysine modifications, which have been shown to play a significant role in metabolic processes. Analogous studies with syntrophic bacteria, however, are relatively unexplored and we hypothesized that highly abundant acylations could exist in S. wolfei proteins, corresponding to the RACS derived from degrading fatty acids. Here, by mass spectrometry-based proteomics (LC-MS/MS), we characterize and compare acylome profiles of two S. wolfei subspecies grown on different carbon substrates. Because modified S. wolfei proteins are sufficiently abundant to analyze post-translational modifications (PTMs) without antibody enrichment, we could identify types of acylations comprehensively, observing six types (acetyl-, butyryl-, 3-hydroxybutyryl-, crotonyl-, valeryl-, and hexanyl-lysine), two of which have not been reported in any system previously. All of the acyl-PTMs identified correspond directly to RACS in fatty acid degradation pathways. A total of 369 sites of modification were identified on 237 proteins. Structural studies and in vitro acylation assays of a heavily modified enzyme, acetyl-CoA transferase, provided insight on the potential impact of these acyl-protein modifications. The extensive changes in acylation-type, abundance, and modification sites with carbon substrate suggest that protein acylation by RACS may be an important regulator of syntrophy.

Metatranscriptomic shifts suggest shared biodegradation pathways for Corexit 9500 components and crude oil in Arctic seawater.

While the genes and pathways responsible for petroleum biodegradation in marine environments have received substantial attention, considerably less is known about those active in the biodegradation of the commonly applied chemical dispersant Corexit 9500. Yet, their fate in the Arctic marine environment is an increasingly important unknown. To elucidate the genes and pathways active in the biodegradation of oil and dispersants, we performed metatranscriptomic sequencing on microbial communities in Arctic seawater exposed to oil, Corexit, or both for 0, 5, and 30 days in a mesocosm incubation experiment. While oil and Corexit stimulated significantly different metatranscriptomic profiles overall, both enriched a suite of fatty acid degradation gene transcripts. Based on the gene transcripts observed and the chemical structures of Corexit 9500 surfactant components, we propose a hypothetical pathway for Corexit surfactant biodegradation in which surfactant ester groups are transformed into fatty acids that are then funnelled into the β-oxidation fatty acid degradation pathway. Several microbial taxa within Oceanospirillales, Pseudomonadales, and Alteromonadales were associated with either oil-only or Corexit-only exposure, potentially implicating them in the degradation of these mixtures. Metabolic gene transcripts were associated with diverse gammaproteobacterial lineages, with many genera exhibiting functional redundancy. These findings offer new insight into the potential genes, pathways, and microbial consortia involved in the biodegradation of Corexit 9500 in the Arctic marine environment.

Research Progress on the Construction of Artificial Pathways for the Biosynthesis of Adipic Acid by Engineered Microbes

Adipic acid is an important bulk chemical used in the nylon industry, as well as in food, plasticizers and pharmaceutical fields. It is thus considered one of the most important 12 platform chemicals. The current production of adipic acid relies on non-renewable petrochemical resources and emits large amounts of greenhouse gases. The bio-production of adipic acid from renewable resources via engineered microorganisms is regarded as a green and potential method to replace chemical conversion, and has attracted attention all over the world. Herein we review the current status of research on several artificial pathways for the biosynthesis of adipic acid, especially the reverse degradation pathway, which is a full biosynthetic method and has achieved the highest titer of adipic acid so far. Other artificial pathways including the fatty acid degradation pathway, the muconic acid conversion pathway, the polyketide pathway, the α-ketopimelate pathway and the lysine degradation pathway are also discussed. In addition, the challenges in the bio-production of adipic acid via these artificial pathways are analyzed and the prospects are presented with the intention of providing some significant points for the promotion of adipic acid biosynthesis.

Strategic thermosonication-mediated modulation of lactic acid bacteria acidification kinetics for enhanced (post)-fermentation performance

This study explored the feasibility of thermosonication (TS)-prestressed inoculum with different fermentation patterns for regulating microbial (post)-fermentation acidification kinetics. Through a Box-Behnken design, stimulative (20 min, 400 W, 33 kHz, 25 °C) and inhibitive (10 min, 600 W, 33 kHz, 20 °C) effects on the acidification capability of Lactobacillus plantarum A3 were achieved without observing greatly activated/inactivated strains growth, further confirmed by lactose fermentation performed by Streptococcus thermophilus and Lactobacillus bulgaricus. Lactic acid was the major contributing factor responsible for TS-induced acidification modifications corresponding to the potential fluctuations of CoA biosynthesis, fatty acid degradation and chain elongation pathways to TS prestress. Microscopy observations and quantitative extracellular substance assays showed palpable stress disturbance on microbes, but causing insignificant effects on product characteristics. This investigation demonstrated the potential of controlled sonication prestress strategies to achieve dual engineering effects on microbial metabolic behavior, for alleviating post-acidification problem or enhancing process efficiencies.

Identification of Differential Expression Genes between Volume and Pressure Overloaded Hearts Based on Bioinformatics Analysis.

Volume overload (VO) and pressure overload (PO) are two common pathophysiological conditions associated with cardiac disease. VO, in particular, often occurs in a number of diseases, and no clinically meaningful molecular marker has yet been established. We intend to find the main differential gene expression using bioinformatics analysis. GSE97363 and GSE52796 are the two gene expression array datasets related with VO and PO, respectively. The LIMMA algorithm was used to identify differentially expressed genes (DEGs) of VO and PO. The DEGs were divided into three groups and subjected to functional enrichment analysis, which comprised GO analysis, KEGG analysis, and the protein–protein interaction (PPI) network. To validate the sequencing data, cardiomyocytes from AR and TAC mouse models were used to extract RNA for qRT-PCR. The three genes with random absolute values of LogFC and indicators of heart failure (natriuretic peptide B, NPPB) were detected: carboxylesterase 1D (CES1D), whirlin (WHRN), and WNK lysine deficient protein kinase 2 (WNK2). The DEGs in VO and PO were determined to be 2761 and 1093, respectively, in this study. Following the intersection, 305 genes were obtained, 255 of which expressed the opposing regulation and 50 of which expressed the same regulation. According to the GO and pathway enrichment studies, DEGs with opposing regulation are mostly common in fatty acid degradation, propanoate metabolism, and other signaling pathways. Finally, we used Cytoscape’s three techniques to identify six hub genes by intersecting 255 with the opposite expression and constructing a PPI network. Peroxisome proliferator-activated receptor (PPARα), acyl-CoA dehydrogenase medium chain (ACADM), patatin-like phospholipase domain containing 2 (PNPLA2), isocitrate dehydrogenase 3 (IDH3), heat shock protein family D member 1 (HSPD1), and dihydrolipoamide S-acetyltransferase (DLAT) were identified as six potential genes. Furthermore, we predict that the hub genes PPARα, ACADM, and PNPLA2 regulate VO myocardial changes via fatty acid metabolism and acyl-Coa dehydrogenase activity, and that these genes could be employed as basic biomarkers for VO diagnosis and treatment.

Enhancing very long chain fatty acids production in Yarrowia lipolytica

BackgroundVery long chain fatty acids (VLCFA) and their derivatives are industrially attractive compounds. The most important are behenic acid (C22:0) and erucic acid (C22:1Δ13), which are used as lubricants, and moisturizers. C22:0 and C22:1Δ13 have also potential for biofuel production. These fatty acids are conventionally obtained from plant oils. Yarrowia lipolytica is an oleaginous yeast with a long history of gene manipulations resulting in the production of industrially interesting compounds, such as organic acids, proteins, and various lipophilic molecules. It has been shown previously that it has potential for the production of VLCFA enriched single cell oils.ResultsThe metabolism of Y. lipolytica was redesigned to achieve increased production of VLCFA. The effect of native diacylglycerol acyltransferases of this yeast YlLro1p, YlDga1p, and YlDga2p on the accumulation of VLCFA was examined. It was found that YlDga1p is the only enzyme with a beneficial effect. Further improvement of accumulation was achieved by overexpression of 3-ketoacyl-CoA synthase (TaFAE1) under 8UAS-pTEF promoter and blockage fatty acid degradation pathway by deletion of YlMFE1. The best-producing strain YL53 (Δmfe, pTEF-YlDGA1, 8UAS-pTEF-TaFAE1) produced 120 µg of very long chain fatty acids per g of produced biomass, which accounted for 34% of total fatty acids in biomass.ConclusionsRecombinant strains of Y. lipolytica have proved to be good producers of VLCFA. Redesign of lipid metabolism pathways had a positive effect on the accumulation of C22:1Δ13 and C22:0, which are technologically attractive compounds.

Lotus seed resistant starch ameliorates high-fat diet induced hyperlipidemia by fatty acid degradation and glycerolipid metabolism pathways in mouse liver

We investigated the potential efficacy and underlying mechanisms of Lotus seed Resistant Starch (LRS) for regulating hyperlipidemia in mice fed a High-fat Diet (HFD). Mouse were fed a normal diet (Normal Control group, NC group), HFD alone (MC group), HFD plus lovastatin (PC group), or HFD with low/medium/high LRS (LLRS, MLRS, and HLRS groups, respectively) for 4 weeks. LRS supplementation significantly decreased body weight and significantly reduced serum levels of total cholesterol, triglycerides, low-density lipoprotein cholesterol, and high-density lipopro-tein cholesterol compared with the MC group. LRS also significantly alleviated hepatic steatosis, especially in the MLRS group, which also showed a significantly reduced visceral fat index. LLRS supplementation significantly regulated genes associated with glycerolipid metabolism and steroid hormone biosynthesis (Lpin1 and Ugt2b38), MLRS significantly regulated genes related to fatty acid degradation, fatty acid elongation, and glycerolipid metabolism (Lpin1, Hadha, Aldh3a2, and Acox1), whereas HLRS significantly regulated genes related to fatty acid elongation and glycerolipid metabolism (Lpin1, Elovl3, Elovol5, and Agpat3). The fatty acid-degradation pathway regulated by MLRS thus exerts better control of serum lipid levels, body weight, visceral fat index, and liver steatosis in mice compared with LLRS- and HLRS-regulated pathways.

Host-virus interactions in PK-15 cells infected with Pseudorabies virus Becker strain based on RNA-seq

Pseudorabies is a highly contagious viral disease caused by the pseudorabies virus (PRV), and it is one of the most devastating diseases for the swine industry worldwide. However, the host-virus interaction and virus-related host factors at the mRNA level in virus natural host (pig) cells, are not fully understood. Here, we performed time-course RNA sequencing of the PK-15 cells infected with a recombinant strain PRV-Becker-GFP to study the dynamic competition between the host and the virus. At early stage of infection (3 hpi), our results suggested that the activation of cytosolic DNA-sensing pathway and NOD-like receptor signaling pathway might play a role in recognition of PRV, and the activation of NF-kappa B signaling pathway and TNF signaling pathway might be involved in immune response against the virus. However, all these pathways were subsequently inhibited by PRV. Additionally, our data indicated the fatty acid degradation pathway was significantly downregulated during late stage of infection (9 hpi), which was likely to accumulate fatty acids for viral envelope synthesis. Moreover, we verified the expression of 5 representative genes (ALDH1B1, ACAA2, ACSL3, ADH5, and EHHADH) related to fatty acid degradation pathway by RT-qPCR. Overall, our findings provide valuable information to better understand host-virus interactions and the immune escape mechanism of PRV-Becker as a virulent strain, offering novel targets for porcine anti-PRV breeding research and potential clinical treatment.

ITRAQ-Based Quantitative Proteomic Analysis of Antibacterial Mechanism of Milk-Derived Peptide BCp12 against Escherichia coli.

BCp12 is a novel casein-derived antibacterial peptide with a broad-spectrum antibacterial effect. However, its action mechanism against E. coli is unknown. In this study, the growth curve showed that BCp12 had excellent antibacterial activity against E. coli. Red (propidium iodide staining) and green (fluorescein isothiocyanate staining) fluorescence signals were detected at the edges of the E. coli cells treated with BCp12. scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images showed that E. coli cells became rough and shrunken, and part of the cell contents leaked to form a cavity. Furthermore, the iTRAQ proteome analysis showed that 193 and 174 proteins were significantly up-regulated and down-regulated, respectively, after BCp12 treatment. Four enzymes involved in fatty acid degradation of E. coli were down-regulated, disrupting the synthesis of cell membranes. Molecular docking and gel retardation assays showed that BCp12 could bind to genes encoding four key enzymes involved in the fatty acid degradation pathway through hydrogen bonding and hydrophobic interactions, thus significantly inhibiting their activities. Overall, the results indicate that BCp12 inhibits the growth of E. coli, causing metabolic disorders, thus destroying the structure of cell membranes.

Preliminary study on differentially expressed proteins in a mouse model of secondary alveolar echinococcosis based on data independent acquisition proteomics

To identify the differentially expressed proteins in different liver tissues in the mouse model of alveolar echinococcosis using high-resolution mass spectrometry with data independent acquisition (DIA), and to identify the key proteins contributing to the pathogenesis of alveolar echinococcosis. Protoscoleces were isolated from Microtus fuscus with alveolar echinococcosis and the experimental model of alveolar echinococcosis was established in female Kunming mice aged 6 to 8 weeks by infection with Echinococcus multilocularis protoscoleces. Mice were divided into the experimental and control groups, and animals in the experimental group was injected with approximately 3 000 protoscoleces, while mice in the control group were injected with the same volume of physiological saline. Mouse liver specimens were sampled from both groups one year post-infection and subjected to pathological examinations. In addition, the lesions (the lesion group) and peri-lesion specimens (the peri-lesion group) were sampled from the liver of mice in the experimental group and the normal liver specimens (the normal group) were sampled from mice in the control group for DIA proteomics analysis, and the differentially expressed proteins were subjected to bioinformatics analysis. A total of 1 020 differentially expressed proteins were identified between the lesion group and the normal group, including 671 up-regulated proteins and 349 down-regulated proteins, and 495 differentially expressed proteins were identified between the peri-lesion group and the normal group, including 327 up-regulated proteins and 168 down-regulated proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these differentially expressed proteins were involved in peroxisome, peroxisome proliferator-activated receptor (PPAR) and fatty acid degradation pathways, and the peroxisome and PPAR signaling pathways were found to correlate with liver injury. Several differentially expressed proteins that may contribute to the pathogenesis of alveolar echinococcosis were identified in these two pathways, including fatty acid binding protein 1 (Fabp1), Acyl-CoA synthetase long chain family member 1 (Acsl1), Acyl-CoA oxidase 1 (Acox1), Enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (Ehhadh) and Acetyl-Coenzyme A acyltransferase 1B (Acaa1b), which were down-regulated in mice in the experimental group. A large number of differentially expressed proteins are identified in the liver of the mouse model of alveolar echinococcosis, and Fabp1, Acsl1, Acox1, Ehhadh and Acaa1b may contribute to the pathogenesis of alveolar echinococcosis.

Transcriptome and Metabolome Analyses Provide Insights Into the Composition and Biosynthesis of Grassy Aroma Volatiles in White-Fleshed Pitaya.

Aroma is one of the major inherent quality characteristics in fruits. Understanding the composition of aroma volatiles and their biosynthesis mechanism is crucial to improving fruit quality. However, the biosynthesis mechanism of aroma volatiles has not been characterized yet in white-fleshed pitaya (Hylocereus undatus). This study was performed to investigate aroma volatiles and related gene expression patterns in the pulp of “mild grassy” and “strong grassy” aroma cultivars. Analysis of volatile composition and concentration showed that aldehydes, alcohols, esters, and alkenes were predominant in both cultivars. However, comparative analysis revealed a significant difference in the concentration of several metabolites, particularly hexanal and 1-hexanol. The results of the comparative transcriptome identified a large number of aroma-related differentially expressed genes. The majority of these genes were enriched in fatty acid and isoleucine degradation pathways. According to integrative analyses, changes in the expression of lipoxygenase pathway genes, specifically FAD, LOXs, HPLs, and ADHs, probably lead to the difference in strength of “grassy” aroma between both cultivars. The qRT-PCR of 18 aroma-related genes was performed to validate the transcriptome analysis. Our results identified key genes and pathways connected with the biosynthesis of aroma volatiles in white-fleshed pitaya. These results will be useful to dissect the genetic mechanism of fruit aroma in white-fleshed pitaya.

Population Genomics of Megalobrama Provides Insights into Evolutionary History and Dietary Adaptation.

Simple SummaryMegalobrama is the economically most important freshwater fish genus in China. In recent years, germplasm resources of Megalobrama have been depleting as a result of environmental degradation and artificial factors. In this study, we established the whole genome database of Megalobrama populations using the whole genome re-sequencing technology, explored population genetic structure, and inferred comprehensive evolutionary relationships using principal component analysis and population structure analysis. Furthermore, employing selective sweep analysis, we identified candidate genes related to variations in feeding habits, revealing the molecular mechanisms of environmental adaptability in Megalobrama populations. Taken together, this study describes the population history and genetic diversity of Megalobrama populations and also the molecular mechanisms likely involved their environmental adaptability. These findings will make a substantial contribution to conservation and utilization of Megalobrama germplasm resources. Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. pellegrini. Population structure indicated that geographically divergent Megalobrama populations were separated into six subgroups. A phylogenetic tree showed that M. skolkovii was more closely related to M. pellegrini than other species and M. hoffmanni was clustered apart from other Megalobrama species, showing a high nucleotide diversity in geographic groups. Treemix validated gene flow from M. amblycephala to M. skolkovii, suggesting that introgression may provide an important source of genetic variation in the M. skolkovii populations. According to the demographic history analysis, it is speculated that Megalobrama might have been originally distributed in the Pearl River with some spread to Hainan Island and northern China due to lower sea levels during the glacial period. Whole-genome selective sweeps analysis demonstrated that M. amblycephala likely developed an enhanced energy metabolism mostly through fatty acid degradation pathways whereas M. hoffmanni possibly regulate lipid absorption via the cholesterol metabolism pathway. Taken together, this study provides a valuable genomic resource for future genetic investigations aiming to improve genome-assisted breeding of Megalobrama species.

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis.

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

In situ Metabolomics of Metabolic Reprogramming Involved in a Mouse Model of Type 2 Diabetic Kidney Disease.

The in situ metabolic profiling of the kidney is crucial to investigate the complex metabolic reprogramming underlying diabetic kidney disease (DKD) and to allow exploration of potential metabolic targets to improve kidney function. However, as the kidney is a highly heterogeneous organ, traditional metabolomic methods based on bulk analysis that produce an averaged measurement are inadequate. Herein, we employed an in situ metabolomics approach to discover alternations of DKD-associated metabolites and metabolic pathways. A series of histology-specific metabolic disturbances were discovered in situ using airflow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI–MSI). In combination with integrated metabolomics analysis, five dysfunctional metabolic pathways were identified and located in the kidneys of type-2 DKD mice simultaneously for the first time, including taurine metabolism, arginine and proline metabolism, histidine metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways. As crucial nodes of metabolic pathways, five dysregulated rate-limiting enzymes related to altered metabolic pathways were further identified. These findings reveal alternations from metabolites to enzymes at the molecular level in the progression of DKD and provide insights into DKD-associated metabolic reprogramming.