Along with team at the NCBI and collaborators at the International Center for Genetic Engineering and Biotechnology, New Delhi, India Dr Aravind characterized the role of the multiple enzymatic activities of ParB/Srx superfamily in mediating sexual conflict among conjugative plasmids. Conjugative plasmids are typically locked in intergenomic and sexual conflicts with co-resident rivals, whose translocation they block using fertility inhibition factors (FINs). They described the first crystal structure of an enigmatic FIN Osa deployed by the proteobacterial plasmid pSa. Osa contains a catalytically active version of the ParB/Sulfiredoxin fold with both ATPase and DNase activity, the latter being regulated by an ATP-dependent switch. Using the Agrobacterium tumefaciens VirB/D4 type IV secretion system (T4SS), a relative of the conjugative T4SS, they demonstrated that catalytically active Osa blocks T-DNA transfer into plants. With a partially reconstituted T4SS in vitro, they showed that Osa degrades T-DNA in the T-DNA-VirD2 complex before its translocation. Further, they presented evidence for conservation and interplay between ATPase and DNase activities throughout the ParB/Sulfiredoxin fold, using other members of the family, namely P1 ParB and RK2 KorB, which have general functional implications across diverse biological contexts. Dr Aravind and his team did computational analysis of bacterial genomes to identify the mechanism by which bacteria sense the metal Manganese. They obtained evidence that the ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. The highly structured, cis-encoded RNA elements known as riboswitches modify gene expression upon binding a wide range of molecules. The yybP-ykoY motif was one of the most broadly distributed and numerous bacterial riboswitches for which the cognate ligand was unknown. Having predicted it as the potential Mn-sensor Dr. Aravind teamed up with Dr. Storz and Dr. Waters at the NICHD and using a combination of in vivo reporter and in vitro expression assays, equilibrium dialysis, and northern analysis, showed that the yybP-ykoY motif responds directly to manganese ions in both Escherichia coli and Bacillus subtilis. The identification of the yybP-ykoY motif as a manganese ion sensor suggests that the genes that are preceded by this motif and encode a diverse set of poorly characterized membrane proteins have roles in metal homeostasis. Dr. Aravind predicted the DNA N6-adenine methylase in C.elegans and provided evidence for the first time for the role of this modification in animal epigenetic information coding. Teaming up with Dr. Yang Shis group at the Harvard University, he was able obtain evidence for this enzymes role in active DNA modification. In mammalian cells, DNA methylation on the fifth position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC, as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, they demonstrated the presence of adenine N6-methylation (6mA) in i DNA. They further demonstrated that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, they identified a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylations of histone H3K4 and adenines and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data confirmed for the first time a DNA modification in C. elegans and raised the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes. Dr. Aravinds work in evolution of insect transcription factors provided new evidence regarding the body plan plasticity in the Hemiptera which include bugs, cicadas and aphids. Availability of complete genomes provides a means to explore the evolution of enormous developmental, morphological, and behavioral diversity among insects. Hemipterans in particular show great diversity of both morphology and life history within a single order. To better understand the role of transcription regulators in the diversification of hemipterans, using sequence profile searches and hidden Markov models Dr. Aravind and his team computationally analyzed transcription factors (TFs) and chromatin proteins (CPs) in the recently available Rhodnius prolixus genome along with 13 other insect and 4 non-insect arthropod genomes. They generated a comprehensive collection of TFs and CPs across arthropods including 303 distinct types of domains in TFs and 139 in CPs. This, along with the availability of two hemipteran genomes, R. prolixus and Acyrthosiphon pisum, helped them identify possible determinants for their dramatic morphological and behavioral divergence. They identified five domain families (i.e. Pipsqueak, SAZ/MADF, THAP, FLYWCH and BED finger) as having undergone differential patterns of lineage-specific expansion in hemipterans or within hemipterans relative to other insects. These expansions appear to be at least in part driven by transposons, with the DNA-binding domains of transposases having provided the raw material for emergence of new TFs. their analysis suggests that while R. prolixus probably retains a state closer to the ancestral hemipteran, A. pisum represents a highly derived state, with the emergence of asexual reproduction potentially favoring genome duplication and transposon expansion. Both hemipterans are predicted to possess active DNA methylation systems. However, in the course of their divergence, aphids seem to have expanded the ancestral hemipteran DNA methylation along with a distinctive linkage to the histone methylation system, as suggested by expansion of SET domain methylases, including those fused to methylated CpG recognition domains. Thus, differential use of DNA methylation and histone methylation might have played a role in emergence of polyphenism and cyclic parthenogenesis from the ancestral hemipteran. Dr. Iyers work was at the forefront of expanding the understanding of human and plant diseases. His work received over 4,800 citations in the scientific literature in the year 2015. Additionally, Dr. Iyer was asked to serve as a peer reviewer for several manuscripts submitted to the journals Biology Direct, Cell, Nature, Science, Nucleic Acids Research, Current Opinions in Structural Biology, Current Topics in Microbiology and Immunology, Frontiers in Genetics, and PNAS. As an invited speaker at two conferences, he also presented several aspects of his research.
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