Crystal Structure of the Lamprey Variable Lymphocyte Receptor C Reveals an Unusual Feature in Its N-Terminal Capping Module

Jawless vertebrates represented by lampreys and hagfish use variable lymphocyte receptors (VLRs) as antigen receptors to mount adaptive immune responses. VLRs generate diversity that is comparable to immunoglobulins and T-cell receptors by a gene conversion-like mechanism, which is mediated by cytosine deaminases. Currently, three types of VLRs, VLRA, VLRB, and VLRC, have been identified in lampreys. Crystal structures of VLRA and VLRB in complex with antigens have been reported recently, but no structural information is available for VLRC. Here, we present the first crystal structure of VLRC from the Japanese lamprey (Lethenteron japonicum). Similar to VLRA and VLRB, VLRC forms a typical horseshoe-like solenoid structure with a variable concave surface. Strikingly, its N-terminal cap has a long loop with limited sequence variability that protrudes toward the concave surface, which is the putative antigen-binding surface. Furthermore, as predicted previously, its C-terminal cap lacks a highly variable protruding loop that plays an important role in antigen recognition by lamprey VLRA and VLRB. Recent work suggests that VLRC+ lymphocytes in jawless vertebrates might be akin to γδ T cells in jawed vertebrates. Structural features of lamprey VLRC described here suggest that it may recognize antigens in a unique manner.     

Immune Related Genes Underpin the Evolution of Adaptive Immunity in Jawless Vertebrates

The study of immune related genes in lampreys and hagfish provides a unique perspective on the evolutionary genetic underpinnings of adaptive immunity and the evolution of vertebrate genomes. Separated from their jawed cousins at the stem of the vertebrate lineage, these jawless vertebrates have many of the gene families and gene regulatory networks associated with the defining morphological and physiological features of vertebrates. These include genes vital for innate immunity, inflammation, wound healing, protein degradation, and the development, signaling and trafficking of lymphocytes. Jawless vertebrates recognize antigen by using leucine-rich repeat (LRR) based variable lymphocyte receptors (VLRs), which are very different from the immunoglobulin (Ig) based T cell receptor (TCR) and B cell receptor (BCR) used for antigen recognition by jawed vertebrates. The somatically constructed VLR genes are expressed in monoallelic fashion by T-like and B-like lymphocytes. Jawless and jawed vertebrates thus share many of the genes that provide the molecular infrastructure and physiological context for adaptive immune responses, yet use entirely different genes and mechanisms of combinatorial assembly to generate diverse repertoires of antigen recognition receptors.     

日本七鳃鳗(Lampetra japonica)VLRB的克隆表达及单克隆抗体制备

七鳃鳗(Lampetra japonica)和盲鳗(Hyperotreti)作为现存的无颌类脊椎动物的代表,其适应性免疫系统中的受体分子与哺乳动物的抗原受体分子不同,这种独特的受体分子称为可变淋巴细胞受体VLRs(Variable lym-phocyte receptors)。目前VLRs分为3类,分别是VLRA、VLRB、VLRC,而VLRB由七鳃鳗类B淋巴细胞产生,是其体液免疫中主要成分,与IgM结构和功能类似。文章对日本七鳃鳗VLRB基因保守的C末端进行克隆、原核表达和重组蛋白纯化后,免疫Balb/c小鼠,通过细胞融合及间接酶联免疫吸附实验(Enzyme-linked immu-nosorbent assay,ELISA)筛选技术得到针对VLRB保守区的单克隆抗体细胞株。将杂交瘤细胞接种小鼠腹腔得到大量的单抗腹水,经Protein G亲和纯化后的单抗进行ELISA与Western blotting检测。经ELISA检测抗体效价为1:40000。Western blotting结果显示该单克隆抗体能够特异的检测重组VLRB蛋白及七鳃鳗血清中分泌型VLRB。流式细胞实验证明该单抗能特异识别七鳃鳗类淋巴细胞表面表达的膜型VLRB。VLRB单克隆抗体的成功制备和建株,为研究日本七鳃鳗基于VLR的适应性免疫系统提供了重要的工具。     

Structural diversity of the hagfish variable lymphocyte receptors

Variable lymphocyte receptors (VLRs) are recently discovered leucine-rich repeat (LRR) family proteins that mediate adaptive immune responses in jawless fish. Phylogenetically it is the oldest adaptive immune receptor and the first one with a non-immunoglobulin fold. We present the crystal structures of one VLR-A and two VLR-B clones from the inshore hagfish. The hagfish VLRs have the characteristic horseshoe-shaped structure of LRR family proteins. The backbone structures of their LRR modules are highly homologous, and the sequence variation is concentrated on the concave surface of the protein. The conservation of key residues suggests that our structures are likely to represent the LRR structures of the entire repertoire of jawless fish VLRs. The analysis of sequence variability, prediction of protein interaction surfaces, amino acid composition analysis, and structural comparison with other LRR proteins suggest that the hypervariable concave surface is the most probable antigen binding site of the VLR.     

七鳃鳗鳃黏膜免疫系统类淋巴细胞免疫应答遗传基础

近年来,在无颌类脊椎动物七鳃鳗体内发现了以可变淋巴细胞受体(Variable lymphocyte receptors, VLR)为基础的抗原识别机制。为揭示七鳃鳗鳃黏膜免疫系统中类淋巴细胞适应性免疫应答的遗传基础,探索无颌类与有颌类脊椎动物在适应性免疫应答机制上的进化关系,本文构建了日本七鳃鳗(Lampetra japonica)鳃囊组织免疫前后cDNA文库并进行了高通量转录组测序及分析。通过对组装得到的88 525个独立基因(Unigene)进行功能注释,分别有21 704和9769个unigene在GO(Gene Ontology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库得到注释。999个unigene参与免疫系统的多个通路,其中184个与高等脊椎动物TCR(T cell receptor)和BCR(B cell receptor)信号通路的51个分子具有较高的同源关系,说明七鳃鳗体内存在高等脊椎动物适应性免疫应答信号通路的相关分子。本文还发现5个VLRA、7个VLRB和4个VLRC分子,说明七鳃鳗鳃黏膜免疫组织内至少分布3种类淋巴细胞亚群。实时荧光定量PCR结果显示,Lck、Fyn和Zap70基因在免疫激发后表达量显著上调,而Syk、Btk和Blnk基因表达没有显著变化,说明七鳃鳗鳃组织受到抗原刺激后,类似T淋巴细胞的信号转导途径被激活。本研究初步证明,尽管无颌类和有颌类脊椎动物的适应性免疫系统在抗原识别机制上存在不同,但具有共同的遗传基础。研究结果为探讨七鳃鳗VLRA⁺、VLRB⁺和VLRC⁺淋巴细胞免疫应答信号传导过程提供了有价值的线索。     

新型靶向药物研究的重要分子：可变淋巴细胞受体

自从2004年可变淋巴细胞受体（variable lymphocyte receptor, VLR）在七鳃鳗中首次发现以来,因VLR能识别多种抗原、具有简单的分子结构、物理化学性质稳定、对蛋白质以及聚糖的高亲和力和强特异性等多方面优点,学术界对于VLR的研究和改造十分火热。近年来,随着研究的不断深入,由VLR构建的重组分子广泛用于各领域的基础研究和应用研究。本文对近年来VLR面向下游的最新应用研究进行综述。在肿瘤研究中,VLR可特异性地精准识别碳水化合物,并能够区分只有1个官能团不同的多糖,可作为灵敏抗多糖试剂,用于识别肿瘤细胞上独特的糖复合物,为肿瘤的靶向治疗提供新的策略;VLR也可与其他经典的治疗方法进行结合。例如,将嵌合抗原受体进行改造,经过改造后可表达一种合成受体。这种合成受体可将T细胞的细胞靶向杀伤作用重新定位到所选择的靶点;VLR经重组改造后,也可用于改良分离纯化试剂或在水生生物疾病上发挥作用。这些新开发的VLR的作用有可能作为新型的识别、诊断和治疗试剂。本文将从VLR多样性产生的机制、VLR与糖生物学和生物医药研究上的关系、VLR用于改良分离纯化试剂的作用、VLR在水生生物疾病研究等方面进行阐述,以期为VLR用于疾病药物研发等相关应用提供参考。     

Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47

SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1 (SHPS-1 or SIRPα/BIT) is an immunoglobulin (Ig) superfamily transmembrane receptor and a member of the signal regulatory protein (SIRP) family involved in cell-cell interaction. SHPS-1 binds to its ligand CD47 to relay an inhibitory signal for cellular responses, whereas SIRPβ, an activating member of the same family, does not bind to CD47 despite sharing a highly homologous ligand-binding domain with SHPS-1. To address the molecular basis for specific CD47 recognition by SHPS-1, we present the crystal structure of the ligand-binding domain of murine SHPS-1 (mSHPS-1). Folding topology revealed that mSHPS-1 adopts an I2-set Ig fold, but its overall structure resembles IgV domains of antigen receptors, although it has an extended loop structure (C′E loop), which forms a dimer interface in the crystal. Site-directed mutagenesis studies of mSHPS-1 identified critical residues for CD47 binding including sites in the C′E loop and regions corresponding to complementarity-determining regions of antigen receptors. The structural and functional features of mSHPS-1 are consistent with the human SHPS-1 structure except that human SHPS-1 has an additional β-strand D. These results suggest that the variable complementarity-determining region-like loop structures in the binding surface of SHPS-1 are generally required for ligand recognition in a manner similar to that of antigen receptors, which may explain the diverse ligand-binding specificities of SIRP family receptors.     

Pseudomonas evades immune recognition of flagellin in both mammals and plants

The building blocks of bacterial flagella, flagellin monomers, are potent stimulators of host innate immune systems. Recognition of flagellin monomers occurs by flagellin-specific pattern-recognition receptors, such as Toll-like receptor 5 (TLR5) in mammals and flagellin-sensitive 2 (FLS2) in plants. Activation of these immune systems via flagellin leads eventually to elimination of the bacterium from the host. In order to prevent immune activation and thus favor survival in the host, bacteria secrete many proteins that hamper such recognition. In our search for Toll like receptor (TLR) antagonists, we screened bacterial supernatants and identified alkaline protease (AprA) of Pseudomonas aeruginosa as a TLR5 signaling inhibitor as evidenced by a marked reduction in IL-8 production and NF-κB activation. AprA effectively degrades the TLR5 ligand monomeric flagellin, while polymeric flagellin (involved in bacterial motility) and TLR5 itself resist degradation. The natural occurring alkaline protease inhibitor AprI of P. aeruginosa blocked flagellin degradation by AprA. P. aeruginosa aprA mutants induced an over 100-fold enhanced activation of TLR5 signaling, because they fail to degrade excess monomeric flagellin in their environment. Interestingly, AprA also prevents flagellin-mediated immune responses (such as growth inhibition and callose deposition) in Arabidopsis thaliana plants. This was due to decreased activation of the receptor FLS2 and clearly demonstrated by delayed stomatal closure with live bacteria in plants. Thus, by degrading the ligand for TLR5 and FLS2, P. aeruginosa escapes recognition by the innate immune systems of both mammals and plants.     

Crystal structure of the C‐terminal domain of mouse TLR9

Toll‐like receptors (TLRs) are important pattern recognition receptors that function in innate immunity. Elucidating the structure and signaling mechanisms of TLR9, a sensor of foreign and endogenous DNA, is essential for understanding its key role in immunity against microbial pathogens as well as in autoimmunity. Abundant evidence suggests that the TLR9‐CTD (C‐terminal domain) by itself is capable of DNA binding and signaling. The crystal structure of unliganded mouse TLR9‐CTD is presented. TLR9‐CTD exhibits one unique feature, a cluster of stacked aromatic and arginine side chains on its concave face. Overall, its structure is most related to the TLR8‐CTD, suggesting a similar mode of ligand binding and signaling. Proteins 2014; 82:2874–2878. © 2014 Wiley Periodicals, Inc.     

Two nonadjacent regions in enteroaggregative Escherichia coli flagellin are required for activation of toll-like receptor 5

Flagellin is the major structural protein of the flagella of Gram-negative bacteria. Recent work has demonstrated that flagellin is a potent trigger of innate immune responses in a number of eukaryotic cells and organisms, including both mammals and plants. In several different human epithelial cell lines, this innate immune response involves toll-like receptor 5 (TLR5). The mechanisms by which flagellin activates TLR5 and the importance of this interaction in other model systems of flagellin-induced inflammation remain unknown. In this work, random and site-directed mutagenesis of the inflammatory flagellin from enteroaggregative Escherichia coli identified two regions in the conserved D1 domain that are required for interleukin-8 release and TLR5 activation. In contrast, large regions of the variable domain could be excised without reducing the inflammatory activity. In addition, regions of the protein analogous to epitopes that trigger innate immune responses in plants are not involved in Caco-2 flagellin responses. These results highlight the complexity of the interaction between bacterial flagellin and its eukaryotic recognition partners and provide the basis for further studies to characterize the innate immune response to flagellin.     

一种蛋白质B细胞表位展示系统的构建及验证

目的:建立一种能够有效展示蛋白质B细胞表位的载体系统,以用于表位特异性抗体的制备和表位疫苗的设计。方法:选用抗体的可变区作为蛋白质B细胞表位展示的骨架蛋白,B细胞表位的展示部位为CDR3区。全基因合成骨架蛋白基因,通过重叠PCR将B细胞表位编码序列插入到骨架蛋白基因中,原核表达目的蛋白,利用Sephacryl S-100层析柱进行蛋白纯化,用纯化的蛋白按常规方法免疫小鼠,采用ELISA法检测免疫血清的滴度及特异性,通过Western blot和间接免疫荧光技术进一步验证免疫血清对目的蛋白的识别。结果:成功构建了3种表位展示蛋白,均表现出了很好的抗原性,表位展示蛋白免疫血清具有较好的特异性,能够特异识别所展示的B细胞表位。结论:抗体可变区作为骨架蛋白能够很好地展示B细胞表位,免疫小鼠后获得的免疫血清表现出了较好的特异性。     

Evolutionary Analysis for Functional Divergence of the Toll-Like Receptor Gene Family and Altered Functional Constraints

The Toll-like receptor (TLR) gene family consists of type 1 transmembrane receptors, which play essential roles in both innate immunity and adaptive immune response by ligand recognition and signal transduction. Using all available vertebrate TLR protein sequences, we inferred the phylogenetic tree and then characterized critical amino acid residues for functional divergence by detecting altered functional constraints after gene duplications. We found that the extracellular domain of TLR genes showed higher functional divergence than that of the cytoplasmic domain, particularly in the region between leucine-rich repeat (LRR) 10 and LRR 15 of TLR 4. Our finding supports the concept that sequence evolution in the extracellular domain may be responsible for the broad diversity of TLR ligand-binding affinity, providing a testable hypothesis for potential targets that could be verified by further experimentation.     

Extracellular HSP70 binding to surface receptors present on antigen presenting cells and endothelial/epithelial cells

Extracellular HSP70 has been found to participate in both innate and adaptive immune responses. However, little is known about the molecular mechanisms that mediate this process. Previous reports suggest that HSP70 interacts with antigen presenting cells (APC) through a plethora of surface receptors. In this study, we have examined the relative binding of potential HSP70 receptors and found high affinity binding to LOX-1 but not other structures with a role in HSP70-APC interactions such as LRP/CD91, CD40, TLR2, TLR4 or another c-type lectin family member (DC-SIGN) closely related to LOX-1. In addition to APC, HSP70 can avidly bind to non-APC cell lines, especially those from epithelial or endothelial background.     

Human CD4+ T cells express TLR5 and its ligand flagellin enhances the suppressive capacity and expression of FOXP3 in CD4+CD25+ T regulatory cells

Germline encoded pattern recognition receptors, such as TLRs, provide a critical link between the innate and adaptive immune systems. There is also evidence to suggest that pathogen-associated molecular patterns may have the capacity to modulate immune responses via direct effects on CD4+ T cells. Given the key role of both CD4+CD25+ T regulatory (Treg) cells and the TLR5 ligand flagellin in regulating mucosal immune responses, we investigated whether TLR5 may directly influence T cell function. We found that both human CD4+CD25+ Treg and CD4+CD25- T cells express TLR5 at levels comparable to those on monocytes and dendritic cells. Costimulation of effector T cells with anti-CD3 and flagellin resulted in enhanced proliferation and production of IL-2, at levels equivalent to those achieved by costimulation with CD28. In contrast, costimulation with flagellin did not break the hyporesponsiveness of CD4+CD25+ Treg cells, but rather, potently increased their suppressive capacity and enhanced expression of FOXP3. These observations suggest that, in addition to their APC-mediated indirect effects, TLR ligands have the capacity to directly regulate T cell responses and modulate the suppressive activity of Treg cells.     

Escherichia coli‐based cell free production of flagellin and ordered flagellin display on virus‐like particles

Bacterial flagellin has been explored as a potential vaccine adjuvant for enhancing immune responses. In this article, we describe Escherichia coli‐based cell‐free protein synthesis (CFPS) as a method to rapidly produce soluble phase 1 flagellin (FliC) protein from Salmonella typhimurium. The yield was about 300 µg/mL and the product had much higher affinity for the TLR5 receptor (EC50 = 2.4 ± 1.4 pM) than previously reported. The flagellin coding sequence was first optimized for cell‐free expression. We then found that the D0 domain at the C‐terminus of flagellin was susceptible to proteolytic degradation in the CFPS system. Proteolysis was reduced by protease inhibitors, the use of protease‐deficient cell extracts or deletion of the flagellin D0 domain. A human Toll‐Like Receptor 5 (hTLR5)‐specific bioactivity analysis of purified flagellin demonstrated that, although the D0 domain is far from the TLR5 recognition region, it is important for flagellin bioactivity. We next incorporated a non‐natural amino acid displaying an alkyne moiety into flagellin using the CFPS system and attached flagellin to hepatitis B core virus‐like particles (VLPs) using bioorthogonal azide‐alkyne cycloaddition reactions. The ordered and oriented VLP display of flagellin increased its specific TLR5 stimulation activity by approximately 10‐fold. Biotechnol. Bioeng. 2013; 110: 2073–2085. © 2013 Wiley Periodicals, Inc.     

Molecular evolution of vertebrate Toll-like receptors: evolutionary rate difference between their leucine-rich repeats and their TIR domains

Toll-like receptors (TLRs) that initiate an innate immune response contain an extracellular leucine rich repeat (LRR) domain and an intracellular Toll IL-receptor (TIR) domain. There are fifteen different TLRs in vertebrates. The LRR domains, which adopt a solenoid structure, usually have higher rates of evolution than do the TIR globular domains. It is important to understand the molecular evolution and functional roles of TLRs from this standpoint. Both pairwise genetic distances and Ka/Ks's (the ratios between non synonymous and synonymous substitution rates) were compared between the LRR domain and the TIR domain of 366 vertebrate TLRs from 96 species (from fish to primates). In fourteen members (TLRs 1, 2, 3, 4, 5, 6, 7, 8, 9, 11/12, 13, 14, 21, and 22/23) the LRR domains evolved significantly more rapidly than did the corresponding TIR domains. The evolutionary rates of the LRR domains are significantly different among these members; LRR domains from TLR3 and TLR7 from primates to fishes have the lowest rate of evolution. In contrast, the fifteenth member, TLR10, shows no significant differences; its TIR domain is not highly conserved. The present results suggest that TLR10 may have a different function in signaling from those other members and that a higher conservation of TLR3 and TLR7 may reflect a more ancient mechanism and/or structure in the innate immune response system. Gene conversions are suggested to have occurred in platypus TLR6 and TLR10. This study provides new insight about structural and functional diversification of vertebrate TLRs.     

How Location Governs Toll-Like Receptor Signaling

Toll-like receptors (TLRs) are a family of innate immune system receptors responsible for recognizing conserved pathogen-associated molecular patterns (PAMPs). PAMP binding to TLRs initiates intracellular signaling pathways that lead to the upregulation of a variety of costimulatory molecules and the synthesis and secretion of various cytokines and interferons by cells of the innate immune system. TLR-induced innate immune responses are a prerequisite for the generation of most adaptive immune responses, and in the case of B cells, TLRs directly regulate signaling from the antigen-specific B-cell receptor. The outcome of TLR signaling is determined, in part, by the cells in which they are expressed and by the selective use of signaling adaptors. Recent studies suggest that, in addition, both the ligand recognition by TLRs and the functional outcome of ligand binding are governed by the subcellular location of the TLRs and their signaling adaptors. In this review we describe what is known about the intracellular trafficking and compartmentalization of TLRs in innate system's dendritic cells and macrophages and in adaptive system's B cells, highlighting how location regulates TLR function.     

临床诊断与治疗的新工具——可变淋巴细胞受体

单克隆抗体(Monoclonal antibody, mAb)在癌症以及自身免疫等疾病的诊断与治疗中得到广泛应用, 并且取得了重大进展。当今应用于临床的单克隆抗体是在免疫球蛋白的基础上进行改造研发而得。然而近期发现的无颌类脊椎动物的特异性抗原受体-可变淋巴细胞受体(Variable lymphocyte receptor, VLR), 为抗体类试剂或药物的研发提供了新的视角。与免疫球蛋白(Immunoglobulins, Ig)相比, VLR与抗原结合的特异性、亲和力及稳定性都优于Ig类抗体, 并且抗原特异性单克隆VLR的制备技术日趋成熟。因此, VLR在临床诊断和治疗中具有更高的应用价值, 并可能成为新一代的抗体药物。文章就VLR的基本特征、制备方法及其应用前景进行综述, 为实现VLR在临床诊断与治疗等领域中的应用提供有益参考。