Evolutionary trajectories of DNA/RNA-editing enzymes involved in adaptive and innate immunity

脊椎动物免疫细胞通过特定的DNA/RNA编辑酶有目的地诱导其基因组或入侵病毒基因组的突变。胞苷脱氨酶的激活诱导的胞苷脱氨酶/载脂蛋白B编辑催化样多肽（AID/APOBEC）家族是免疫中的核心参与者。AID作用于内源性免疫球蛋白基因并启动抗体亲和力成熟，而APOBECs使病毒的基因组突变以使其编码能力丧失。由于AID/APOBECs在免疫中的功能，它们受到的进化压力使它们在物种之间高度多样化，使它们成为酶结构：功能进化的迷人主题。然而，与其他参与免疫的分子一样，虽然人类和小鼠的版本已经得到了深入的研究，但我们对远距离进化物种中AID/APOBEC（或类似）酶的理解存在明显的差距。 我们率先研究了不同的AID/APOBECs。专注于代表关键进化节点的物种，我们贡献了几个进展：1。发现并鉴定了新的酶2.共同发现了同一物种内酶多样性的现象3.发现了与抗体应答缺陷相关的天然AID失活的第一例，以及与扩展的先天免疫相关的补偿性共同进化的新模式4。进行了第一次祖先重建（ASR）的酶参与免疫破译其进化轨迹在这里，我们提出：目标1。研究现存和祖先进化远缘物种的DNA/RNA编辑酶的功能，并检查它们与免疫的协同进化我们将重点了解无脊椎动物，无颌和有颌脊椎动物关键进化节点的AID/APOBEC酶的进化及其与免疫的协同进化。现存的和预测的祖先酶的关键进化节点将在酶测定和基于细胞的功能测定进行研究。酶的性质，然后将被认为是在每一个物种的适应性和先天免疫组件的上下文中。目标2.酶学，结构生物学和人工智能的结合应用，以破译DNA/RNA编辑酶的结构：功能关系我们将应用机器学习来破译结构：功能特征，这些特征是酶特性进化适应的基础。为此，我们将在广度（直系同源物的数量）和深度（生化参数）方面产生任何酶的最大数据集。高通量生化分析将通过对3D结构的计算和实验见解来补充。冲击 我们将发现新的酶和结构：功能关系，并深入了解未知的进化遥远的免疫系统。我们的工作也将代表机器学习在酶学中的新应用。

Vertebrate immune cells purposefully induce mutations in their genomes, or in the genomes of invading viruses, through specific DNA/RNA-editing enzymes. The Activation-induced cytidine deaminase/Apolipoprotein B editing catalytic like polypeptide (AID/APOBEC) family of cytidine deaminase enzymes are central players in immunity. AID acts on the endogenous immunoglobulin genes and initiates antibody affinity maturation, while APOBECs mutate the genomes of viruses to incapacitate their coding ability. The evolutionary pressure imposed on AID/APOBECs due to their functions in immunity has made these highly diverse among species, making them a fascinating subject for enzyme structure:function evolution. However, as with other molecules involved in immunity, while the human and mouse versions have been intensely studied, there is a glaring gap in our understanding of AID/APOBEC (or similar) enzymes in distantly evolved species. We pioneered the study of divergent AID/APOBECs. Focusing on species representing key evolutionary junctures, we contributed several advances: 1. discovered and characterized new enzymes 2. co-discovered the phenomenon of enzyme diversification within the same species 3. discovered the first instance of natural AID inactivation correlating with a deficiency in antibody response, and a novel mode of compensatory co-evolution with expanded innate immunity 4. Carried out the first ancestral reconstruction (ASR) of an enzyme involved in immunity to decipher its evolutionary trajectory Here we propose to: Objective 1. Study the function of DNA/RNA-editing enzymes from extant and ancestral evolutionary distant species, and examine their co-evolution with immunity We will focus on understanding the evolution and co-evolution with immunity, of AID/APOBEC enzymes from key evolutionary junctures of invertebrates, jawless and jawed vertebrates. Extant and predicted ancestral enzymes of key evolutionary nodes will be studied in enzyme assays and cell-based assays of function. Enzyme properties will then be considered in the context of the adaptive and innate immune components of each species. Objective 2. Combined application of enzymology, structural biology and artificial intelligence to decipher structure:function relationships in DNA/RNA-editing enzymes We will apply machine learning to decipher the structure:function features that underlie evolutionary adaptations of enzyme properties. To this end, we will produce the largest dataset of any enzyme in terms of breadth (number of orthologs) and depth (biochemical parameters). High throughput biochemical analysis will be complemented by computational and experimental insights into 3D structures. Impact. We will discover new enzymes and structure:function relationships, and gain insights into unknown evolutionary distant immune systems. Our work will also represent a novel application of machine learning in enzymology.