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通过构建和利用专门的基因组规模代谢模型揭示人类病原体的新特征。

Unveiling new features of the human pathogen through the reconstruction and exploitation of a dedicated genome-scale metabolic model.

作者信息

Viana Romeu, Couceiro Diogo, Newton William, Coutinho Luís, Dias Oscar, Coelho Carolina, Teixeira Miguel Cacho

机构信息

Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisboa 1049-001, Portugal.

iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, Lisboa 1049-001, Portugal.

出版信息

Comput Struct Biotechnol J. 2025 May 23;27:2336-2346. doi: 10.1016/j.csbj.2025.05.034. eCollection 2025.

Abstract

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.

摘要

因引起严重的肺部和中枢神经系统感染而臭名昭著,尤其是在免疫功能低下的患者中。高死亡率与其嗜性、对脑微环境的适应性及其耐药性特征相关,使这种病原体成为公共卫生威胁和世界卫生组织(WHO)的优先关注对象。本研究提出了首个针对[病原体名称未给出]的重建基因组规模代谢模型(GSMM),即iRV890,它包含890个基因、2598个反应以及四个区室中的2047种代谢物。GSMM iRV890模型是使用开源软件工具merlin 4.0.2重建的,以成熟的系统生物学标记语言(SBML)格式公开可用,并使用特定生长和葡萄糖消耗率以及222种氮和碳同化源的实验数据进行了验证,预测率为85%。基于与其他致病酵母可用的GSMMs的比较,预测了[病原体名称未给出]的独特代谢特征,包括塑造[病原体名称未给出]与人类宿主之间动态关系的关键途径,以及其对脑环境的潜在适应性。最后,对经过验证的模型中预测的96个必需基因作为潜在的新型抗真菌药物靶点进行了研究,包括Erg4、Chs1、Fol1和Fas1,由于它们在人类细胞中不存在,这些基因是靶向药物开发的有希望的候选者。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/accf/12167027/3cfe51d278e6/ga1.jpg

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