Evolutionary Reconfiguration of Regulatory Circuitry

所有生物的生存都严重依赖于感知环境并做出适当反应的能力。因此，所有细胞都有复杂的系统来做到这一点。此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之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、获取营养以及在不同的环境压力下生存所需的，例如温度变化，甚至接触毒素、污染物和化学农药。这些调节回路在进化过程中的变化对于在当前物种中观察到的形式和功能的显着多样性至关重要。调节回路的进化可能涉及控制细胞信号传导的蛋白质的变化，或其靶标的序列或背景的改变。了解驱动调节电路重新配置的机制是生物学的核心挑战之一，我们现在可以通过利用测序和功能基因组学的进步以前所未有的力量来解决这一挑战。该研究计划的中心目标是剖析支持调节电路重新配置的机制，该调节电路控制着对生存至关重要的两个特征：响应环境线索的形态发生和对环境压力的抵抗力。我们研究了两种在实验上最容易处理的与人类密切相关的生物体，即模型酵母酿酒酵母和最常见的人类共生酵母和机会性真菌病原体白色念珠菌。首先，我们将重点关注控制从单细胞酵母到多细胞丝的形态转变的电路，这使得能够获取营养、侵入表面和组织、形成生物膜以及逃避免疫系统。我们对酿酒酵母丝状生长所需的基因进行了首次全球规模的分析，并鉴定了许多新的调控因子，包括以前未表征的基因 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，这三个调节器的目标在不同物种之间几乎完全不同。其次，我们将重点关注抵抗各种压力所需的电路，例如接触广泛应用于医学和农业的抗真菌剂。我们确定基因表达的全局调节因子（赖氨酸脱乙酰酶或 KDAC）Hda1 和 Rpd3 控制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作用，但我们发现电路发生了改变，使得 Hda1 和 Rpd3 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节电路如何在进化过程中重新连接。这项研究将建立控制获取营养和环境生态位、引起传染病、形成生物膜以及适应环境压力（例如暴露于抗真菌剂、盐和重金属）所需电路的机制。最终，这项工作将揭示如何利用这些机制来预防微生物感染和污染，阻止对医学和农业至关重要的抗菌药物耐药性的进化，并进化出具有增强耐受压力和修复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.