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: 9564629
• 负责人: Aravind Iyer
• 金额: $ 107.08万
• 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/9564629
• 关键词: ATP phosphohydrolase; Adenine; Affect; Animal Model; Animals; Architecture; Bacterial DNA; Binding; Biological; Biological Process; Biology; Blood; C-terminal; CDC6 gene; Cells; Chagas Disease; Characteristics; Chromosomes; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Codon Nucleotides; Conflict (Psychology); Coupled; Cytokinins; DNA; DNA Restriction Enzymes; DNA-Directed DNA Polymerase; Development; Digestion; Dioxygenases; Elements; Enzymes; Epigenetic Process; Eukaryota; Evaluation; Evolution; Family; Genes; Genetic; Genetic Recombination; Genome; Genomics; Head; Horizontal Gene Transfer; Immune; Immune response; Immune signaling; Immunity; Immunology; Insecta; Interferons; Journals; Life; Life Style; Ligase; Link; Literature; Manuscripts; Mediating; Membrane; Methods; Methylation; Methyltransferase; Microbiology; Microscopic; Modification; Molecular; N-terminal; Nature; Neighborhoods; Nucleic Acids; Nucleotides; ORC1L gene; Oligonucleotides; Oomycetes; Pancreatic ribonuclease; Parasites; Pathway interactions; Pattern; Peptide Hydrolases; Periodicity; Physiology; Plant Diseases; Play; Polymerase; Prokaryotic Cells; Protein Analysis; Protein Binding Domain; Protein Kinase; Proteins; RNA; RNA-Directed DNA Polymerase; Reader; Recruitment Activity; Research; Rhodnius; Role; Science; Selenocysteine; Sequence Analysis; Signal Transduction; Signaling Molecule; Structure; System; Tertiary Protein Structure; Toxic effect; Transposase; Tribolium; Trypanosoma cruzi; Ubiquitin; Vibrio cholerae; Wolbachia; Work; base; comparative; comparative genomics; disorder control; endonuclease; experience; feeding; frontier; fungus; genome analysis; glutathione peroxidase; gut microbiota; human disease; innovation; killings; member; novel; nuclease; nucleoside triphosphatase; pathogen; peer; prototype; selenoprotein; sensor; structural biology; symposium; tRNA Methyltransferases; trafficking; vector; whole genome

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