Evolutionary multispecies transcriptomics to reveal genes that govern fungal spore germination and pathogenesis

进化多物种转录组学揭示控制真菌孢子萌发和发病机制的基因

• 批准号: 10612374
• 负责人: Anita Sil
• 金额: $ 73.37万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-16 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10612374
• 关键词: Aspergillus fumigatus; Aspergillus nidulans; Biological Assay; Biology; Candidate Disease Gene; Chaetomium; Coccidioides; Coccidioides posadasii; Data; Development; Developmental Biology; Diagnostic; Disease; Disease Progression; Disparate; Environment; Event; Evolution; Fungal Genes; Fungal Genome; Fungal Spores; Fungal Vaccines; Fusarium; Gene Expression; Genes; Genomics; Germination; Goals; Growth; Histoplasma; Histoplasma capsulatum; Human; Infection; Intervention; Knock-out; Knowledge; Macrophage; Mammals; Modeling; Mycoses; Neurospora crassa; Organism; Pathogenesis; Pathogenicity; Pattern; Phenotype; Phylogenetic Analysis; Plants; Publications; Publishing; Reproduction spores; Research; Role; Sexual Development; Technology; Temperature; Time; Vaccines; Work; comparative; comparative genomics; diagnostic tool; dimorphism; experimental study; fungus; gene function; host colonization; human pathogen; innovation; interest; knockout gene; novel diagnostics; opportunistic pathogen; pathogen; pathogenic fungus; prophylactic; trait; transcriptome sequencing; transcriptomics; vector-borne

Project Summary Fungal pathogens of humans are prevalent in the environment, and commonly come into contact with hosts via dispersal of vegetative spores. Although spore germination and subsequent development are recognized as critical to the initiation of fungal-host interactions, little is known about the fungal genes that govern these events. Our goal is to leverage comparative genomics, evolutionary biology and fungal pathogenesis to define genes that are essential for spore germination, subsequent growth, and host colonization in an evolutionarily diverse group of fungi. We have chosen fungi with a range of abilities to cause disease upon interaction of spores with mammalian hosts, including primary, opportunistic, and nonpathogenic species. We will take advantage of a highly effective and innovative pipeline that reveals genes whose evolving roles have led to phenotypic differences among these species. PIs Trail and Townsend have defined a paradigm that brings together comparative genomics, developmental biology, and transcriptomics into a single, unified phylogenetic framework that will identify key genes that govern spore germination and outgrowth in these fungi. The linchpin of our approach is use of the evolutionary relationship between the fungi to infer genes whose expression has been altered during evolution from their ancestral state to each present-day lineage, thus allowing specific traits (such as pathogenesis) to evolve. In our recently published work and preliminary data, this approach was immensely powerful for identifying genes whose evolving role led to developmental and phenotypic differences among species during (1) fungal sexual development and (2) spore germination and early infection during fungal pathogenesis of plants. We will use a common medium to germinate spores from the following fungi: the primary pathogens Histoplasma capsulatum and Coccidioides posadasii, the opportunistic pathogens Aspergillus fumigatus, Fusarium oxysporum, and Chaetomium elatum, the infrequent opportunistic pathogen Aspergillus nidulans, and the non-pathogenic Neurospora crassa. We will subject these fungi to transcriptomics over a time-course of germination and subsequent development under temperature conditions relevant to germination in the environment vs. in a mammalian host. We will reconstruct evolutionary changes of gene expression across these multiple species to identify genes that have undergone recent shifts in gene expression, in particular shifts that occurred along the shared ancestral branches where key traits (such as the ability to colonize mammals) have evolved. These experiments will yield a high-confidence set of candidate genes whose function is expected to be critical for spore germination and development in each organism. We will use gene knock-out technology to interrogate the function of these candidate genes in spore germination and development. These studies will identify potential targets for diagnostic, prophylactic, and vaccine interventions for ubiquitous fungal infections of humans.

项目概要 人类的真菌病原体在环境中普遍存在，并且通常与宿主接触 通过营养孢子的传播。尽管孢子萌发和随后的发育被认为是 对于真菌与宿主相互作用的启动至关重要，但人们对控制这些事件的真菌基因知之甚少。 我们的目标是利用比较基因组学、进化生物学和真菌发病机制来定义基因 这对于孢子萌发、随后的生长和进化多样化的宿主定植至关重要 真菌群。我们选择了具有一系列能力的真菌，这些真菌可以在孢子与孢子相互作用时引起疾病。 哺乳动物宿主，包括初级物种、机会性物种和非致病性物种。我们将利用 高效和创新的管道，揭示了其进化作用导致表型的基因 这些物种之间的差异。 PIs Trail 和 Townsend 定义了一个范例，将 将比较基因组学、发育生物学和转录组学整合到一个统一的系统发育框架中 这将鉴定出控制这些真菌孢子萌发和生长的关键基因。我们的关键 方法是利用真菌之间的进化关系来推断其表达已被 在从祖先状态到当今每个谱系的进化过程中发生了改变，从而允许特定的特征（例如 作为发病机制）进化。在我们最近发表的工作和初步数据中，这种方法非常有效 对于识别其进化作用导致发育和表型差异的基因非常有用 (1) 真菌有性发育期间的物种和 (2) 真菌期间孢子萌发和早期感染的物种 植物的发病机制。 我们将使用通用培养基使以下真菌的孢子发芽： 主要病原体 荚膜组织胞浆菌和波萨达球孢子菌，机会性病原体烟曲霉， 尖孢镰刀菌 (Fusarium oxysporum) 和毛壳菌 (Chaetomium elatum)、罕见的机会性病原体构巢曲霉 (Aspergillus nidulans)，以及 非致病性粗糙脉孢菌。我们将在一段时间内对这些真菌进行转录组学研究 在与发芽相关的温度条件下发芽和随后的发育 环境与哺乳动物宿主中。我们将重建这些基因表达的进化变化 多个物种来识别近期基因表达发生变化的基因，特别是 沿着共同的祖先分支发生，其中关键特征（例如殖民哺乳动物的能力）具有 进化了。这些实验将产生一组高置信度的候选基因，其功能预计 对于每个生物体的孢子萌发和发育至关重要。我们将利用基因敲除技术 询问这些候选基因在孢子萌发和发育中的功能。这些研究将 确定针对普遍存在的真菌感染的诊断、预防和疫苗干预的潜在目标 人类。

项目成果

Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa.

粗糙脉孢菌的无性生长、分生孢子和有性发育过程中，次生代谢基因簇表现出越来越动态和差异的表达。

• 发表时间: 2022-06-28
• 影响因子: 6.4
• 作者: Wang, Zheng;Lopez;Slot, Jason;Yarden, Oded;Trail, Frances;Townsend, Jeffrey P
• 通讯作者: Townsend, Jeffrey P

Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.

谱系特异性基因与 HET 域基因聚集在一起，并对调节脉孢菌繁殖的环境和遗传操作做出反应。

• 发表时间: 2023-11
• 影响因子: 4.5
• 作者: Wang, Zheng;Wang, Yen;Kasuga, Takao;Lopez;Zhang, Yang;Zhang, Zhang;Wang, Yaning;Dong, Caihong;Sil, Anita;Trail, Frances;Yarden, Oded;Townsend, Jeffrey P
• 通讯作者: Townsend, Jeffrey P

Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa.

通过粗糙脉孢菌中的基因复制、重新定位和区域重排来起源谱系特异性元件。

• DOI: 10.1111/mec.17168
• 发表时间: 2023-10-16
• 期刊: Molecular ecology
• 影响因子: 4.9
• 作者: Zheng Wang;Yen;Takao Kasuga;H. Hassler;F. López;C. Dong;O. Yarden;Jeffrey P. Townsend
• 通讯作者: Jeffrey P. Townsend