Evolutionary Reconfiguration of Regulatory Circuitry

为了生存，所有的生物都依赖于能够感知环境并做出适当的反应。因此，所有细胞都有复杂的系统来完成这一任务。这种系统包括感知环境变化的蛋白质，然后将这种变化信号传递给与之相互作用的其他蛋白质、RNA或DNA目标。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，这些反应需要利用新环境，获取营养物质，并在暴露于不同的环境压力（如温度变化，甚至暴露于毒素，污染物和化学农药）下存活。在进化过程中，这些调节回路的变化对于产生在当前物种中观察到的形态和功能的显著多样性至关重要。调控回路的进化可能涉及控制细胞信号传导的蛋白质的变化，或其目标序列或背景的改变。理解驱动调控电路重构的机制是生物学的核心挑战之一，我们现在可以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个问题。本研究项目的中心目标是剖析调控回路重构的机制，调控回路控制着对生存至关重要的两个特征，即响应环境信号的形态发生和对环境压力的抵抗。我们的研究对象是与人类密切相关的两种实验上最容易处理的生物，即酿酒酵母菌和最普遍的人类共生酵母菌和机会性真菌病原体白色念珠菌。首先，我们将关注控制从单细胞酵母到多细胞细丝的形态转变的电路，这使得营养物质的觅食、表面和组织的入侵、生物膜的形成和免疫系统的逃避成为可能。我们对酿酒葡萄球菌丝状生长所需的基因进行了首次全球范围的分析，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控因子（转录因子）Flo8和Mss11结合，并控制酿酒葡萄球菌和白色念珠菌的形态发生。引人注目的是，这三种调节因子的目标在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，例如暴露于广泛应用于医学和农业的抗真菌剂。我们确定了基因表达的全局调控因子（赖氨酸去乙酰化酶，或kdac） Hda1和Rpd3控制酿酒葡萄球菌对药物诱导的细胞应激的抗性进化。尽管使用药物抑制物种之间的kdac具有保守作用，但我们发现改变的电路使得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控电路是如何在进化过程中重新连接的。这项研究将建立控制通路所需的机制，以获取营养和环境生态位，引起传染病，形成生物膜，并适应环境压力，如暴露于抗真菌剂，盐和重金属。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素的耐药性进化，并使微生物进化出更强的承受压力和修复污染环境的能力，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.