Evolutionary Analysis and Comparative Genomics of Protein Superfamilies

蛋白质超家族的进化分析和比较基因组学

• 批准号: 8149617
• 负责人: Aravind Iyer
• 金额: $ 137.11万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8149617
• 关键词: Comparative Genomic Analysis; Proteins

1) Dr. Aravind and his group performed research to identify novel nucleic acid modification enzymes. Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity of the conventional bases. Recently, members of the 2-oxoglutarate- and iron(II)-dependent dioxygenase super-family, which modify diverse substrates from small molecules to biopolymers, were predicted and subsequently confirmed to catalyze oxidative modification of bases in nucleic acids. Of these, two distinct families, namely the AlkB and the kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation of bases in nucleic acids. Using sensitive computational analysis of sequences, structures and contextual information from genomic structure and protein domain architectures, they reported five distinct families of 2-oxoglutarate- and iron(II)-dependent dioxygenase that they predict to be involved in nucleic acid modifications. Among the DNA-modifying families, they showed that the dioxygenase domains of the kinetoplastid base J-binding proteins belong to a larger family that includes the Tet proteins, prototyped by the human oncogene Tet1, and proteins from basidiomycete fungi, chlorophyte algae, heterolobosean amoeboflagellates and bacteriophages. They presented evidence that some of these proteins are likely to be involved in oxidative modification of the 5-methyl group of cytosine leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs from basidiomycete fungi such as Laccaria and Coprinopsis show large lineage-specific expansions and a tight linkage with genes encoding a novel and distinct family of predicted transposases, and a member of the Maelstrom-like HMG family. They proposed that these fungal members are part of a mobile transposon. This is the first report of a eukaryotic transposable element that encodes its own DNA-modification enzyme with a potential regulatory role. Through a wider analysis of other poorly characterized DNA-modifying enzymes they also showed that the phage Mu Mom-like proteins, which catalyze the N6-carbamoylmethylation of adenines, are also linked to diverse families of bacterial transposases, suggesting that DNA modification by transposable elements might have a more general presence than previously appreciated. Among the other families of 2-oxoglutarate- and iron(II)-dependent dioxygenases identified in this study, one which is found in algae, is predicted to mainly comprise of RNA-modifying enzymes and shows a striking diversity in protein domain architectures suggesting the presence of RNA modifications with possibly unique adaptive roles. The results presented here are likely to provide the means for future investigation of unexpected epigenetic modifications, such as hydroxymethyl cytosine, that could profoundly impact our understanding of gene regulation and processes such as DNA demethylation. 2)DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development. In a computational search for enzymes that could modify 5-methylcytosine (5mC), Dr. Aravind identified TET proteins as mammalian homologs of the trypanosome proteins JBP1 and JBP2, which have been proposed to oxidize the 5-methyl group of thymine. In conjunction with his collaborator Dr. Anjana Rao, Immune Disease Institute, Harvard Medical School it was shown that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro. hmC is present in the genome of mouse embryonic stem cells, and hmC levels decrease upon RNA interference-mediated depletion of TET1. Thus, TET proteins have potential roles in epigenetic regulation through modification of 5mC to hmC. 3)Dr. Aravind initiated a project on chromatin proteins that lead to the discovery of a novel histone chaperone that function as part of the Hir-Asf1 histone chaperone complex. Using protein sequence profile analyses methods he investigated the evolution of Hir-Asf1 complex proteins and showed that they have a much wider phyletic pattern than was previously known. He established the animal histone-deacetylase-complex-interacting proteins, CAIN/CABIN, to be orthologs of Hir3p. They contain a conserved core of around 30 TPR-like bi-helical repeats that are likely to form a super-helical scaffold. He also identified a conserved domain, the HUN domain, in all Hpc2p homologs, including animal ubinuclein/yemanuclein and the recently discovered vertebrate cell-cycle regulator FLJ25778. The HUN domain has a characteristic pattern of conserved acidic residues based on which he predicted that it is a previously unrecognized histone-tail-binding chaperone. By analyzing various high-throughput data sets, such as RNAi knock-downs, genetic and protein interaction maps and cell-cycle-specific gene expression data, we present evidence that Hpc2p homologs might be deployed in specific processes of chromatin dynamics relating to cell-cycle progression in vertebrates and schizogony in Plasmodium.

第一章 博士Aravind和他的团队进行了研究，以确定新的核酸修饰酶。核酸中的修饰碱基提供了一层信息，其指导生物功能超过并超出常规碱基的编码能力。最近，2-酮戊二酸和铁（II）依赖性双加氧酶超家族的成员，修改从小分子到生物聚合物的不同底物，被预测和随后证实催化氧化修饰核酸中的碱基。其中，两个不同的家族，即AlkB和动质体碱基J结合蛋白（JBP）催化核酸中碱基的原位羟基化。通过对来自基因组结构和蛋白质结构域架构的序列、结构和上下文信息进行敏感的计算分析，他们报告了5个不同的2-酮戊二酸和铁（II）依赖性双加氧酶家族，他们预测这些家族参与核酸修饰。在DNA修饰家族中，他们发现动质体碱基J结合蛋白的双加氧酶结构域属于一个更大的家族，该家族包括以人类癌基因Tet 1为原型的泰特蛋白，以及来自担子菌真菌、绿藻、异裂体变形虫和噬菌体的蛋白。他们提出的证据表明，这些蛋白质中的一些可能涉及胞嘧啶的5-甲基的氧化修饰，导致5-羟甲基胞嘧啶的形成。泰特/JBP同系物从担子菌真菌，如蜡蘑和鬼伞显示大的谱系特异性的扩展和紧密连锁的基因编码一个新的和独特的家庭预测的转座酶，和Maelstrom样HMG家族的成员。他们提出这些真菌成员是移动的转座子的一部分。这是第一次报告的真核转座因子，编码自己的DNA修饰酶具有潜在的调节作用。通过对其他特征不佳的DNA修饰酶进行更广泛的分析，他们还表明，催化腺嘌呤的N6-氨基甲酰基甲基化的噬菌体Mu Mom样蛋白也与不同的细菌转座酶家族有关，这表明转座因子对DNA的修饰可能比以前认识的更普遍。在其他家庭的2-酮戊二酸和铁（II）的依赖性双加氧酶在这项研究中确定，其中一个是在藻类中发现的，预计主要包括RNA修饰酶，并显示出显着的多样性，在蛋白质结构域的架构，这表明存在的RNA修饰可能具有独特的适应性作用。这里提出的结果可能为未来研究意外的表观遗传修饰提供手段，如羟甲基胞嘧啶，这可能会深刻影响我们对基因调控和DNA去甲基化等过程的理解。 2)DNA胞嘧啶甲基化对逆转录转座子沉默和哺乳动物发育至关重要。在一项对能够修饰5-甲基胞嘧啶（5 mC）的酶的计算机搜索中，Aravind博士将泰特蛋白鉴定为锥虫蛋白JBP 1和JBP 2的哺乳动物同源物，后者被认为可以氧化胸腺嘧啶的5-甲基。与他的合作者Anjana Rao博士（哈佛医学院免疫疾病研究所）一起，研究表明TET 1（急性髓性白血病中MLL基因的融合伴侣）是一种2-酮戊二酸（2 OG）和Fe（II）依赖性酶，可在培养细胞和体外催化5 mC转化为5-羟甲基胞嘧啶（hmC）。hmC存在于小鼠胚胎干细胞的基因组中，并且hmC水平在RNA干扰介导的TET 1消耗后降低。因此，泰特蛋白通过将5 mC修饰为hmC而在表观遗传调控中具有潜在的作用。 3）Aravind博士发起了一个关于染色质蛋白的项目，该项目导致发现了一种新型组蛋白伴侣，其功能是Hir-Asf 1组蛋白伴侣复合物的一部分。使用蛋白质序列分析方法，他研究了Hir-Asf 1复合蛋白的进化，并表明它们具有比以前已知的更广泛的系统模式。他建立了动物组蛋白脱乙酰酶复合物相互作用蛋白CAIN/CABIN，作为Hir 3 p的直系同源物。它们包含约30个TPR样双螺旋重复序列的保守核心，这些重复序列可能形成超螺旋支架。他还在所有Hpc 2 p同源物中鉴定了一个保守的结构域，匈奴结构域，包括动物ubinuclein/yemanuclein和最近发现的脊椎动物细胞周期调节因子FLJ 25778。匈奴结构域具有保守的酸性残基的特征模式，基于此，他预测它是以前未识别的组蛋白尾结合伴侣。通过分析各种高通量数据集，如RNAi敲除，遗传和蛋白质相互作用图和细胞周期特异性基因表达数据，我们提出的证据表明，Hpc 2 p同源物可能部署在特定的染色质动力学过程中与脊椎动物的细胞周期进展和疟原虫的胚胎发育。