Comparative genomic study of arachnid immune systems indicates loss of beta-1,3-glucanase-related proteins and the immune deficiency pathway

Abstract

Analyses of arthropod genomes have shown that the genes in the different innate humoral immune responses are conserved. These genes encode proteins that are involved in immune signalling pathways that recognize pathogens and activate immune responses. These immune responses include phagocytosis, encapsulation of the pathogen and production of effector molecules for pathogen elimination. So far, most studies have focused on insects leaving other major arthropod groups largely unexplored. Here, we annotate the immune-related genes of six arachnid genomes and present evidence for a conserved pattern of some immune genes, but also evolutionary changes in the arachnid immune system. Specifically, our results suggest that the family of recognition molecules of beta-1,3-glucanase-related proteins (βGRPs) and the genes from the immune deficiency (IMD) signalling pathway have been lost in a common ancestor of arachnids. These findings are consistent with previous work suggesting that the humoral immune effector proteins are constitutively produced in arachnids in contrast to insects, where these have to be induced. Further functional studies are needed to verify this. We further show that the full haemolymph clotting cascade found in the horseshoe crab is retrieved in most arachnid genomes. Tetranychus lacks at least one major component, although it is possible that this cascade could still function through recruitment of a different protein. The gel-forming protein in horseshoe crabs, coagulogen, was not recovered in any of the arachnid genomes; however, it is possible that the arachnid clot consists of a related protein, spätzle, that is present in all of the genomes.

Keywords: Arachnida; coagulation; genomics; immunity; signalling pathway.

Figure 1

Key components searched for in five investigated immune related pathways. The tri-spine horseshoe crab Tachypleus tridentatus model of clotting is redrawn from (Iwanaga & Lee, 2005), and the fruit fly Drosophila melanogaster models of signalling pathways are redrawn from (Bier & Guichard, 2012). Clotting: dark blue represents pathogen surface molecules that initiate the clotting pathway, brown represents cascade molecules, and grey represents end product. Toll: dark blue represents pathogen surface molecules that initiate the Toll pathway, dark green represents recognition molecules, blue represents signalling molecules, and red represents transcription factor. IMD: dark blue represents pathogen surface molecules that initiate the Toll pathway, green represents recognition molecules, orange represents signalling molecules, and purple represents transcription factor. JNK: light green represents signalling molecules, and light brown represents transcription factors. JAK/STAT: yellow represents ligand of domeless released upon infection (not searched for), pink represents signalling molecules, and turquoise represents transcription factor.

Figure 2

Phylogenetic relationships of the major arthropod groups including the six arachnids of this study. The relationships among the arachnids are based on (Sanggaard et al., 2014).

Figure 3

Copy numbers identified in six arachnid and three insect genomes (in Drosophila melanogaster numbers originate from www.flybase.org) of the genes involved in different humoral innate immune responses. On top is a representation of the phylogeny of the focal species. The relationships among arachnids are based on (Sanggaard et al., 2014). The identification of tube is difficult (see text), and it is uncertain whether we identified a tube homolog in the arachnids, indicated by 0/1 in this figure. The colour coding is the same as in Figure 1, where a detailed description can be found.

Figure 4

Domain structure of the clotting cascade factors of the tri-spine horseshoe crab Tachypleus tridentatus. A) shows the domain structure of factor C, and B) shows the domain structure of factor B, factor G and proclotting enzyme. Signal: signal peptide, EGF: epidermal growth factor-like domain, CCP: Domain abundant in complement control proteins; SUSHI repeats; short complement-like repeats (SCR), LCCL: named after Limulus Factor C, CLECT: C-type lectin (CTL) or carbohydrate-recognition domain, Tryp_SPc: trypsin-like serine protease, CLIP: clip or disulphide knot domain.

Figure 5

Alignment of identified defensins. Six cysteines (marked in red) are conserved among all loci. The species names are followed by identifiers from the respective gene lists, except for Stegodyphus mimosarum, where the genome sequence scaffold carrying the defensin loci is given.