Defining the Interplay Between Viral Adaptation and Host Proteostasis

极高的突变率使大多数RNA病毒能够快速探索蛋白质序列空间。另一方面，高突变率也导致病毒蛋白变异体的广泛产生，具有较差的生物物理性质和严重的折叠缺陷。不能成功折叠的蛋白质变体被从种群中移除，即使它们本来可以赋予有益的适应功能。最近的工作表明，宿主细胞蛋白质折叠和质量控制机制(蛋白质平衡网络)的组成和活动在确定快速进化的RNA病毒蛋白所能获得的氨基酸序列空间中起着核心作用。到目前为止，这种现象在很大程度上是通过蛋白质平衡调节本身作为选择压力来探索的。目前尚不清楚宿主细胞伴侣是否通过增强病毒蛋白折叠直接影响病毒适应和逃避来自宿主适应性免疫系统、抗病毒药物或其他因素的外部选择压力的能力。以流感为模型系统，该方案综合了最新的化学生物学、遗传学、生物化学、生物物理学和计算方法，在分子水平上全面评估和阐明了在不同选择压力下宿主蛋白平衡和病毒适应之间新出现的和复杂的相互作用。目的1重点研究被劫持的宿主伴侣蛋白促进流感病毒逃避天然免疫系统因素的机制，建立宿主伴侣蛋白依赖在流感核蛋白进化中的生物物理起源，阐明病毒是否以及如何容易地适应挑战宿主蛋白平衡的环境。目的2确定宿主细胞内质网蛋白平衡网络的组成和活性如何影响流感血凝素的能力，流感血凝素是流感中和抗体的主要靶标，以逃避适应性免疫系统的选择压力。AIM 3在更广泛的范围内运作，以了解宿主蛋白调控网络如何影响全基因组的突变耐受性和流感错误灾难，这是一种病毒变异率超过一定阈值导致种群灭绝的现象。所有这些目的的实验结果都与蛋白质生物物理研究和计算模型相结合，以阐明宿主蛋白稳定依赖的病毒适应的分子起源。这项工作有望将宿主蛋白平衡确立为形成病毒适应的决定性力量，特别是在高度相关的选择压力的背景下。除了从根本上阐明病毒的进化，这些发现将极大地提高对病毒适应宿主选择压力所涉及的因素的理解，并从长远来看，提高准确预测病毒进化的能力。预计这些发现还将突出针对宿主伴侣的治疗佐剂的潜力，以实现病毒不易产生耐药性的治疗方案。贡献将影响从基础病毒学和疫苗和抗病毒药物开发到进化生物学和蛋白质折叠生物物理学等领域。

Exceedingly high mutation rates permit most RNA viruses to rapidly explore protein sequence space. On the other hand, high mutation rates also result in widespread production of viral protein variants with poor biophysical properties and severe folding defects. Protein variants that cannot fold successfully are removed from the population, even if they could otherwise confer a beneficial adaptive function. Recent work has revealed that the composition and activities of the host cell’s protein folding and quality control machinery (the proteostasis network) play a central role in defining the amino acid sequence space accessible to rapidly evolving RNA viral proteins. This phenomenon has so far largely been explored using proteostasis modulation itself as the selection pressure. It is not yet clear whether host cell chaperones are directly – by enhancing viral protein folding – impacting the ability of viruses to adapt to and escape from external selection pressures stemming from the host’s adaptive immune system, antiviral drugs, or other factors. Using influenza as a model system, this proposal integrates state-of-the-art chemical biology, genetic, biochemical, biophysical, and computational methods to comprehensively evaluate and elucidate, at the molecular-level, the emerging and complex interplay between host proteostasis and viral adaptation in the context of diverse selection pressures. Aim 1 focuses on the mechanism by which hijacked host chaperones promote influenza escape from innate immune system factors, establishing biophysical origins of host chaperone-dependence in influenza nucleoprotein evolution and elucidating whether and how the virus can readily adapt to challenging host proteo- stasis environments. Aim 2 establishes how the composition and activities of the host cell’s endoplasmic reticulum proteostasis network impact the ability of influenza hemagglutinin, the primary target of influenza-neutralizing antibodies, to escape selection pressure from the adaptive immune system. Aim 3 operates on a broader scale to understand how host proteostasis networks impact genome-wide mutational tolerance and influenza error catastrophe, a phenomenon in which increasing viral mutation rates past a certain threshold causes population extinction. Experimental findings from all these Aims are integrated with protein biophysical studies and computational modeling to illuminate molecular origins of host proteostasis-dependent viral adaptation. This work is expected to establish host proteostasis as a defining force that shapes viral adaptation, particularly in the context of highly relevant selection pressures. Beyond fundamental elucidation of viral evolution, findings will greatly enhance understanding of the factors involved in viral adaptation to host selection pressures and, in the longer-term, improve the ability to accurately predict viral evolution. Discoveries are also expected to highlight the potential of therapeutic adjuvants targeting host chaperones to enable treatment regimens to which viruses cannot easily evolve resistance. Contributions will impact fields ranging from basic virology and vaccine and antiviral drug development to evolutionary biology and protein folding biophysics.