98%
921
2 minutes
20
is notorious for causing severe pulmonary and central nervous system infections, particularly in immunocompromised patients. High mortality rates, associated with its tropism and adaptation to the brain microenvironment and its drug resistance profile, make this pathogen a public health threat and a World Health Organization (WHO) priority. This study presents the first reconstructed genome-scale metabolic model (GSMM), iRV890, for , which comprises 890 genes, 2598 reactions, and 2047 metabolites across four compartments. The GSMM iRV890 model was reconstructed using the open-source software tool merlin 4.0.2, is openly available in the well-established systems biology markup language (SBML) format and underwent validation using experimental data for specific growth and glucose consumption rates, and 222 nitrogen and carbon assimilation sources, with a 85 % prediction rate. Based on the comparison with GSMMs available for other pathogenic yeasts, unique metabolic features were predicted for , including key pathways shaping dynamics between and human host, as well as its underlying adaptions to the brain environment. Finally, the 96 predicted essential genes from the validated model are investigated as potential novel antifungal drug targets-including Erg4, Chs1, Fol1, and Fas1-which represent promising candidates for targeted drug development due to their absence in human cells.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167027 | PMC |
http://dx.doi.org/10.1016/j.csbj.2025.05.034 | DOI Listing |
NPJ Biofilms Microbiomes
September 2025
Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel University, Kiel, Schleswig-Holstein, Germany.
Urinary tract infections (UTIs) are among the most common bacterial infections and are increasingly complicated by multidrug resistance (MDR). While Escherichia coli is frequently implicated, the contribution of broader microbial communities remains less understood. Here, we integrate metatranscriptomic sequencing with genome-scale metabolic modeling to characterize active metabolic functions of patient-specific urinary microbiomes during acute UTI.
View Article and Find Full Text PDFmSystems
September 2025
Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Genome-scale metabolic models (GEMs) are widely used in systems biology to investigate metabolism and predict perturbation responses. Automatic GEM reconstruction tools generate GEMs with different properties and predictive capacities for the same organism. Since different models can excel at different tasks, combining them can increase metabolic network certainty and enhance model performance.
View Article and Find Full Text PDFNew Phytol
September 2025
Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
Comparative molecular and physiological analyses of organisms from one taxonomic group grown under similar conditions offer a strategy to identify gene targets for trait improvement. While this strategy can also be performed in silico using genome-scale metabolic models for the compared organisms, we continue to lack solutions for the de novo generation of such models, particularly for eukaryotes. To facilitate model-driven identification of gene targets for growth improvement in green algae, here we present a semiautomated platform for de novo generation of genome-scale algal metabolic models.
View Article and Find Full Text PDFmSystems
September 2025
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
SC05-UT is an anaerobic, heterogenous microbial enrichment culture that reduces chloroform to dichloromethane through reductive dechlorination, which it further mineralizes to carbon dioxide. This dichloromethane mineralization yields electron equivalents that are used to reduce chloroform without the addition of exogenous electron donor. By studying this self-feeding chloroform-amended culture and a dichloromethane-amended enrichment subculture (named DCME), we previously found the genomic potential to perform both biodegradation steps in two distinct strains: SAD and Dehalobacter alkaniphilus DAD.
View Article and Find Full Text PDFPlant Commun
September 2025
Guizhou University of Traditional Chinese Medicine Guiyang 550025 Guizhou, China; Guizhou Key Laboratory for Germplasm Innovation and Resource-Efficient Utilization of Dao-di Herbs, Guiyang 550025, Guizhou, China. Electronic address:
Nitrogen and auxin uptake plays pivotal roles in seed germination and development. Gastrodia elata, a fully mycoheterotrophic plant, depends entirely on its symbiotic association with Mycena for early growth and seed germination. The process by which Mycena enables the supply of nitrogen nutrients and auxin, which are deficient in G.
View Article and Find Full Text PDF