Comparative Genomics And Evolution Of IL17R And TLR Signaling Pathways Components

The Toll/IL1receptor (TIR) domain was first characterized on the basis of homology between the intracellular region of mammalian IL1receptor (IL1R) and the Drosophila Toll protein. TIR domain consists of three "boxes" of conserved residues set in a core sequence ranging200amino acids. So far, TIR domain-containing proteins are found in plants, bacteria, archaeabacteria, eukaryotes and viruses. They play key roles in immune response. The isoforms of IL17receptors (IL17Rs) and their adaptor protein CIKS (connection to IKK and SAPK/JNK) contain a conserved segment that shares similar amino acid sequence and secondary structures with the TIR domains. Novatchkova et al. named this segment SEF/IL17R (SEFIR) domain. The similarity between SEFIR and TIR domains also involves the conserved boxes of the TIR domain. Therefore, Novatchkova et al. speculated that both domains may function in a similar way. Like the TIR domain, SEFIR domain also mediates homologous protein-protein interactions between components involved in innate immune response against pathogen infections and adaptive immue system. Here, we focus on evolution of TIR domain-containing proteins (TICAM-1/-2,TIRAP and TLR/TOLL) and SEFIR domain-containing proteins (IL17R,CIKS/ACT1/TRAF3IP2and prokaryotic SEFIR proteins).1. The human interleukin17receptor (IL17R) family plays a critical role in inflammatory responses and contributes to the pathology of many autoimmune diseases. So far, five members, IL17RA to IL17RE, have been identified. Here, we concentrated on the IL17R evolution in chordates. There are two IL17Rs in the genome of the basal chordate amphioxus:IL17RA and IL17RD. After two rounds of whole genome duplications, these two IL17R genes expanded into five early vertebrate IL17R genes, IL17RA to IL17RE. IL17RA and IL17RD are found in most vertebrates, whereas the other three, IL17RB, ILR17RC, and IL17RE, underwent some loss in vertebrates during evolution. Our sequence and structure analyses reveal functional similarities and distinctions between the different IL17Rs and identify new functional domains, such as CPD(C-terminus Phosphorylation Domain). Based on similarity searches for IL17R-like proteins within chordate sequences, a group of IL17RE-like (IL17REL) proteins were identified from mammalians to lower vertebrates. In silico and expression analyses on the novel IL17RELs showed that this group of receptors is highly conserved across species, indicating that IL17REL may represent a unique subfamily of IL17Rs.2. CIKS (TRAF3IP2/Actl) is important for inflammatory responses and autoimmunity control through its dual functions in CD40L/BAFF and IL17signaling in mammalians. In this study, we performed comparative and evolutionary analyses of CIKSs from metazoans. Although nematode (Caenorabditis elegans) and sea urchin (Strongylocentrotus purpuratus) have IL17and IL17receptors, we found no CIKS in their genomes. The ancient CIKS-like (CIKSL) genes from the invertebrates lottia (Lottia gigantea) and amphioxus (Branchiostoma floridae) have an additional DEATH domain compared with other CIKSLs/CIKSs. Our data suggest that the ancient CIKSL evolved into early chordate CIKS possibly through gene tandem duplication and gene fission. Based on phylogenetic and synteny analyses, vertebrate CIKS genes are divided into two groups, one of which is orthologous to human CIKS and the other is paralogous. Expression analysis indicated that cephalochordata amphioxus IL17together with CIKS might play an ancient and conserved role in host defense against bacterial infections. During the evolutionary process, the CIKS genes have obtained more and more functions through cooperation with other genes.3. SEF/IL17receptor (SEFIR) domains are mainly found in IL17receptors (IL17Rs) and their adaptor proteins CIKS (connection to IKK and SAPK/JNK), which exert a host defense role in numbers of infectious diseases and promote inflammatory pathology in autoimmunity. Exploring the evolutionary pathway of SEFIR domains will provide further insight into their functions. Here, we have identified84SEFIR domain-containing proteins from more than1400prokaryotic genomes. As most SEFIR domain-containing bacterial genomes possess a single SEFIR encoding gene and the SEFIR protein domain forms homodimeric complexes like the Toll/IL1receptor (TIR) domain, the single bacterial SEFIR proteins may receive binding partners from other organisms. Through comparative and phylogenetic sequence analyses, we show that bacterial SEFIR domain is more similar to that of vertebrate CIKS than IL17R, and it possibly emerges via a lateral gene transfer (LGT) from animals. In addition, our secondary and three-dimensional structural predictions of SEFIR domains reveal that human and pathogenic bacterial SEFIR domains share similar structural and electrostatic features. Our findings provide important clues for further experimental researches on determining the functions of SEFIR proteins in pathogenic prokaryotes.4. Domain shuffling, which is an important mechanism in the evolution of multi-domain proteins, has shaped the evolutionary development of the immune system in animals. Toll and Toll-like receptors (TLRs) are a class of proteins that play a key role in the innate and adaptive immune systems. In this study, we investigated the combination of Toll/interleukin-1receptor (TIR) and leucine-rich repeat (LRR) domains of metazoan Toll/TLRs. Before Toll with both domains occurred in Cnidaria (sea anemone, Nematostella vectensis), through domain combinations, TIR-only and LRR-only proteins had already appeared in sponges (Amphimedon queenslandica). Although vertebrate-like TIR (V-TIR) domain already appeared in Cnidaria, the vertebrate-like TLR (V-TLR) with both domains appeared much later. The first combination between V-TIR domain and vertebrate-like LRR (V-LRR) domain for V-TLR may have occurred after the divergence of Cnidaria and bilateria. Then, another combination for V-TLR, a recombination of both domains, possibly occurred before or during the evolution of primitive vertebrates. Taken together, two rounds of domain combinations may thus have co-shaped the vertebrate TLRs. Our research offers a clue to chimeric TLR.5. In this study, comparative and evolutionary analyses were performed for TICAM-1, TICAM-2and TIRAP within the range of25representative species. Our data show that the origin of the TICAM-like and TIRAP-like genes may coincide with the origin of chordates (amphioxus). Several putative TICAMs and TIRAPs were identified for different chordate species. Shark is the only non-mammalian species whose genome contains a TICAM-2gene. The variations in TIC AM-1sequences might not affect their antiviral activity in vertebrates, and the variability of the important sites among vertebrate TIRAPs have affected their function. Analysis of vertebrate TIR domain structures suggested the TIR domain might interact with other molecules through a direct point-to-point mode. Together with analyses of other genes involved in the TLR signaling pathways, we speculate that TICAM-1, TICAM-2and TIRAP might have co-evolved with the TLR3/22antivirus signaling, the LPS-specific TLR4signaling and the Gram-positive bacteria-induced TLR2signaling pathways, respectively. Our results are valuable contributions to the understanding of TIC AM/TIRAP evolutional functions and may provide targets for therapeutic intervention in TLR-mediated vertebrate diseases.Based on our analyses, we propose possible scenario for the evolution of IL17R and TLR signaling pathways components, and provide clues about these genes function. Moreover, Our findings provide important clues for SEFIR-associated microbial subversion of host immunity and could set the stage for design of new therapeutic opportunities for infectious diseases.