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，高突变率也导致广泛产生具有较差生物物理特性和严重折叠缺陷的病毒蛋白变体。不能成功折叠的蛋白质变异从种群中移除，即使它们可以赋予有益的适应功能。最近的研究表明，宿主细胞的蛋白质折叠和质量控制机制（蛋白质静止网络）的组成和活动在确定快速进化的RNA病毒蛋白可接近的氨基酸序列空间方面起着核心作用。到目前为止，这一现象已经在很大程度上被研究了，研究人员利用蛋白质平衡调节本身作为选择压力。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。本研究以流感为模型系统，整合了最先进的化学生物学、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在不同选择压力背景下，宿主蛋白酶平衡和病毒适应之间新兴的复杂相互作用。目的1侧重于劫持宿主伴侣蛋白促进流感逃避先天免疫系统因子的机制，建立流感核蛋白进化中宿主伴侣蛋白依赖的生物物理起源，阐明病毒是否以及如何容易适应具有挑战性的宿主蛋白质停滞环境。目的2建立宿主细胞内质网蛋白静止网络的组成和活性如何影响流感血凝素（流感中和抗体的主要目标）逃避适应性免疫系统选择压力的能力。Aim 3在更广泛的范围内开展工作，以了解宿主蛋白质平衡网络如何影响全基因组突变耐受性和流感错误灾难，这是一种病毒突变率超过一定阈值导致种群灭绝的现象。所有这些目标的实验结果与蛋白质生物物理研究和计算模型相结合，以阐明宿主蛋白酶依赖病毒适应的分子起源。这项工作有望确立宿主蛋白酶静止是塑造病毒适应的决定性力量，特别是在高度相关的选择压力背景下。除了从根本上阐明病毒进化，这些发现将极大地增强对病毒适应宿主选择压力的因素的理解，并从长远来看，提高准确预测病毒进化的能力。这些发现还有望突出针对宿主伴侣的治疗性佐剂的潜力，从而使病毒不易产生耐药性的治疗方案成为可能。贡献将影响从基本病毒学、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.