The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss

Genome Biology e2VMt0oia0luls7e.mreea8r,cIshsue 4, Article R59 Re The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss David J Miller*, Georg Hemmrich, Eldon E Ball, David C Hayward, Konstantin Khalturin, Noriko Funayama, Kiyokazu Agata and Thomas CG Bosch Correspondence: Thomas CG Bosch. Email: 0 Zoological Institute, Christian-Albrechts-University Kiel , Olshausenstrasse, 24098 Kiel , Germany 1 ARC Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University , Canberra ACT 2601 , Australia 2 ARC Centre of Excellence in Coral Reef Studies and Comparative Genomics Centre, James Cook University , Townsville, Queensland 4811 , Australia 3 Department of Biophysics, Kyoto University , Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502 , Japan Background: Characterization of the innate immune repertoire of extant cnidarians is of both fundamental and applied interest - it not only provides insights into the basic immunological 'tool kit' of the common ancestor of all animals, but is also likely to be important in understanding the global decline of coral reefs that is presently occurring. Recently, whole genome sequences became available for two cnidarians, Hydra magnipapillata and Nematostella vectensis, and large expressed sequence tag (EST) datasets are available for these and for the coral Acropora millepora. Results: To better understand the basis of innate immunity in cnidarians, we scanned the available EST and genomic resources for some of the key components of the vertebrate innate immune repertoire, focusing on the Toll/Toll-like receptor (TLR) and complement pathways. A canonical Toll/TLR pathway is present in representatives of the basal cnidarian class Anthozoa, but neither a classic Toll/TLR receptor nor a conventional nuclear factor (NF)-B could be identified in the anthozoan Hydra. Moreover, the detection of complement C3 and several membrane attack complex/perforin domain (MAC/PF) proteins suggests that a prototypic complement effector pathway may exist in anthozoans, but not in hydrozoans. Together with data for several other gene families, this implies that Hydra may have undergone substantial secondary gene loss during evolution. Such losses are not confined to Hydra, however, and at least one MAC/PF gene appears to have been lost from Nematostella. Conclusion: Consideration of these patterns of gene distribution underscores the likely significance of gene loss during animal evolution whilst indicating ancient origins for many components of the vertebrate innate immune system. These authors contributed equally to this work - Background The innate immune system is the first line of defense against pathogens, and in non-chordates is assumed to be the sole means by which any non-self cells are detected and either killed or contained [1]. Innate immunity in vertebrates is essentially a two-tier system consisting on one hand of phagocyte activation by the interaction of specialized surface receptors with pathogens or pathogen-derived components, and on the other of the direct opsonization and lysis of pathogens via the complement cascade. Whilst the vertebrate innate immune system has been the subject of intense investigation and is relatively well understood, studies of invertebrate immunity, which have focused primarily on the arthropods Drosophila and various horseshoe crab species [2-4], have revealed some striking similarities. For example, in both Drosophila and vertebrates, the Toll/Toll-like receptor (TLR) mediates the activation of appropriate response genes to microbial challenge [5,6]. Toll and the TLRs are transmembrane proteins with a characteristic domain structure consisting of an extracellular amino-terminal domain containing leucine-rich repeats (LRRs) responsible for pattern recognition and an intracellular Toll interleukin receptor (TIR) domain that mediates signal transmission. Although the Toll and TLR families of arthropods and mammals are thought to have independently diversified [7,8], all Tolls and TLRs signal via a common pathway that is conserved between Drosophila and mammals. The ultimate step in this pathway is translocation of nuclear factor (NF)-B or its fly counterpart (the Dif/Rel heterodimer) into the nucleus, where it stimulates transcription of appropriate response genes. The immune repertoire of the horseshoe crab Carcinoscorpius includes a complex complement pathway that has both opsonic and lytic effector functions [9]. Horseshoe crab complement C3 is functionally homologous with mammalian C3, mediating phagocytosis of bacteria (by hemocytes) in a strikingly similar manner. Whilst these specific studies imply that at least some innate immune mechanisms have been conserved, broader comparative studies highlight the extent of gene loss and divergence in various metazoan lineages. For example, although Carcinoscorpius clearly uses a vertebrate-like complement system, none of the central components of the cascade (C2, C3, C4, C5) are encoded by the genomes of the ecdysozoans Drosophila, Caenorhabditis or Anopheles. Moreover, the sole Toll/TLR in Caenorhabditis elegans and C. brigssae is not known to function in the context of immunity, nor does that reported in the horseshoe crab Tachypleus tridentatus [10]. There are also important differences between the Toll/TLR systems of Drosophila and mammals. For example, some mammalian TLRs themselves act as pattern recognition receptors (PRRs) upon microbial challenge, whereas in fly this is not the case [11]. Moreover, whereas most of the ten or so vertebrate TLRs function primarily in immunity, only one of the nine fly (and ten mosquito) Tolls functions in this context. The others play a role in development [10], most famously in controlling differentiation in the dorsal/ventral axis. The significance of gene loss in animal evolution has recently been brought into focus by preliminary expressed sequence tag (EST) and genomic analyses of some 'basal' animals (Figure 1), particularly the anthozoan cnidarians Acropora millepora and Nematostella vectensis [12,13] and the planarian Dugesia japonica [14]. Paradoxically, the genomes of these morphologically simple animals contain many genes previously thought to have evolved much later in the context of vertebrate complexity, and most of the complexity of signaling pathways and transcription factors associated with higher animals is represented in the anthozoan datasets [13,15-17]. In contrast to Drosophila and Caenorhabditis, which have undergone substantial gene loss, for at least some groups of genes Acropora and Nematostella appear to have preserved much of the genetic complexity of the common metazoan ancestor. For example, whereas fly and worm have each lost approximately half of the ancestral Wnt complement, all but one of the 12 known Wnt subfamilies is represented in Nematostella [15]. The emerging cnidarian EST and genomic dat (...truncated)