Evolutionary Analysis and Comparative Genomics of Protein Superfamilies

1) Aravind博士和他的团队进行了鉴定新型核酸修饰酶的研究。核酸中的修饰碱基呈现出一层信息，该信息指导生物功能，超越传统碱基的编码能力。最近，2-氧戊二酸和铁（II）依赖性双加氧酶超家族的成员，可以修饰从小分子到生物聚合物的各种底物，被预测并随后证实可以催化核酸中碱基的氧化修饰。其中，两个不同的家族，即AlkB和着丝质体碱基J结合蛋白（JBP）催化核酸中碱基的原位羟基化。通过对基因组结构和蛋白质结构域结构的序列、结构和上下文信息进行灵敏的计算分析，他们报道了5个不同的2-氧戊二酸和铁（II）依赖性双加氧酶家族，他们预测这些家族参与了核酸修饰。在dna修饰家族中，他们发现着丝质体碱基j结合蛋白的双加氧酶结构域属于一个更大的家族，该家族包括以人类致癌基因Tet1为原型的Tet蛋白，以及来自担子菌真菌、绿藻、异色虫变形虫鞭毛虫和噬菌体的蛋白。他们提出的证据表明，这些蛋白质中的一些可能参与了胞嘧啶5-甲基的氧化修饰，导致5-羟甲基胞嘧啶的形成。担子菌真菌（如Laccaria和Coprinopsis）的Tet/JBP同源物显示出大的谱系特异性扩展，并与编码一个新的和独特的可预测转座酶家族的基因紧密联系，以及一个类似maelstrom的HMG家族成员。他们提出这些真菌成员是可移动转座子的一部分。这是首次报道真核生物的转座元件，其编码自身的dna修饰酶具有潜在的调节作用。通过对其他特征不明确的DNA修饰酶的更广泛分析，他们还表明，噬菌体Mu mom样蛋白（催化腺嘌呤的n6 -氨基甲酰甲基化）也与细菌转座酶的不同家族有关，这表明转座因子对DNA的修饰可能比以前所认识的更为普遍。在本研究中发现的2-氧戊二酸和铁（II）依赖性双加氧酶的其他家族中，有一个在藻类中发现，预计主要由RNA修饰酶组成，并且在蛋白质结构域结构上显示出惊人的多样性，表明RNA修饰的存在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想不到的表观遗传修饰（如羟甲基胞嘧啶）提供手段，这些修饰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。

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.