Evolutionary Reconfiguration of Regulatory Circuitry

所有的生物都依赖于能够感知环境并做出适当的反应来生存。因此，所有的细胞都有复杂的系统来做到这一点。这些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它们相互作用的其他蛋白质、RNA或DNA靶标。通过这样的相互作用网络，细胞可以协调复杂的形态和细胞反应，这些反应是开发新环境、获取营养物质以及暴露于不同环境压力（如温度变化甚至暴露于毒素、污染物和化学农药）下生存所必需的。这些调节回路在进化过程中的变化是产生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解决这个问题。这项研究计划的中心目标是剖析机制的基础上重新配置的调节电路，控制两个特征的生存，形态发生在响应环境线索和抵抗环境压力至关重要。我们的工作与两个最容易实验的生物体，是密切相关的人类，模式酵母酵母菌和最普遍的人类真菌酵母菌和机会致病真菌，白色念珠菌。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电路，这使得能够觅食营养物质，侵入表面和组织，形成生物膜，以及逃避免疫系统。我们进行了第一次全球规模的基因分析所需的丝状生长在S。酿酒酵母，并确定了许多新的监管机构，包括以前未表征的基因，MFG1。Mfg1与另外两种基因表达调节因子（转录因子）Flo8和Mss11结合，并控制两种S. cerevisiae和C.白色念珠菌引人注目的是，这三种调节剂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节因子（赖氨酸脱乙酰酶，或KDAC）Hda 1和Rpd3控制S.酿酒。尽管使用药物抑制物种之间的KDAC的保守效应，我们发现改变电路，使Hda1和Rpd3不足以控制C的关键应激反应。白色念珠菌。我们将利用最先进的遗传和基因组分析来剖析这些调节电路是如何在进化过程中重新连接的。这项研究将建立机制控制电路所需的获取营养物质和环境生态位，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剂的耐药性的演变，并使微生物进化出更强的耐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.