Evolutionary Analysis and Comparative Genomics of Protein Superfamilies

阿拉文德博士和他的团队参与了许多核苷酸依赖信号系统的发现。环状双核苷酸和线性寡核苷酸信号激活动物免疫系统对侵入性核酸的防御；然而，人们对它们的进化起源知之甚少。通过比较基因组学、序列和结构分析，阿拉文德博士的团队发现了一个由保守的原核基因邻域定义的庞大系统网络，这些基因邻域编码产生此类核苷酸的酶，或者对它们进行加工以产生潜在的信号分子。核苷酸生成酶包括dna聚合酶超家族的几个分支（包括霍乱弧菌DncV）， CRISPR聚合酶的最小版本和disa样环二磷酸腺苷合成酶。核苷酸结合/加工结构域包括TIR结构域和一个由Smf/DprA蛋白和碱基（细胞分裂素）释放LOG酶原型的超家族成员。它们在保守的基因邻区与大量蛋白质超家族的基因结合在一起，Aravind博士的研究小组预测，这些超家族将作为核苷酸传感器和靶向核酸、蛋白质或膜（成孔剂）的效应器。这些系统有时与其他生物冲突系统相结合，如限制性修饰和CRISPR/Cas。有趣的是，一些基因与原核泛素系统或HORMA结构域- pch2样AAA+ atp酶二偶体在互排斥的邻域中偶联。后者是真核生物染色体动力学中等效蛋白的潜在前体。此外，来自这些以核苷酸为中心的系统的组分已被用于其他几种系统，包括具有逆转录酶的新型多样性产生系统。Aravind博士和他的团队还发现这些系统中的Smf/DprA/LOG结构域在真核TRPM通道中作为预测的核苷酸结合结构域被招募。这些发现指出了进化和机制上的联系，将CRISPR/Cas、动物干扰素诱导免疫和其他几种结合了核酸感应和核苷酸依赖信号的系统结合在一起。

Dr. Aravind and his team was involved in the discovery of numerous nucleotide-dependent signaling systems. Cyclic di- and linear oligo-nucleotide signals activate defenses against invasive nucleic acids in animal immunity; however, their evolutionary antecedents are poorly understood. Using comparative genomics, sequence and structure analysis, Dr. Aravind's group uncovered a vast network of systems defined by conserved prokaryotic gene-neighborhoods, which encode enzymes generating such nucleotides or alternatively processing them to yield potential signaling molecules. The nucleotide-generating enzymes include several clades of the DNA-polymerase -like superfamily (including Vibrio cholerae DncV), a minimal version of the CRISPR polymerase and DisA-like cyclic-di-AMP synthetases. Nucleotide-binding/processing domains include TIR domains and members of a superfamily prototyped by Smf/DprA proteins and base (cytokinin)-releasing LOG enzymes. They are combined in conserved gene-neighborhoods with genes for a plethora of protein superfamilies, which Dr. Aravind's group predict to function as nucleotide-sensors and effectors targeting nucleic acids, proteins or membranes (pore-forming agents). These systems are sometimes combined with other biological conflict-systems such as restriction-modification and CRISPR/Cas. Interestingly, several are coupled in mutually exclusive neighborhoods with either a prokaryotic ubiquitin-system or a HORMA domain-PCH2-like AAA+ ATPase dyad. The latter are potential precursors of equivalent proteins in eukaryotic chromosome dynamics. Further, components from these nucleotide-centric systems have been utilized in several other systems including a novel diversity-generating system with a reverse transcriptase. Dr. Aravind and his group also found the Smf/DprA/LOG domain from these systems to be recruited as a predicted nucleotide-binding domain in eukaryotic TRPM channels. These findings point to evolutionary and mechanistic links, which bring together CRISPR/Cas, animal interferon-induced immunity, and several other systems that combine nucleic-acid-sensing and nucleotide-dependent signaling. Dr Aravind was part of an internal team that sequenced and analyzed the genome of the blood-bug Rhodnius prolixus Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. Dr. Aravind and his and the Rhodius sequencing team sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome ( 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. Dr. Aravind and his group carried out the first comprehensive study of adenine methylation in eukaryotes. While N(6) -methyladenosine (m(6) A) is a well-known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well-studied 5-methylcytosine mark. They showed that adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction-modification and counter-restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, m(6) A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m(6) A-binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m(6) A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m(6) A demethylases, this proposal needs more careful evaluation. Dr. Aravind and his group discovered a novel class of effectors deployed by eukaryotic pathogens. Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics Dr. Aravind and his group identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal 'Header' domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora Remarkably, Dr. Aravind and his group also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. Dr. Aravind and his group present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms. Dr. Aravind's 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 2016. Additionally, he 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