Characterization of Metabolite Landscape Distinguishes Medicinal Fungus Cordyceps sinensis and other Cordyceps by UHPLC-Q Exactive HF-X Untargeted Metabolomics
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ABSTRACT:
SUBMITTER: Tang C
PROVIDER: S-EPMC10708286 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Cordyceps sinensis is a second-class, nationally protected, medicinal fungi and serves as a functional nutrient in China. C. sinensis is extremely scarce due to its peculiar growing environment and the extensive gathering practices carried out by humans. A large number of counterfeit products for this fungi have also emerged in the market. At present, there is a lack of research on the differential metabolites of C. sinensis and its counterfeit products. The current study used an LC-MS non-targeted metabolomics method to compare the differences in metabolites between C. sinensis and other Cordyceps. The results indicated that there were significant differences in the metabolites between C. sinensis and the others. The 18 superclasses were found to have differences, involving lipids, organic acids, nucleosides, carbohydrates, amino acids, vitamins, and their derivatives. Compared with the other four groups of Cordyceps, 8 metabolites with significant differences were screened. In addition, the types and abundance of different metabolites of nucleosides of C. sinensis were superior compared to other Cordyceps (e.g., 5-Methyldioxycytidine, didanosine, cytidine, etc.). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the metabolism of arginine and proline, and glycerophosphate metabolism were the two significant differences in the metabolic pathways between C. sinensis and other Cordyceps. The research results provide a reference for identifying the authenticity of C. sinensis using non-targeted metabolic methods.
| S-EPMC11851418 | biostudies-literature
Project description:The diagnosis of Lyme neuroborreliosis (LNB) requires the demonstration of intrathecal synthesis of Borrelia antibodies in a patient's cerebrospinal fluid (CSF), which involves the invasive procedure of a lumbar puncture. This study serves as a feasibility study aimed at exploring the potential of using serum samples, which are easily obtainable routine clinical samples, for LNB diagnostics via advanced metabolomics techniques. Serum samples were collected from confirmed LNB patients before and after treatment, with post-treatment samples serving as controls. The objective of the study was to find stable biomarkers for acute LNB through untargeted metabolomics analysis using ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The study focused on biomarkers that could be reliably detected in serum samples stored under typical clinical conditions, without the need for special handling, ensuring consistent detection over time. The analysis revealed 26,978 molecular features (MFs), of which 1,746 were statistically significant (p < 0.001). Further manual investigation into 91 of the most prominent MFs revealed 53 potential biomarkers for LNB, individually or in combination. The workflow developed provides a comprehensive platform for biomarker detection, with potential applications in both research and clinical settings for LNB and other infections. This minimally invasive diagnostic approach is promising, and additional validation and future studies are needed for it to be considered as a practical alternative or a complement to CSF-based diagnostics of LNB in everyday clinical practice.
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Project description:Five new polyketides, including two pairs of enantiomers and a racemate, were isolated from the fermentation broth of Aspergillus fumigatus, an endophytic fungus isolated from Cordyceps sinensis. Their structures were identified using one-dimensional (1D) and two-dimensional (2D) NMR experiments, and the absolute configurations of the enantiomers were confirmed using electronic circular dichroism (ECD) calculations. Compounds 1a and 2a exhibited inhibitory activity against the MV4-11 cell line in vitro, with IC50 values of 23.95 µM and 32.70 µM, respectively.
| S-EPMC6100219 | biostudies-literature
Project description:As part of a genome sequencing project for Ophiocordyceps sinensis, strain 1229, a complete mitochondrial (mt) genome was assembled as a single circular dsDNA of 157,510 bp, one of the largest reported for fungi. Conserved genes including the large and small rRNA subunits, 27 tRNA and 15 protein-coding genes, were identified. In addition, 58 non-conserved open reading frames (ncORFs) in the intergenic and intronic regions were also identified. Transcription analyses using RNA-Seq validated the expression of most conserved genes and ncORFs. Fifty-two introns (groups I and II) were found within conserved genes, accounting for 68.5% of the genome. Thirty-two homing endonucleases (HEs) with motif patterns LAGLIDADG (21) and GIY-YIG (11) were identified in group I introns. The ncORFs found in group II introns mostly encoded reverse transcriptases (RTs). As in other hypocrealean fungi, gene contents and order were found to be conserved in the mt genome of O. sinensis, but the genome size was enlarged by longer intergenic regions and numerous introns. Intergenic and intronic regions were composed of abundant repetitive sequences usually associated with mobile elements. It is likely that intronic ncORFs, which encode RTs and HEs, may have contributed to the enlarged mt genome of O. sinensis.
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Project description:Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.
| S-EPMC5223169 | biostudies-literature
Project description:BackgroundCordyceps militaris is an insect pathogenic fungus that is prized for its use in traditional medicine. This and other entomopathogenic fungi are understudied sources for the discovery of new bioactive molecules. In this study, PacBio SMRT long read sequencing technology was used to sequence the genome of C. militaris with a focus on the genetic potential for secondary metabolite production in the genome assembly of this fungus.ResultsThis is first chromosome level assembly of a species in the Cordyceps genera. In this seven chromosome assembly of 33.6 Mba there were 9371 genes identified. Cordyceps militaris was determined to have the MAT 1-1-1 and MAT 1-1-2 mating type genes. Secondary metabolite analysis revealed the potential for at least 36 distinct metabolites from a variety of classes. Three of these gene clusters had homology with clusters producing desmethylbassianin, equisetin and emericellamide that had been studied in other fungi.ConclusionOur assembly and analysis has revealed that C. militaris has a wealth of gene clusters for secondary metabolite production distributed among seven chromosomes. The identification of these gene clusters will facilitate the future study and identification of the secondary metabolites produced by this entomopathogenic fungus.
| S-EPMC5702197 | biostudies-literature
Project description:Cordyceps guangdongensis is an edible fungus which was approved as a novel food by the Chinese Ministry of Public Health in 2013. It also has a broad prospect of application in pharmaceutical industries, with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising nine scaffolds with an average GC content of 57.01%. It is predicted to contain a total of 9150 protein-coding genes. Sequence identification and comparative analysis indicated that the assembled scaffolds contained two complete chromosomes and four single-end chromosomes, showing a high level assembly. Gene annotation revealed a diversity of transposons that could contribute to the genome size and evolution. Besides, approximately 15.57% and 12.01% genes involved in metabolic processes were annotated by KEGG and COG respectively. Genes belonging to CAZymes accounted for 3.15% of the total genes. In addition, 435 transcription factors, involved in various biological processes, were identified. Among the identified transcription factors, the fungal transcription regulatory proteins (18.39%) and fungal-specific transcription factors (19.77%) represented the two largest classes of transcription factors. This genomic resource provided a new insight into better understanding the relevance of phenotypic characters and genetic mechanisms in C. guangdongensis.
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Project description:Tongmai Sini decoction (TSD), the classical prescriptions of traditional Chinese medicine, consisting of three commonly used herbal medicines, has been widely applied for the treatment of myocardial infarction and heart failure. However, the absorbed components and their metabolism in vivo of TSD still remain unknown. In this study, a reliable and effective method using ultra-performance liquid chromatography coupled with hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-Q-Exactive-MS/MS) was employed to identify prototype components and metabolites in vivo (rat plasma and urine). Combined with mass defect filtering (MDF), dynamic background subtraction (DBS), and neutral loss filtering (NLF) data-mining tools, a total of thirty-two major compounds were selected and investigated for their metabolism in vivo. As a result, a total of 82 prototype compounds were identified or tentatively characterized in vivo, including 41 alkaloids, 35 phenolic compounds, 6 saponins. Meanwhile, A total of 65 metabolites (40 alkaloids and 25 phenolic compounds) were tentatively identified. The metabolic reactions were mainly hydrogenation, demethylation, hydroxylation, hydration, methylation, deoxylation, and sulfation. These findings will be beneficial for an in-depth understanding of the pharmacological mechanism and pharmacodynamic substance basis of TSD.
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Project description:Cordyceps militaris readily performs sexual reproduction, thus providing a remarkably rich model for understanding the processes involved in sexual development. It could regulate expression of human genes by diet-derived miRNA-like RNAs (milRNAs). However, the study of miRNAs in C. militaris has been limited. In the present study, genes encoding Dicers, Argonautes, and RNA-dependent RNA polymerases were identified. Illumina deep sequencing was performed to characterize the milRNAs in C. militaris at asexual and sexual development stages. Total 38 milRNAs were identified and five milRNAs were validated by northern blot and qRT-PCR, out of which, 19 were specific for sexual development. Importantly, the fungi could not form fruiting bodies after disruption of milR4, while the perithecium was formed in advance after over-expression of milR4. Abnormal pale yellow fruiting body primordium, covered with abnormal primordium, was formed in the strain with miR16 disruption. Although no milR4 or milR16 target genes were identified, differential expression of many different genes involved in mycelium growth and sexual development (mating process, mating signaling, and fruiting body development) among these mutants were found. Overall, milRNAs play vital roles in sexual development in C. militaris.
| S-EPMC6362416 | biostudies-literature
Project description:Cordyceps militaris is a famous traditional edible and medicinal fungus in Asia, and its fruiting body has rich medicinal value. The molecular mechanism of fruiting body development is still not well understood in C. militaris. In this study, phylogenetically analysis and protein domains prediction of the 14 putative chitinases were performed. The transcription level and enzyme activity of chitinase were significant increased during fruiting body development of C. militaris. Then, two chitinase genes (Chi1 and Chi4) were selected to construct gene silencing strain by RNA interference. When Chi1 and Chi4 genes were knockdown, the differentiation of the primordium was blocked, and the number of fruiting body was significantly decreased approximately by 50% compared to wild-type (WT) strain. The length of the single mature fruiting body was shortened by 27% and 38% in Chi1- and Chi4-silenced strains, respectively. In addition, the chitin content and cell wall thickness were significantly increased in Chi1- and Chi4-silenced strains. These results provide new insights into the biological functions of chitinase in fruiting body development of C. militaris.
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