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.
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