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: 8344972
• 负责人: Aravind Iyer
• 金额: $ 119.92万
• 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/8344972
• 关键词: Active Sites; Address; Adenylate Cyclase; Amino Acids; Amino Acyl-tRNA Synthetases; Anabolism; Architecture; Area; Bacteria; Berlin; Binding; Binding Sites; Biological; Biological Process; Biology; Catalysis; Catalytic Domain; Cations; Cells; Citric Acid Cycle; Classification; Collagen; Comparative Genomic Analysis; Computing Methodologies; Consult; Contractor; DNA Sequence Rearrangement; DNA Viruses; DNA-Directed DNA Polymerase; DNA-Directed RNA Polymerase; Dimerization; Dioxygenases; Disease; Dynamin; Enzymatic Biochemistry; Enzymes; Event; Evolution; Family; Ferredoxin; Genes; Genome; Glycine; Guanine Nucleotides; Guanosine Triphosphate; Guanosine Triphosphate Phosphohydrolases; Hydroxylation; Immunity; In Vitro; Intracellular Membranes; Iron; Isomerase; Journals; Life; Lipids; Lymphocyte; Manuscripts; Mediating; Membrane; Metabolism; Metals; Methods; Microscopic; Mixed Function Oxygenases; Modification; Molecular; Monograph; Mutagenesis; Nature; Neighborhoods; Nucleic Acids; Nucleotides; Pathway interactions; Pattern; Peer Review; Peptide Antibiotics; Peptides; Peroxidases; Phenylalanine-Specific tRNA; Play; Polymerase; Polynucleotide 5' -Hydroxyl-Kinase; Polynucleotides; Positioning Attribute; Postdoctoral Fellow; Process; Property; Proteins; Publications; Publishing; RNA; RNA-Directed DNA Polymerase; RNA-Directed RNA Polymerase; Radiation; Reaction; Recording of previous events; Research; Research Project Grants; Role; Science; Scientist; Siderophores; Signal Transduction; Specificity; Structure; Surface; System; Tertiary Protein Structure; Transcriptional Regulation; Transfer RNA; Work; alpha ketoglutarate; apoptosis in lymphocytes; base; comparative genomics; diguanylate cyclase; epimerase; genome sequencing; in vivo; innovation; inorganic phosphate; interest; member; novel; peroxidation; polymerization; programs; protein structure function; repaired; scaffold; sensor; sugar; translation factor; tripolyphosphate; viral RNA; wybutosine

Dr. Aravind has an ongoing interest in using computational methods to decipher various aspects of protein structure, function and evolution. During 2010, Dr. Aravind demonstrated exceptional progress and effective planning and execution of several major research projects along these lines. These research projects cover the areas of molecular enzymology, signal transduction and transcriptional regulation mechanisms using computational methods. His group comprising of 1 staff scientist, 3 post-doctoral fellows and one contractor has over 12 publications in peer-reviewed publications in top scientific journals. He also published a comprehensive monograph on signal sensor domains in bacteria, which is recognized as a major work in this field. In this period, Dr. Aravind was also consulted to serve as a referee for several manuscripts submitted to the journals Science, Cell, Genome Research, JMB and Nucleic Acids Research, Genome Biology. He was an invited to speaker at three venues in course of the year. Some highlights of Dr. Aravinds 2010 research program include the following: Dr. Aravinds group studied GTPases of immunity-associated proteins (GIMAPs), a distinctive family of GTPases, which control apoptosis in lymphocytes and play a central role in lymphocyte maturation and lymphocyte-associated diseases. To explore their function and mechanism, he collaborated with Olivier Daumkes group, Max-Delbrck-Centrum fr Molekulare Medizin, Berlin to determine crystal structures of a representative member, GIMAP2, in different nucleotide-loading and oligomerization states. Nucleotide-free and GDP-bound GIMAP2 were monomeric and revealed a guanine nucleotide-binding domain of the TRAFAC (translation factor associated) class with a unique amphipathic helix 7 packing against switch II. In the absence of 7 and the presence of GTP, GIMAP2 oligomerized via two distinct interfaces in the crystal. GTP-induced stabilization of switch I mediates dimerization across the nucleotide-binding site, which also involves the GIMAP specificity motif and the nucleotide base. Structural rearrangements in switch II appear to induce the release of 7 allowing oligomerization to proceed via a second interface. The unique architecture of the linear oligomer predicted by Dr. Aravinds analysis was confirmed by mutagenesis by Oliver Daumkes group. Furthermore, they showed a function for the GIMAP2 oligomer at the surface of lipid droplets. Although earlier studies indicated that GIMAPs are related to the septins, the current structure also revealed a strikingly similar nucleotide coordination and dimerization mode as in the dynamin GTPase. Based on this, Dr. Aravind reexamined the relationships of the septin- and dynamin-like GTPases and demonstrated that these are likely to have emerged from a common membrane-associated dimerizing ancestor. This ancestral property appears to be critical for the role of GIMAPs as nucleotide-regulated scaffolds on intracellular membranes. Dr. Aravind and his team performed from new analysis elucidating the structure and catalysis of a rather interesting novel class of nucleic acid polymerases. Almost all known nucleic acid polymerases catalyze 5'-3' polymerization by mediating the attack on an incoming nucleotide 5' triphosphate by the 3'OH from the growing polynucleotide chain in a template dependent or independent manner. The only known exception to this rule is the Thg1 RNA polymerase that catalyzes 3'-5' polymerization in vitro and also in vivo as a part of the maturation process of histidinyl tRNA. While the initial reaction catalyzed by Thg1 has been compared to adenylation catalyzed by the aminoacyl tRNA synthetases, the evolutionary relationships of Thg1 and the actual nature of the polymerase reaction catalyzed by it remain unclear. Using sensitive profile-profile comparison and structure prediction methods Dr. Aravind and his group showed that the catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system. They showed just as in these polymerases, Thg1 possesses an active site with three acidic residues that chelate Mg++ cations. Based on this they predicted that Thg1 catalyzes polymerization similarly to the 5'-3' polymerases, but uses the incoming 3' OH to attack the 5' triphosphate generated at the end of the elongating polynucleotide. In addition they identified a distinct set of residues unique to Thg1 that they predicted as comprising a second active site, which catalyzes the initial adenylation reaction to prime 3'-5' polymerization. Based on contextual information from conserved gene neighborhoods they showed that Thg1 might function in conjunction with a polynucleotide kinase that generates an initial 5' phosphate substrate for it at the end of a RNA molecule. In addition to histidinyl tRNA maturation, Thg1 might have other RNA repair roles in representatives from all the three superkingdoms of life as well as certain large DNA viruses. They also present evidence that among the polymerase-like domains Thg1 is most closely related to the catalytic domains of the GGDEF and CRISPR polymerase proteins. Based on this relationship and the phyletic patterns of these enzymes they inferred that the Thg1 protein is likely to represent an archaeo-eukaryotic branch of the same clade of proteins that gave rise to the mobile CRISPR polymerases and in bacteria spawned the GGDEF domains. Thg1 is likely to be close to the ancestral version of this family of enzymes that might have played a role in RNA repair in the last universal common ancestor. A key work by Dr. Aravind and his group resulted in solving the evolutionary classification of the jumonji-like enzymes and predicting of the long elusive catalytic activity of the Wybutosine hydroxylase/peroxidase. Unlike classical 2-oxoglutarate and iron-dependent dioxygenases, which include several nucleic acid modifiers, the structurally similar jumonji-related dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative genomics methods, Dr. Aravind and his team predicted that a family of jumonji-related enzymes catalyzes wybutosine hydroxylation/peroxidation at position 37 of eukaryotic tRNAPhe. Identification of this enzyme raised questions regarding the emergence of protein- and nucleic acid-modifying activities among jumonji-related domains. They addressed these with a natural classification of DSBH domains and reconstructed the precursor of the dioxygenases as a sugar-binding domain. This precursor gave rise to sugar epimerases and metal-binding sugar isomerases. The sugar isomerase active site was exapted for catalysis of oxygenation, with a radiation of these enzymes in bacteria, probably due to impetus from the primary oxygenation event in Earth's history. 2-Oxoglutarate-dependent versions appear to have further expanded with rise of the tricarboxylic acid cycle. They identified previously under-appreciated aspects of their active site and multiple independent innovations of 2-oxoacid-binding basic residues among these superfamilies. They showed that double-stranded -helix dioxygenases diversified extensively in biosynthesis and modification of halogenated siderophores, antibiotics, peptide secondary metabolites and glycine-rich collagen-like proteins in bacteria. Jumonji-related domains diversified into three distinct lineages in bacterial secondary metabolism systems and these were precursors of the three major clades of eukaryotic enzymes. The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily.

Aravind博士对使用计算方法对蛋白质结构，功能和进化的各个方面具有持续的兴趣。在2010年，Aravind博士在这些方面表现出了出色的进度，并有效地计划和执行了几个主要的研究项目。这些研究项目涵盖了使用计算方法的分子酶学，信号转导和转录调控机制的领域。他的小组包括1名员工科学家，3名博士后研究员和一名承包商在高级科学期刊的同行评审出版物中有12个出版物。他还发表了有关细菌信号传感器域的全面专着，该专着被认为是该领域的主要工作。在此期间，还咨询了Aravind博士，担任裁判员，用于裁判，以提交给期刊科学，细胞，基因组研究，JMB和核酸研究，基因组生物学。 在一年中，他受邀在三个场所的演讲者。 Aravinds 2010年研究计划的一些亮点包括以下内容： Aravinds Group博士研究了一种独特的GTPases家族免疫相关蛋白（GIMAPS）的GTPase，该蛋白（GIMAPS）控制淋巴细胞中的凋亡，并在淋巴细胞成熟和淋巴细胞相关的疾病中起核心作用。为了探索他们的功能和机制，他与柏林的Max-Delbrck-Centrum Molekulare Medizin Max-Delbrck-Centrum Fr Melekulare Medizin合作，以确定不同核苷酸载荷和低聚状态的代表成员GIMAP2的晶体结构。无核苷酸和GDP结合的GIMAP2是单体的，并揭示了Trafac的鸟嘌呤核苷酸结合结构域（相关的翻译因子）类，其具有独特的两体性螺旋螺旋7填充开关II。在不存在7和GTP的情况下，GIMAP2通过晶体中的两个不同界面进行了低聚。 GTP诱导的开关I的稳定化介导了整个核苷酸结合位点的二聚化，这也涉及GIMAP特异性基序和核苷酸碱基。开关II中的结构重排似乎诱导了7的释放，从而可以通过第二个接口进行低聚。 Oliver Daumkes Group通过诱变证实了Aravinds分析博士预测的线性低聚物的独特结构。此外，它们在脂质液滴表面显示了GIMAP2低聚物的功能。尽管较早的研究表明GIMAP与SEPTIS有关，但当前的结构还显示出与Dynamin GTPase中相似的核苷酸配位和二聚化模式。基于此，Aravind博士重新审查了Septin和Dynamin样GTPases的关系，并证明这些关系可能是从常见的膜相关二聚体祖先中出现的。这种祖先特性对于gimap的作用至关重要，因为核苷酸调节的支架在细胞内膜上。 Aravind博士和他的团队从新的分析中进行了阐明一类有趣的新型核酸聚合酶的结构和催化。几乎所有已知的核酸聚合酶几乎通过以模板依赖或独立的方式从生长的多核苷酸链中介导3'OH对传入的核苷酸5'的攻击来催化5'-3'聚合。该规则的唯一例外是THG1 RNA聚合酶，该聚合酶在体外催化3'-5'聚合，并且在体内也是组蛋白基TRNA成熟过程的一部分。虽然将THG1催化的初始反应与氨基酰基TRNA合成酶催化的腺苷酸化进行了比较，但THG1的进化关系和由其催化的聚合酶反应的实际性质尚不清楚。 Using sensitive profile-profile comparison and structure prediction methods Dr. Aravind and his group showed that the catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase CRISPR系统。它们与这些聚合酶一样表现出来，THG1具有一个活性位点，其三个酸性残基螯合Mg ++阳离子。基于此，他们预测THG1催化聚合类似于5'-3'聚合酶，但使用传入的3'OH攻击在伸长多核苷酸结束时产生的5磷酸盐。此外，他们确定了THG1独有的一组不同的残基，它们预测为包括第二个活性位点，该位点催化了初始的腺苷酸化反应，对质子3'-5'聚合。基于来自保守基因邻域的上下文信息，他们表明THG1可能与多核苷酸激酶一起起作用，该多核苷酸激酶在RNA分子结束时为其生成最初的5'磷酸基底物。除了组蛋白基tRNA成熟外，THG1在生命的所有三个超级行为以及某些大型DNA病毒的代表中可能还具有其他RNA修复作用。他们还提供了证据表明，在聚合酶样结构域中，THG1与GGDEF和CRISPR聚合酶蛋白的催化结构域密切相关。基于这种关系和这些酶的植物模式，他们推断出THG1蛋白可能代表同一蛋白枝的考古 - 核核分支，从而引起移动CRISPR聚合酶，并在细菌中产生了GGDEF域。 THG1很可能与该酶家族的祖先版本接近，这些酶可能在最后一个普遍的普通祖先中在RNA修复中发挥了作用。 Aravind博士及其小组的一项关键工作导致解决了类似Jumonji的酶的进化分类，并预测了Wybutosine羟化酶/过氧化物酶的长期难以捉摸的催化活性。与经典的2-氧化甲酸和铁依赖性二加氧酶不同，其中包括几种核酸修饰剂，结构相似的Jumonji相关的二氧酶超家族仅催化肽修饰。使用比较基因组学方法，Aravind博士和他的团队预测，与真核生物Trnaphe的位置37处的Jumonji相关酶催化Wybutosine羟基化/过氧化。这种酶的鉴定引发了有关与Jumonji相关结构域之间蛋白质和核酸修饰活性的出现的问题。他们通过DSBH结构域的自然分类来解决这些问题，并将双加氧酶的前体重建为糖结合结构域。该前体产生糖分和金属结合糖异构酶。将糖异构酶活性位点被催化以催化氧合，这些酶在细菌中的辐射可能是由于地球历史上主要的氧合事件的推动力所致。随着三羧酸循环的增加，2-氧化剂依赖性版本似乎进一步扩展。他们确定了这些超家族中2-氧化物结合基本残基的活跃部位的先前不受欢迎的方面以及多次独立的创新。他们表明，在细菌中，双链二氧酶在生物合成和修饰过程中广泛多样化，并修饰了细菌中富含甘氨酸的胶原蛋白样蛋白。 Jumonji相关的结构域在细菌次级代谢系统中分为三个不同的谱系，这些是真核酶的三个主要进化枝的前体。 Wybutosine羟化酶/过氧化物酶的特异性可能与该超家族的祖先氨基酸底物的结构相似性有关。