Original Paper

Immunogenetics

, Volume 55, Issue 8, pp 570-581

Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: “waiting for Godot”

  • Kaoru AzumiAffiliated withDepartment of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University
  • , Rosaria De SantisAffiliated withStazione Zoologica “Anton Dohrn”
  • , Anthony De TomasoAffiliated withDepartment of Pathology, Stanford University School of Medicine
  • , Isidore RigoutsosAffiliated withBioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center
  • , Fumiko YoshizakiAffiliated withDepartment of Biological Sciences, Graduate School of Science, University of Tokyo
  • , Maria Rosaria PintoAffiliated withStazione Zoologica “Anton Dohrn”
  • , Rita MarinoAffiliated withStazione Zoologica “Anton Dohrn”
  • , Kazuhito ShidaAffiliated withCenter for Interdisciplinary Research, Tohoku University
  • , Makoto IkedaAffiliated withCenter for Interdisciplinary Research, Tohoku University
    • , Masami IkedaAffiliated withDepartment of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University
    • , Masafumi AraiAffiliated withDepartment of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University
    • , Yasuhito InoueAffiliated withDepartment of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University
    • , Toshio ShimizuAffiliated withDepartment of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University
    • , Nori SatohAffiliated withDepartment of Zoology, Graduate School of Science, Kyoto University
    • , Daniel S. RokhsarAffiliated withU.S. Department of Energy , Joint Genome Institute
    • , Louis Du PasquierAffiliated withDepartment of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido UniversityDepartment of Zoology, University of Basel
    • , Masanori KasaharaAffiliated withDepartment of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido UniversityDepartment of Biosystems Science, School of Advanced Sciences, The Graduate University for Advanced Studies (Sokendai)
    • , Masanobu SatakeAffiliated withDepartment of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido UniversityDepartment of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University
    • , Masaru NonakaAffiliated withDepartment of Biological Sciences, Graduate School of Science, University of Tokyo Email author 

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Abstract

Genome-wide sequence analysis in the invertebrate chordate, Ciona intestinalis, has provided a comprehensive picture of immune-related genes in an organism that occupies a key phylogenetic position in vertebrate evolution. The pivotal genes for adaptive immunity, such as the major histocompatibility complex (MHC) class I and II genes, T-cell receptors, or dimeric immunoglobulin molecules, have not been identified in the Ciona genome. Many genes involved in innate immunity have been identified, including complement components, Toll-like receptors, and the genes involved in intracellular signal transduction of immune responses, and show both expansion and unexpected diversity in comparison with the vertebrates. In addition, a number of genes were identified which predicted integral membrane proteins with extracellular C-type lectin or immunoglobulin domains and intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based activation motifs (ITAMs) (plus their associated signal transduction molecules), suggesting that activating and inhibitory receptors have an MHC-independent function and an early evolutionary origin. A crucial component of vertebrate adaptive immunity is somatic diversification, and the recombination activating genes (RAG) and activation-induced cytidine deaminase (AID) genes responsible for the Generation of diversity are not present in Ciona. However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot.

Keywords

Genome analysis Immunological genes Urochordate Evolution