title: Novel genes dramatically alter regulatory network topology in amphioxus.
abstract: BACKGROUND
  Regulation in protein networks often utilizes specialized domains that 'join' (or 'connect') the network through specific protein-protein interactions. The innate immune system, which provides a first and, in many species, the only line of defense against microbial and viral pathogens, is regulated in this way. Amphioxus (Branchiostoma floridae), whose genome was recently sequenced, occupies a unique position in the evolution of innate immunity, having diverged within the chordate lineage prior to the emergence of the adaptive immune system in vertebrates.
  
  
  RESULTS
  The repertoire of several families of innate immunity proteins is expanded in amphioxus compared to both vertebrates and protostome invertebrates. Part of this expansion consists of genes encoding proteins with unusual domain architectures, which often contain both upstream receptor and downstream activator domains, suggesting a potential role for direct connections (shortcuts) that bypass usual signal transduction pathways.
  
  
  CONCLUSIONS
  Domain rearrangements can potentially alter the topology of protein-protein interaction (and regulatory) networks. The extent of such arrangements in the innate immune network of amphioxus suggests that domain shuffling, which is an important mechanism in the evolution of multidomain proteins, has also shaped the development of immune systems.
authors.affiliation: Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.forename: Christian M
authors.initials: CM
authors.lastname: Zmasek
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Dishaw
authors.forename: M Gail
authors.initials: MG
authors.lastname: Mueller
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Ye
authors.forename: Gary W
authors.initials: GW
authors.lastname: Litman
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D000818:Animals; D002816:Chordata, Nonvertebrate / Q000235:genetics* / Q000276:immunology; D019143:Evolution, Molecular; D015870:Gene Expression; D007113:Immunity, Innate / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D050506:Mutant Chimeric Proteins / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D051192:Receptors, Pattern Recognition / Q000737:chemistry / Q000235:genetics*; D015398:Signal Transduction
chemical_list: D050506:Mutant Chimeric Proteins; D051192:Receptors, Pattern Recognition