Evolutionary Reconfiguration of Regulatory Circuitry

所有生物都严重依赖于能够感知他们的环境并做出适当的反应才能生存。因此，所有细胞都有复杂的系统来完成这一任务。这类系统包括感知环境变化的蛋白质，然后将这种变化信号发送给与其相互作用的其他蛋白质、RNA或DNA靶标。通过这种相互作用网络，细胞可以协调复杂的形态和细胞反应，这些反应是利用新环境、获取营养和在各种环境压力下生存所必需的，例如温度变化，甚至暴露在毒素、污染物和化学农药中。随着进化时间的推移，这些调节回路的变化是产生在当前物种中观察到的形式和功能的显着多样性的基础。调控电路的进化可能涉及控制细胞信号的蛋白质的变化，或者其靶标的序列或背景的变化。了解推动调控电路重新配置的机制是生物学中的核心挑战之一，我们现在可以通过利用测序和功能基因组学的进展来以前所未有的力量应对这一挑战。这项研究计划的中心目标是剖析支持调控电路重新配置的机制，调控电路控制着两个对生存至关重要的性状，即响应环境线索的形态发生和对环境压力的抗性。我们与两种与人类关系密切的、在实验上最容易驯化的生物--模型酵母--酿酒酵母--以及最普遍的人类共生酵母和机会性真菌病原体--白色念珠菌--合作。首先，我们将专注于控制从单细胞酵母到多细胞细丝的形态转变的回路，这使得能够觅食营养、入侵表面和组织、形成生物膜和逃避免疫系统。我们首次对酿酒酵母丝状生长所需的基因进行了全球范围的分析，并确定了许多新的调节因子，包括以前未描述的基因MFG1。Mfg1与另外两个基因表达调节因子(转录因子)Flo8和Mss11结合，并控制酿酒酵母和白色念珠菌的形态发生。引人注目的是，这三个监管机构的目标在不同物种之间几乎完全不同。其次，我们将重点介绍抵抗不同应激所需的电路，例如广泛应用于医药和农业中的抗真菌药物。我们发现，基因表达的全局调节因子(赖氨酸脱乙酰酶，KDACs)Hda1和Rpd3控制着酿酒酵母对药物诱导的细胞应激的抗性进化。尽管使用药物抑制KDAC在物种之间具有保守的效果，但我们发现Hda1和Rpd3的电路改变不足以控制白色念珠菌的关键应激反应。我们将利用尖端的遗传和基因组分析来剖析这些调控电路是如何随着进化时间的推移而重新连接的。这项研究将建立控制电路的机制，这些电路需要获取营养物质和环境利基，导致传染病，形成生物膜，并适应环境应激，如抗真菌药物、盐和重金属的暴露。最终，这项工作将揭示如何利用这些机制来防止微生物感染和污染，阻止对医药和农业至关重要的抗菌剂耐药性的演变，并进化出具有增强耐受压力和修复受污染环境能力的微生物，从而改善加拿大人的生活。

All living creatures depend critically on being able to sense their environment and mount the appropriate responses in order to survive. As a consequence, all cells have intricate systems to do this. Such systems include proteins that sense environmental change and then signal this change to other proteins, RNA, or DNA targets that they interact with. Through such interaction networks, cells can orchestrate complex morphological and cellular responses that are required to exploit new environments, acquire nutrients, and survive exposure to diverse environmental stresses such as changes in temperature or even exposure to toxins, pollutants, and chemical pesticides. Changes in these regulatory circuits over evolutionary time are fundamental to generating the remarkable diversity of form and function observed in current species. Evolution of regulatory circuits can involve changes in the proteins that control cellular signaling, or alterations in the sequence or context of their targets. Understanding the mechanisms that drive the reconfiguration of regulatory circuitry is one of the central challenges in biology, and one that we can now address with unprecedented power by exploiting advances in sequencing and functional genomics. The central goal of this research program is to dissect mechanisms underpinning the reconfiguration of regulatory circuitry that controls two traits crucial for survival, morphogenesis in response to environmental cues and resistance to environmental stress. We work with two of the most experimentally tractable organisms that are closely related to humans, the model yeast Saccharomyces cerivisiae and the most prevalent human commensal yeast and opportunistic fungal pathogen, Candida albicans. First, we will focus on circuitry governing a morphological transition from single-celled yeast to multicellular filaments, which enables foraging for nutrients, invasion of surfaces and tissues, formation of biofilms, and evasion of the immune system. We performed the first global scale analysis of genes required for filamentous growth in S. cerevisiae, and identified many novel regulators, including a previously uncharacterized gene, MFG1. Mfg1 binds to two other regulators of gene expression (transcription factors), Flo8 and Mss11, and controls morphogenesis in both S. cerevisiae and C. albicans. Strikingly, the targets of these three regulators are almost entirely distinct between the species. Second, we will focus on circuitry required for resistance to diverse stresses such as exposure to antifungal agents widely deployed in medicine and agriculture. We established that the global regulators of gene expression (lysine deacetylases, or KDACs) Hda1 and Rpd3 govern the evolution of resistance to drug-induced cellular stress in S. cerevisiae. Despite conserved effects of using drugs to inhibit KDACs between the species, we found altered circuitry such that Hda1 and Rpd3 are not sufficient to control key stress responses in C. albicans. We will exploit cutting edge genetic and genomic analyses to dissect how these regulatory circuitries have been rewired over evolutionary time. This research will establish mechanisms controlling circuitry required to access nutrients and environmental niches, cause infectious disease, form biofilms, and adapt to environmental stresses such as exposure to antifungal agents, salts, and heavy metals. Ultimately, this work will reveal the ways in which these mechanisms can be harnessed to prevent microbial infection and contamination, block the evolution of resistance to antimicrobials crucial for medicine and agriculture, and evolve microbes with enhanced capacity to tolerate stress and remediate contaminated environments, thereby improving the lives of Canadians.