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 Azumi
  • Rosaria De Santis
  • Anthony De Tomaso
  • Isidore Rigoutsos
  • Fumiko Yoshizaki
  • Maria Rosaria Pinto
  • Rita Marino
  • Kazuhito Shida
  • Makoto Ikeda
  • Masami Ikeda
  • Masafumi Arai
  • Yasuhito Inoue
  • Toshio Shimizu
  • Nori Satoh
  • Daniel S. Rokhsar
  • Louis Du Pasquier
  • Masanori Kasahara
  • Masanobu Satake
  • Masaru Nonaka
Original Paper

DOI: 10.1007/s00251-003-0606-5

Cite this article as:
Azumi, K., De Santis, R., De Tomaso, A. et al. Immunogenetics (2003) 55: 570. doi:10.1007/s00251-003-0606-5

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 analysisImmunological genesUrochordateEvolution

Supplementary material

Methods

supp_meth.pdf (36 kb)
(PDF 32 KB)

Tables S1-6

supp_tabl_1-6.pdf (52 kb)
(PDF 53 KB)

Figure Legends S1-9

supp_fig_leg.pdf (55 kb)
(PDF 60 KB)

Figures S1-7

supp_fig_1-7.pdf (29 kb)
(PDF 30 KB)

Figures S8-9

supp_fig_8_9.pdf (48 kb)
(PDF 50 KB)

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Kaoru Azumi
    • 1
  • Rosaria De Santis
    • 2
  • Anthony De Tomaso
    • 3
  • Isidore Rigoutsos
    • 4
  • Fumiko Yoshizaki
    • 5
  • Maria Rosaria Pinto
    • 2
  • Rita Marino
    • 2
  • Kazuhito Shida
    • 6
  • Makoto Ikeda
    • 6
  • Masami Ikeda
    • 7
  • Masafumi Arai
    • 7
  • Yasuhito Inoue
    • 7
  • Toshio Shimizu
    • 7
  • Nori Satoh
    • 8
  • Daniel S. Rokhsar
    • 9
  • Louis Du Pasquier
    • 10
  • Masanori Kasahara
    • 11
  • Masanobu Satake
    • 12
  • Masaru Nonaka
    • 5
  1. 1.Department of Biochemistry, Graduate School of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
  2. 2.Stazione Zoologica “Anton Dohrn”NaplesItaly
  3. 3.Department of PathologyStanford University School of MedicineStanfordUSA
  4. 4.Bioinformatics and Pattern Discovery GroupIBM Thomas J. Watson Research CenterYorktown HeightsUSA
  5. 5.Department of Biological Sciences, Graduate School of ScienceUniversity of TokyoTokyoJapan
  6. 6.Center for Interdisciplinary ResearchTohoku UniversitySendaiJapan
  7. 7.Department of Electronic Information System Engineering, Faculty of Science and TechnologyHirosaki UniversityHirosakiJapan
  8. 8.Department of Zoology, Graduate School of ScienceKyoto UniversityKyotoJapan
  9. 9.U.S. Department of Energy Joint Genome InstituteWalnut CreekUSA
  10. 10.Department of ZoologyUniversity of BaselBaselSwitzerland
  11. 11.Department of Biosystems Science, School of Advanced SciencesThe Graduate University for Advanced Studies (Sokendai)HayamaJapan
  12. 12.Department of Molecular Immunology, Institute of Development, Aging and CancerTohoku UniversitySendaiJapan