The role of post-translational modifications in resistance to viral diseases in farmed fish

水产养殖是世界上发展最快的食品工业，在不耗尽海洋自然资源的情况下为世界提供食物方面发挥着关键作用（粮农组织2020年，http://www.fao.org/documents/card/en/c/ca9229en）。然而，水产养殖面临着重大的动物健康和福利挑战，传染病构成持续的风险。病毒性病原体目前是对水产养殖可持续性的主要威胁，通常疫苗或治疗方案有限。在这种情况下，抗病性的遗传改良，包括选择性育种和基因组编辑，是解决水产养殖种群病毒性疾病的一种非常有前途的方法（Houston et al. 2020 Nat Rev Genet 21:389-409）。我们之前对大西洋鲑鱼和鲤鱼的研究（例如Palaiokostas et al. 2018 G3 8:3507-3513）表明，参与翻译后修饰（泛素和泛素样分子附着在蛋白质上）的基因（如TRIM25）可能在抵抗病毒性疾病中发挥重要作用。TRIM25在哺乳动物中负责干扰素途径的激活，并且是流感的直接靶向以避免宿主免疫反应。然而，这种基因在鱼类中经历了多次复制，在鲑鱼中有63个拷贝，在鲤鱼中有83个拷贝，这表明了巨大的功能多样化。虽然我们知道其中一些拷贝与免疫有关（Langevin et al. 2019 Fish Shellfish Immunol 86:724-733），但它们的具体功能尚不清楚。该项目的主要目的是了解与翻译后修饰相关的基因在大西洋鲑鱼和鲤鱼对病毒疾病的抗性中的作用。为了做到这一点，博士生将使用这两个物种的永生化细胞培养物来研究宿主-病毒的相互作用。CRISPR/Cas9将用于敲除或上调TRIM25和其他感兴趣基因的不同拷贝，评估它们对两种物种对各种病毒性疾病的抗病能力的影响。这些基因的分子功能将使用分子生物学、病毒学、转录组学和蛋白质组学技术进行进一步评估，以找到它们的直接靶点、对它们泛素化/泛素样状态的影响以及这如何影响下游分子途径。还将评估病毒与这一分子级联的相互作用（即病毒是否靶向或被这些基因靶向）。从这些实验中鉴定出的基因和分子将成为体内基因组编辑的目标，有可能培育出抗病的鱼类。总之，该项目将帮助我们了解翻译后修饰在鱼类病毒性疾病反应中的作用，并有助于制定应对水产养殖病毒性疾病的策略。这个为期四年的学生将提供一个优秀的跨学科培训机会，涵盖基因组学和遗传学，分子生物学，病毒学和生物信息学方面，并应用各种各样的技术。该学生将成为爱丁堡大学（https://www.ed.ac.uk/roslin/aquaculture）水产养殖遗传学大型多学科和多样化团队的一员，并与阿伯丁大学（https://www.abdn.ac.uk/sfirc/）苏格兰鱼类免疫学研究中心的世界专家密切合作。

Aquaculture is the fastest growing food industry worldwide, playing a critical role in feeding the world without exhausting oceans natural resources (FAO 2020, http://www.fao.org/documents/card/en/c/ca9229en). However, aquaculture faces major animal health and welfare challenges, and infectious diseases pose a constant risk. Viral pathogens are current a major threat to aquaculture sustainability, often with limited vaccine or treatment options. In this context, genetic improvement of disease resistance, including selective breeding and genome editing, constitute a highly promising approach to tackle viral diseases of aquaculture stocks (Houston et al. 2020 Nat Rev Genet 21:389-409).Our previous research in Atlantic salmon and common carp (e.g. Palaiokostas et al. 2018 G3 8:3507-3513) suggests that genes involved in post-translational modifications (the attachment of ubiquitin and ubiquitin-like molecules to proteins) such as TRIM25 may play an important role in resistance to viral diseases. TRIM25 is responsible for the activation of the interferon pathway in mammals, and is directly targeted by Influenza to avoid the host immune response. However, this gene has undergone multiple duplications in fish, with 63 copies in salmon and 83 in carp, pointing towards a huge functional diversification. While we know several of these copies are involved in immunity (Langevin et al. 2019 Fish Shellfish Immunol 86:724-733), their specific function is unknown.The main aim of this project in to understand the role of genes related to posttranslational modifications in resistance to viral diseases in Atlantic salmon and carp. To do so, the PhD student will work with immortalised cell cultures of both species to study host-virus interactions. CRISPR/Cas9 will be used to knockout or up-regulate the different copies of TRIM25 and other genes of interest, evaluating their impact on disease resistance to various viral diseases in both species. The molecular function of these genes will be further evaluated using a combination of molecular biology, virology, transcriptomic and proteomic techniques, in order to find their direct targets, the impact on their ubiquitination / ubiquitin-like status and how this affects downstream molecular pathways. The interaction of the virus with this molecular cascade will also be evaluated (i.e. if the virus targets or is targeted by these genes). The identified genes and molecules from these experiments will form targets for genome editing in vivo, with potential for developing disease resistant fish. In sum, this project will help us understand the role of posttranslational modifications in response to viral diseases in fish and contribute to the development of strategies to tackle viral diseases in aquaculture.This 4-year studentship will provide an excellent inter-disciplinary training opportunity, covering aspects of genomics and genetics, molecular biology, virology and bioinformatics, and applying a wide variety of techniques. The student will be part of a large multidisciplinary and diverse team working in aquaculture genetics at the University of Edinburgh (https://www.ed.ac.uk/roslin/aquaculture), in close collaboration with world experts in the Scottish Fish Immunology Research Centre, at the University of Aberdeen (https://www.abdn.ac.uk/sfirc/).