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，有目的地在它们的基因组中或在入侵病毒的基因组中诱导突变。激活诱导型胞苷脱氨酶/载脂蛋白B编辑类催化多肽(AID/APOBEC)家族胞苷脱氨酶家族在免疫过程中起重要作用。AID作用于内源性免疫球蛋白基因，启动抗体亲和力成熟，而APOBEC突变病毒基因组，使其丧失编码能力。由于AID/APOBEC在免疫中的功能而施加在进化上的压力使它们在物种之间具有高度的多样性，使它们成为酶结构的一个迷人的主题：功能进化。然而，与其他参与免疫的分子一样，尽管人类和小鼠的版本已经得到了深入的研究，但我们对遥远进化物种中的AID/APOBEC(或类似)酶的理解存在着明显的差距。我们开创了AID/APOBECs分化研究的先河。围绕代表进化关键节点的物种，我们取得了一些进展：1.发现并表征了新的酶；2.共同发现了同一物种内酶的多样化现象；3.发现了与抗体反应缺陷有关的首例自然艾滋病失活；4.对一种参与免疫的酶进行了首次祖先重建(ASR)，以破译其进化轨迹。我们建议：1.研究现存和祖先进化的远缘物种中DNA/RNA编辑酶的功能。我们将重点了解无脊椎动物、无颌脊椎动物和有颌骨脊椎动物的AID/APOBEC酶的关键进化节点的进化和与免疫的协同进化。现有的和预测的关键进化节点的祖先酶将在酶分析和基于细胞的功能分析中进行研究。然后将在每个物种的适应性和先天免疫成分的背景下考虑酶的特性。目标2.结合应用酶学、结构生物学和人工智能来破译结构：DNA/RNA编辑酶中的功能关系我们将应用机器学习来破译结构：酶特性进化适应的功能特征。为此，我们将在广度(同源基因的数量)和深度(生化参数)方面产生任何酶中最大的数据集。高通量生化分析将得到对3D结构的计算和实验洞察的补充。冲击力。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远程免疫系统。我们的工作也将代表机器学习在酶学中的一种新应用。

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.