人类真菌病原体新型隐球菌的基本生长景观和氟康唑耐药基因。

IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences
R Blake Billmyre, Caroline J Craig, Joshua W Lyon, Claire Reichardt, Amy M Kuhn, Michael T Eickbush, Sarah E Zanders
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引用次数: 0

摘要

真菌可引起毁灭性的侵袭性感染,特别是在免疫功能低下的患者中。由于人类和真菌的进化相似性以及耐药性的频繁出现,治疗变得复杂。由于缺乏模式生物中常见的高通量工具和社区资源,真菌病原体的研究长期以来一直进展缓慢。在这里,我们展示了一种新型隐球菌的高通量转座子突变和测序(TN-seq)系统,该系统能够在全基因组范围内确定基因的必要性。我们采用随机森林机器学习方法将C. neoformmans基因组分类为必需或非必需,预测了1,465个必需基因,其中包括302个缺乏人类同源物的基因。这些基因是开发新型抗真菌药物的理想靶点。n -seq还可以实现基因对感兴趣表型的适应度贡献的全基因组测量。作为原理的证明,我们展示了基因对氟康唑生长的全基因组贡献,氟康唑是一种临床使用的抗真菌药物。我们展示了在氟康唑易感性中被充分研究的RIM101通路的新作用。我们还表明,转座子插入到5'上游区域可以驱动必要基因的敏化,从而可以对基因组的必要和非必要成分进行类似筛选的分析。使用这种方法,我们证明了线粒体功能在氟康唑敏感性中的作用,例如通过5'插入下调许多必需的线粒体基因可以驱动对氟康唑的抗性。我们的分析系统将在未来的研究中有价值的新生梭菌,特别是在检查基因型多样性的后果。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans.

Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system in Cryptococcus neoformans that enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify the C. neoformans genome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studied RIM101 pathway in fluconazole susceptibility. We also show that insertions of transposons into the 5' upstream region can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5' insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies of C. neoformans, particularly in examining the consequences of genotypic diversity.

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来源期刊
PLoS Biology
PLoS Biology BIOCHEMISTRY & MOLECULAR BIOLOGY-BIOLOGY
CiteScore
15.40
自引率
2.00%
发文量
359
审稿时长
3-8 weeks
期刊介绍: PLOS Biology is the flagship journal of the Public Library of Science (PLOS) and focuses on publishing groundbreaking and relevant research in all areas of biological science. The journal features works at various scales, ranging from molecules to ecosystems, and also encourages interdisciplinary studies. PLOS Biology publishes articles that demonstrate exceptional significance, originality, and relevance, with a high standard of scientific rigor in methodology, reporting, and conclusions. The journal aims to advance science and serve the research community by transforming research communication to align with the research process. It offers evolving article types and policies that empower authors to share the complete story behind their scientific findings with a diverse global audience of researchers, educators, policymakers, patient advocacy groups, and the general public. PLOS Biology, along with other PLOS journals, is widely indexed by major services such as Crossref, Dimensions, DOAJ, Google Scholar, PubMed, PubMed Central, Scopus, and Web of Science. Additionally, PLOS Biology is indexed by various other services including AGRICOLA, Biological Abstracts, BIOSYS Previews, CABI CAB Abstracts, CABI Global Health, CAPES, CAS, CNKI, Embase, Journal Guide, MEDLINE, and Zoological Record, ensuring that the research content is easily accessible and discoverable by a wide range of audiences.
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