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Pattern Recognition Receptors (PRRs, [110]) (nomenclature as agreed by NC-IUPHAR sub-committee on Pattern Recognition Receptors, [20]) participate in the innate immune response to microbial agents, the stimulation of which leads to activation of intracellular enzymes and regulation of gene transcription. PRRs express multiple leucine-rich regions to bind a range of microbially-derived ligands, termed PAMPs or pathogen-associated molecular patterns or endogenous ligands, termed DAMPS or damage-associated molecular patterns. These include peptides, carbohydrates, peptidoglycans, lipoproteins, lipopolysaccharides, and nucleic acids. PRRs include both cell-surface and intracellular proteins. PRRs may be divided into signalling-associated members, identified here, and endocytic members, the function of which appears to be to recognise particular microbial motifs for subsequent cell attachment, internalisation and destruction. Some are involved in inflammasome formation, and modulation of IL-1β cleavage and secretion, and others in the initiation of the type I interferon response. PRRs included in the Guide To PHARMACOLOGY are:Catalytic PRRs (see links below this overview)Toll-like receptors (TLRs)Nucleotide-binding oligomerization domain, leucine-rich repeat containing receptors (NLRs, also known as NOD (Nucleotide oligomerisation domain)-like receptors)RIG-I-like receptors (RLRs)Caspase 4 and caspase 5 Non-catalytic PRRsAbsent in melanoma (AIM)-like receptors (ALRs)C-type lectin-like receptors (CLRs)Other pattern recognition receptorsAdvanced glycosylation end-product specific receptor (RAGE)

The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15541. Catalytic receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, ion channels, nuclear hormone receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.

Pattern Recognition Receptors (PRRs, [104]) (nomenclature as agreed by NC-IUPHAR sub-committee on Pattern Recognition Receptors, [18]) participate in the innate immune response to microbial agents, the stimulation of which leads to activation of intracellular enzymes and regulation of gene transcription. PRRs express multiple leucine-rich regions to bind a range of microbially-derived ligands, termed PAMPs or pathogen-associated molecular patterns or endogenous ligands, termed DAMPS or damage-associated molecular patterns. These include peptides, carbohydrates, peptidoglycans, lipoproteins, lipopolysaccharides, and nucleic acids. PRRs include both cell-surface and intracellular proteins. PRRs may be divided into signalling-associated members, identified here, and endocytic members, the function of which appears to be to recognise particular microbial motifs for subsequent cell attachment, internalisation and destruction. Some are involved in inflammasome formation, and modulation of IL-1β cleavage and secretion, and others in the initiation of the type I interferon response. PRRs included in the Guide To PHARMACOLOGY are:Catalytic PRRs (see links below this overview)Toll-like receptors (TLRs)Nucleotide-binding oligomerization domain, leucine-rich repeat containing receptors (NLRs, also known as NOD (Nucleotide oligomerisation domain)-like receptors)RIG-I-like receptors (RLRs)Caspase 4 and caspase 5 Non-catalytic PRRsAbsent in melanoma (AIM)-like receptors (ALRs)C-type lectin-like receptors (CLRs)Other pattern recognition receptorsAdvanced glycosylation end-product specific receptor (RAGE)

Summary Zoonotic pathogens, such as COVID-19, reside in animal hosts before jumping species to infect humans. The Carnivora, like mink, carry many zoonoses, yet how diversity in host immune genes across species affect pathogen carriage is poorly understood. Here, we describe a progressive evolutionary downregulation of pathogen-sensing inflammasome pathways in Carnivora. This includes the loss of nucleotide-oligomerization domain leucine-rich repeat receptors (NLRs), acquisition of a unique caspase-1/-4 effector fusion protein that processes gasdermin D pore formation without inducing rapid lytic cell death, and the formation of a caspase-8 containing inflammasome that inefficiently processes interleukin-1β. Inflammasomes regulate gut immunity, but the carnivorous diet has antimicrobial properties that could compensate for the loss of these immune pathways. We speculate that the consequences of systemic inflammasome downregulation, however, can impair host sensing of specific pathogens such that they can reside undetected in the Carnivora., Graphical abstract, Highlights • Carnivorans lack key NLRs and express a unique caspase-1/-4 hybrid protein • This protein is defective in mediating activation of common inflammasome pathways • What little activity occurs is driven by caspase-8, rather than caspase-1/-4, Species of the order Carnivora have evolutionarily acquired the expression of a unique caspase-1/-4 hybrid protein. Digby et al. show that this protein is a poor mediator of NLRP3- and caspase-4-dependent inflammasome activation. This downregulation in inflammasome pathways could impair pathogen detection and facilitate transmission of zoonotic infections.

Zoonotic infections, such as COVID-19, reside in animal hosts before jumping species to humans. The Carnivora, like mink, carry many zoonoses yet how diversity in host immune genes across species impact upon pathogen carriage are poorly understood. Here we describe a progressive evolutionary downregulation of pathogen sensing inflammasome pathways in Carnivora. This includes the loss of nucleotide-oligomerisation domain leucine rich repeat receptors (NLRs), acquisition of a unique caspase-1/-4 effector fusion protein that processes gasdermin D pore formation without inducing lytic cell death and the formation of an NLRP3-caspase-8 containing inflammasome that inefficiently processes interleukin-1β (IL-1β). Inflammasomes regulate gut immunity, but the carnivorous diet is antimicrobial suggesting a tolerance to the loss of these immune pathways. The consequences of systemic inflammasome downregulation, however, can reduce the host sensing of specific pathogens such that they can reside undetected in the Carnivora.

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Pattern Recognition Receptors (PRRs, [83]) (nomenclature as agreed by NC-IUPHAR sub-committee on Pattern Recognition Receptors, [15]) participate in the innate immune response to microbial agents, the stimulation of which leads to activation of intracellular enzymes and regulation of gene transcription. PRRs express multiple leucine-rich regions to bind a range of microbially-derived ligands, termed PAMPs or pathogen-associated molecular patterns or endogenous ligands, termed DAMPS or damage-associated molecular patterns. These include peptides, carbohydrates, peptidoglycans, lipoproteins, lipopolysaccharides, and nucleic acids. PRRs include both cell-surface and intracellular proteins. PRRs may be divided into signalling-associated members, identified here, and endocytic members, the function of which appears to be to recognise particular microbial motifs for subsequent cell attachment, internalisation and destruction. Some are involved in inflammasome formation, and modulation of IL-1β cleavage and secretion, and others in the initiation of the type I interferon response. PRRs included in the Guide To PHARMACOLOGY are:Catalytic PRRs (see links below this overview)Toll-like receptors (TLRs)Nucleotide-binding oligomerization domain, leucine-rich repeat containing receptors (NLRs, also known as NOD (Nucleotide oligomerisation domain)-like receptors)RIG-I-like receptors (RLRs)Caspase 4 and caspase 5 Non-catalytic PRRsAbsent in melanoma (AIM)-like receptors (ALRs)C-type lectin-like receptors (CLRs)Other pattern recognition receptorsAdvanced glycosylation end-product specific receptor (RAGE)

Since the discovery of Toll, in the fruit fly Drosophila melanogaster, as the first described pattern recognition receptor (PRR) in 1996, many families of these receptors have been discovered and characterized. PRRs play critically important roles in pathogen recognition to initiate innate immune responses that ultimately link to the generation of adaptive immunity. Activation of PRRs leads to the induction of immune and inflammatory genes, including proinflammatory cytokines and chemokines. It is increasingly clear that many PRRs are linked to a range of inflammatory, infectious, immune, and chronic degenerative diseases. Several drugs to modulate PRR activity are already in clinical trials and many more are likely to appear in the near future. Here, we review the different families of mammalian PRRs, the ligands they recognize, the mechanisms of activation, their role in disease, and the potential of targeting these proteins to develop the anti-inflammatory therapeutics of the future.

We report a 12-year-old girl who presented with bilateral granulomatous anterior uveitis accompanied by boggy arthritis of knee and ankle joints, intermittent fever, and nodular skin rash. She was diagnosed with sporadic Blau syndrome (early-onset sarcoidosis) based on above clinical signs and presence of non-necrotising granuloma on iris biopsy. DNA sequencing revealed a previously unreported heterozygous mutation consisting of a G>A transition in exon 4 of the NOD2 gene. This resulted in a glutamic acid to lysine substitution in helical domain 2 of the nucleotide binding and oligomerization (NACHT) region, possibly reducing efficiency of auto-inhibition in NOD2 signaling. Interestingly, the ocular inflammation resolved completely following therapeutic vitrectomy in both eyes whereas the systemic symptoms of fever and arthritis continued to wax and wane while on treatment with oral methotrexate and corticosteroids.

The inflammasome is a multi-molecular platform crucial to the induction of an inflammatory response to cellular danger. Recognition in the cytoplasm of endogenously and exogenously derived ligands initiates conformational change in sensor proteins, such as NLRP3, that permits the subsequent rapid recruitment of adaptor proteins, like ASC, and the resulting assembly of a large-scale inflammatory signalling platform. The assembly process is driven by sensor-sensor interactions as well as sensor-adaptor and adaptor-adaptor interactions. The resulting complex, which can reach diameters of around 1 micron, has a variable composition and stoichiometry. The inflammasome complex functions as a platform for the proximity induced activation of effector caspases, such as caspase-1 and caspase-8. This ultimately leads to the processing of the inflammatory cytokines pro-IL1β and pro-IL18 into their active forms, along with the cleavage of Gasdermin D, a key activator of cell death via pyroptosis.

Highlights • NOD2 SNPs that cause Blau syndrome cluster in two regions of the NACHT. • The ATP/Mg2+ binding pocket cluster are likely to dysregulate ATP hydrolysis. • SNPs in helical domain 1 are predicted to influence receptor autoinhibition. • Complementary mutations in NOD1 do not all result in hyperactivation., Understanding how single nucleotide polymorphisms (SNPs) lead to disease at a molecular level provides a starting point for improved therapeutic intervention. SNPs in the innate immune receptor nucleotide oligomerisation domain 2 (NOD2) can cause the inflammatory disorders Blau Syndrome (BS) and early onset sarcoidosis (EOS) through receptor hyperactivation. Here, we show that these polymorphisms cluster into two primary locations: the ATP/Mg2+-binding site and helical domain 1. Polymorphisms in these two locations may consequently dysregulate ATP hydrolysis and NOD2 autoinhibition, respectively. Complementary mutations in NOD1 did not mirror the NOD2 phenotype, which indicates that NOD1 and NOD2 are activated and regulated by distinct methods.

Pathogen recognition by nucleotide-binding oligomerization domain-like receptor (NLR) results in the formation of a macromolecular protein complex (inflammasome) that drives protective inflammatory responses in the host. It is thought that the number of inflammasome complexes forming in a cell is determined by the number of NLRs being activated, with each NLR initiating its own inflammasome assembly independent of one another; however, we show here that the important foodborne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) simultaneously activates at least two NLRs, whereas only a single inflammasome complex is formed in a macrophage. Both nucleotide-binding domain and leucine-rich repeat caspase recruitment domain 4 and nucleotide-binding domain and leucine-rich repeat pyrin domain 3 are simultaneously present in the same inflammasome, where both NLRs are required to drive IL-1β processing within the Salmonella-infected cell and to regulate the bacterial burden in mice. Superresolution imaging of Salmonella-infected macrophages revealed a macromolecular complex with an outer ring of apoptosis-associated speck-like protein containing a caspase activation and recruitment domain and an inner ring of NLRs, with active caspase effectors containing the pro-IL-1β substrate localized internal to the ring structure. Our data reveal the spatial localization of different components of the inflammasome and how different members of the NLR family cooperate to drive robust IL-1β processing during Salmonella infection.

Nucleotide-binding oligomerization domain–like receptors (NLRs) detect pathogens and danger-associated signals within the cell. Salmonella enterica serovar Typhimurium, an intracellular pathogen, activates caspase-1 required for the processing of the proinflammatory cytokines, pro–IL-1β and pro–IL-18, and pyroptosis. In this study, we show that Salmonella infection induces the formation of an apoptosis-associated specklike protein containing a CARD (ASC)–Caspase-8–Caspase-1 inflammasome in macrophages. Caspase-8 and caspase-1 are recruited to the ASC focus independently of one other. Salmonella infection initiates caspase-8 proteolysis in a manner dependent on NLRC4 and ASC, but not NLRP3, caspase-1 or caspase-11. Caspase-8 primarily mediates the synthesis of pro-IL-1β, but is dispensable for Salmonella-induced cell death. Overall, our findings highlight that the ASC inflammasome can recruit different members of the caspase family to induce distinct effector functions in response to Salmonella infection.

Contains fulltext : 177770.pdf (Publisher’s version ) (Open Access) Bicomponent pore-forming leukocidins are a family of potent toxins secreted by Staphylococcus aureus, which target white blood cells preferentially and consist of an S- and an F-component. The S-component recognizes a receptor on the host cell, enabling high-affinity binding to the cell surface, after which the toxins form a pore that penetrates the cell lipid bilayer. Until now, six different leukocidins have been described, some of which are host and cell specific. Here, we identify and characterise a novel S. aureus leukocidin; LukPQ. LukPQ is encoded on a 45 kb prophage (PhiSaeq1) found in six different clonal lineages, almost exclusively in strains cultured from equids. We show that LukPQ is a potent and specific killer of equine neutrophils and identify equine-CXCRA and CXCR2 as its target receptors. Although the S-component (LukP) is highly similar to the S-component of LukED, the species specificity of LukPQ and LukED differs. By forming non-canonical toxin pairs, we identify that the F-component contributes to the observed host tropism of LukPQ, thereby challenging the current paradigm that leukocidin specificity is driven solely by the S-component.

The immune system is an evolutionarily ancient network that invokes the activation of specific cellular changes and events in response to danger. The innate immune system represents a conserved and repetitive set of responses to danger in which the nature of the response is identical, each time the same threat is encountered. In contrast, the adaptive immune response, which is found in vertebrates, provides a specific response to each threat and induces protective memory to enable rapid and efficient clearance of danger. Proper function of the adaptive response requires effective recognition of threat by the innate immune system. Inappropriate activation of the immune system, however, is often associated with the development of long-term chronic inflammatory disorders. This book provides an overview of the key components and the key molecular players and processes involved in the functioning of the innate immune system. Here, we begin with a brief tour of the historical aspects of innate immunity before providing a basic introduction to the different cell types and molecules involved. This is followed with a brief overview of the mucosa-associated immune response and an introduction to homeostatic processes that have also been shown to contribute to the innate immune response.

Activation of the innate immune system is an integral part of disease progression. It is critical to the resolution and clearance of many disease states, particularly those with exogenous and/or infectious elements. The innate immune response is also central to the establishment and progression of autoimmune, autoinflammatory, and chronic disease. Earlier sections of this book have provided insights into the compositional and functional makeup of the innate immune response, as well as highlighting how different components come together to facilitate a coordinated response to threats and dangers. The importance of understanding how the innate immune response helps combat infection is crucial. It has also become apparent that to successfully manage and treat many of the diseases in the developed world also requires an understanding of innate immunity and inflammation. In this section, I provide a brief introduction to the connections between the innate immune response and chronic inflammatory conditions, such as rheumatoid arthritis, atherosclerosis, and inflammatory bowel disease.

The inflammasome is a multi-molecular platform crucial to the induction of an inflammatory response to cellular danger. Recognition in the cytoplasm of endogenously and exogenously derived ligands initiates conformational change in sensor proteins, such as NLRP3, that permits the subsequent rapid recruitment of adaptor proteins, like ASC, and the resulting assembly of a large-scale inflammatory signalling platform. The assembly process is driven by sensor-sensor interactions as well as sensor-adaptor and adaptor-adaptor interactions. The resulting complex, which can reach diameters of around 1 micron, has a variable composition and stoichiometry. The inflammasome complex functions as a platform for the proximity induced activation of effector caspases, such as caspase-1 and caspase-8. This ultimately leads to the processing of the inflammatory cytokines pro-IL1β and pro-IL18 into their active forms, along with the cleavage of Gasdermin D, a key activator of cell death via pyroptosis.

Activation of the innate immune response is a conserved response upon repeat exposure to endogenous and exogenous danger signals. These responses can therefore be broadly considered through a relatively concise set of core functions and effector molecules. It is these elements that form the focus of this section. Here, I provide a basic introduction to the major types of cytokine secreted in response to stimulation of the innate immune system; introduce acute phase proteins and the nature of the acute phase response; provide an overview of a number of the key enzymatic cascades involved in the innate immune response; and discuss the major types of cell death than can result from innate immune activation. These include apoptosis, necrosis, necroptosis, and pyroptosis. Together this section provides a broad overview of the major innate immune effector mechanisms and the cellular outputs that are required to initiate and activate them.

The previous sections have provided an overview of the main functional components, the response systems, and the effector mechanisms of the innate immune system. This has included, amongst others, the immune cells, the complement system, inflammatory mediators, pattern recognition receptors, cell death, cytokines, and chemokines. These elements were previously introduced in isolation. However, the innate response to infection, damage, or danger does not occur in an isolated manner. Many immune stimuli will activate a variety of different response pathways and induce the activation of a multitude of effector functions. In this section, I will look in more depth at some of the key mechanisms that combine the activation of the immune response and the induction of effector molecules to clear the danger and initiate resolution and the restoration of homeostatic balance. The primary focus will be upon pathways involving pattern recognition processes as because these are both fundamental and integral to the whole innate immune response. In particular I will describe the extracellular and intracellular detection of lipopolysaccharide, the production of IL-1β following activation of the inflammasome, and the responses to infection with the bacterium Salmonella and the virus Influenza A .

It is true to say that the innate and adaptive immune systems have their own distinct elements. However, it is not appropriate to view them as being completely functionally independent of one another. There is, without question, an intricate and complex relationship between the two systems that directly influences the overall nature and success of the immune response. Many other resources have provided a comprehensive coverage of the adaptive immune response, particularly in relation to the functionality of B and T cells. In this section, I shall briefly highlight some of the key processes by which the innate immune system can communicate with, influence, and affect the performance of the adaptive response. This includes by regulating transcription of major histocompatibility complex genes, by utilizing components of the complement cascade and the process of autophagy to influence B- and T-cell functions, through the action of dendritic cells and the provision of adjuvant function in the process of vaccination.

The β subunits of voltage-gated sodium (Nav) channels possess an extracellular immunoglobulin (Ig) domain that is related to the L1 family of cell-adhesion molecules (CAMs). Here we show that in HEK293 cells, secretion of the free Ig domain of the β3 subunit is reduced significantly when it is coexpressed with the full-length β3 and β1 subunits but not with the β2 subunit. Using immunoprecipitation, we show that the β3 subunit can mediate trans homophilic-binding via its Ig domain and that the β3-Ig domain can associate heterophilically with the β1 subunit. Evolutionary tracing analysis and structural modeling identified a cluster of surface-localized amino acids fully conserved between the Ig domains of all known β3 and β1 sequences. A notable feature of this conserved surface cluster is the presence of two adjacent cysteine residues that previously we have suggested may form a disulfide bond. We now confirm the presence of the disulfide bond in β3 using mass spectrometry, and we show that its integrity is essential for the association of the full-length, membrane-anchored β3 subunit with itself. However, selective reduction of this surface disulfide bond did not inhibit homophilic binding of the purified β3-Ig domain in free solution. Hence, the disulfide bond itself is unlikely to be part of the homophilic binding site. Rather, we suggest that its integrity ensures the Ig domain of the membrane-tethered β3 subunit adopts the correct orientation for productive association to occur in vivo.—Yereddi, N. R., Cusdin, F. S., Namadurai, S., Packman, L. C., Monie, T. P., Slavny, P., Clare, J. C., Powell, A. J., Jackson, A. P. The immunoglobulin domain of the sodium channel β3 subunit contains a surface-localized disulfide bond that is required for homophilic binding.

Crohn’s disease is a chronic inflammatory condition most commonly affecting the ileum and colon. The aetiology of Crohn’s disease is complex and may include defects in peptidoglycan recognition, and/or failures in the establishment of intestinal tolerance. We have recently described a novel constitutive endogenous delivery system for the translocation of nanomineral-antigen-peptidoglycan (NAP) conjugates to antigen presenting cells (APCs) in intestinal lymphoid patches. In mice NAP conjugate delivery to APCs results in high surface expression of the immuno-modulatory molecule programmed death receptor ligand 1 (PD-L1). Here we report that NAP conjugate positive APCs in human ileal tissues from individuals with ulcerative colitis and intestinal carcinomas, also have high expression of PD-L1. However, NAP-conjugate positive APCs in intestinal tissue from patients with Crohn’s disease show selective failure in PD-L1 expression. Therefore, in Crohn’s disease intestinal antigen taken up by lymphoid patch APCs will be presented without PD-L1 induced tolerogenic signalling, perhaps initiating disease.

The innate immune response provides our first line of defence against infection. Over the course of evolution, pathogens have evolved numerous strategies to either avoid activating or to limit the effectiveness of the innate immune system. The Kaposi's sarcoma-associated herpesvirus (KSHV) contains tegument proteins in the virion that contribute to immune evasion and aid the establishment of viral infection. For example, the KSHV tegument protein ORF63 modulates inflammasome activation to inhibit the innate immune response against the virus. Understanding the likely structure of proteins involved in immune evasion enables potential mechanisms of action to be proposed. To understand more fully how ORF63 modulates the innate immune system we have utilized widely available bioinformatics tools to analyze the primary protein sequence of ORF63 and to predict its secondary and tertiary structure. We found that ORF63 is predicted to be almost entirely alpha-helical and may possess similarity to HEAT repeat containing proteins. Consequently, ORF63 is unlikely to be a viral homolog of the NLR protein family. ORF63 may inhibit the innate immune response by flexibly interacting with its target protein and inhibiting the recruitment of protein co-factors and/or conformational changes required for immune signaling.

Background: Nucleotide binding and oligomerization domain-containing protein 2 (NOD2) is a protein involved in the recognition of bacterial pathogens through detection of muramyl dipeptide. Results: Purified recombinant NOD2 was found to bind ATP and muramyl dipeptide. Conclusion: NOD2 is an intracellular signaling receptor for muramyl dipeptide. Significance: These results help to define the molecular events involved in NOD2 signaling., Nucleotide binding and oligomerization domain-containing protein 2 (NOD2/Card15) is an intracellular protein that is involved in the recognition of bacterial cell wall-derived muramyl dipeptide. Mutations in the gene encoding NOD2 are associated with inherited inflammatory disorders, including Crohn disease and Blau syndrome. NOD2 is a member of the nucleotide-binding domain and leucine-rich repeat-containing protein gene (NLR) family. Nucleotide binding is thought to play a critical role in signaling by NLR family members. However, the molecular mechanisms underlying signal transduction by these proteins remain largely unknown. Mutations in the nucleotide-binding domain of NOD2 have been shown to alter its signal transduction properties in response to muramyl dipeptide in cellular assays. Using purified recombinant protein, we now demonstrate that NOD2 binds and hydrolyzes ATP. Additionally, we have found that the purified recombinant protein is able to bind directly to muramyl dipeptide and can associate with known NOD2-interacting proteins in vitro. Binding of NOD2 to muramyl dipeptide and homo-oligomerization of NOD2 are enhanced by ATP binding, suggesting a model of the molecular mechanism for signal transduction that involves binding of nucleotide followed by binding of muramyl dipeptide and oligomerization of NOD2 into a signaling complex. These findings set the stage for further studies into the molecular mechanisms that underlie detection of muramyl dipeptide and assembly of NOD2-containing signaling complexes.

Initiation of the innate immune response requires agonist recognition by a pathogen recognition receptor. Following ligand binding, conformational rearrangement of the receptor creates a molecular scaffold from which signal transduction is propagated via complex cellular signaling pathways. This in turn leads to the induction of a pro-inflammatory immune response. A critical component of these signaling pathways is the homotypic interaction of receptor and adapter proteins via specific protein interaction domains. Within the innate immune signaling cascade, homotypic interactions between members of the death domain family and the Toll/interleukin-1 receptor domain are particularly important. Here we discuss the current understanding of the molecular basis of these homotypic receptor:adapter interactions and their role in innate immune signal transduction.

Pattern recognition receptors (PRRs) provide a crucial function in the detection of exogenous and endogenous danger signals. The Toll-like receptors (TLRs) were the first family of PRRs to be discovered and have been extensively studied since. Whilst TLRs remain the best characterized family of PRRs there is still much to be learnt about their mode of activation and the mechanisms of signal transduction they employ. Much of our understanding of these processes has been gathered through the use of cell based signaling assays utilizing specific gene-reporters or cytokine secretion based readouts. More recently it has become apparent that the repertoire of ligands recognized by these receptors may be wider than originally assumed and that their activation may be sensitized, or at least modulated by the presence of common household allergens such as the cat dander protein Fel d 1, or the house dust mite allergen Der p 2. In this chapter we provide an overview of the cell culture and stimulation processes required to study TLR signaling in HEK293 based assays and in bone marrow-derived macrophages.

Continual advancements in computing power and sophistication, coupled with rapid increases in protein sequence and structural information, have made bioinformatic tools an invaluable resource for the molecular and structural biologists. With the degree of sequence information continuing to expand at an almost exponential rate, it is essential that scientists today have a basic understanding of how to utilise, manipulate, and analyse this information for the benefit of their own experiments. In the context of Toll-interleukin-1 receptor (TIR) domain containing proteins, we describe here a series of the more common and user-friendly bioinformatic tools available as internet-based resources. These will enable the identification and alignment of protein sequences, the identification of functional motifs, the characterisation of protein secondary structure, the identification of protein structural folds and distantly homologous proteins, and the validation of the structural geometry of modelled protein structures.

Pattern recognition receptors (PRRs) provide a crucial function in the detection of exogenous and endogenous danger signals. The Toll-like receptors (TLRs) were the first family of PRRs to be discovered and have been extensively studied since. Whilst TLRs remain the best characterized family of PRRs there is still much to be learnt about their mode of activation and the mechanisms of signal transduction they employ. Much of our understanding of these processes has been gathered through the use of cell based signaling assays utilizing specific gene-reporters or cytokine secretion based readouts. More recently it has become apparent that the repertoire of ligands recognized by these receptors may be wider than originally assumed and that their activation may be sensitized, or at least modulated by the presence of common household allergens such as the cat dander protein Fel d 1, or the house dust mite allergen Der p 2. In this chapter we provide an overview of the cell culture and stimulation processes required to study TLR signaling in HEK293 based assays and in bone marrow-derived macrophages.

Caspase-8 is an apical component of cell death pathways. Activated caspase-8 can drive classical caspase-dependent apoptosis and actively inhibits cell death mediated by RIPK3-driven necroptosis. Genetic deletion of Casp8 results in embryonic lethality as a result of uncontrolled necroptosis. This lethality can be rescued by simultaneous deletion of Ripk3. Recently, caspase-8 has been additionally connected to inflammatory pathways within the cell. In particular, caspase-8 has been shown to be crucially involved in the induction of pro-IL-1β synthesis and processing via both non-canonical and canonical pathways. In this review, we bring together current knowledge regarding the role of caspase-8 in cellular inflammation with a particular emphasis on the interplay between caspase-8 and the classical and non-canonical inflammasomes.

SummaryThe polypyrimidine tract binding protein (PTB) is an RNA binding protein that normally functions as a regulator of alternative splicing but can also be recruited to stimulate translation initiation by certain picornaviruses. High-resolution structures of the four RNA recognition motifs (RRMs) that make up PTB have previously been determined by NMR. Here, we have used small-angle X-ray scattering to determine the low-resolution structure of the entire protein. Scattering patterns from full-length PTB and deletion mutants containing all possible sequential combinations of the RRMs were collected. All constructs were found to be monomeric in solution. Ab initio analysis and rigid-body modeling utilizing the high-resolution models of the RRMs yielded a consistent low-resolution model of the spatial organization of domains in PTB. Domains 3 and 4 were found to be in close contact, whereas domains 2 and especially 1 had loose contacts with the rest of the protein.

The polypyrimidine tract binding protein (PTB) is an important regulator of alternative splicing that also affects mRNA localization, stabilization, polyadenylation, and translation. NMR structural analysis of the N-terminal half of PTB (residues 55–301) shows a canonical structure for RRM1 but reveals novel extensions to the β strands and C terminus of RRM2 that significantly modify the β sheet RNA binding surface. Although PTB contains four RNA recognition motifs (RRMs), it is widely held that only RRMs 3 and 4 are involved in RNA binding and that RRM2 mediates homodimerization. However, we show here not only that the RRMs 1 and 2 contribute substantially to RNA binding but also that full-length PTB is monomeric, with an elongated structure determined by X-ray solution scattering that is consistent with a linear arrangement of the constituent RRMs. These new insights into the structure and RNA binding properties of PTB suggest revised models of its mechanism of action.

The formation of genomic RNA dimers during the retroviral life cycle is essential for optimal viral replication and infectivity. The sequences and RNA structures responsible for this interaction are located in the untranslated 5' leader RNA, along with other cis-acting signals. Dimer formation occurs by specific interaction between identical structural motifs. It is believed that an initial kissing hairpin forms following self-recognition by autocomplementary RNA loops, leading to formation of an extended stable duplex. The dimerization initiation site (DIS) of the deltaretrovirus human T-cell lymphotropic virus type-I (HTLV-I) has been previously localized to a 14-nucleotide sequence predicted to contain an RNA stem loop. Biochemical probing of the monomeric RNA structure using RNAse T1, RNAse V1, RNAse U2, lead acetate, and dimethyl sulfate has led to the generation of the first structural map of the HTLV-I DIS. A comprehensive data set of individual nucleotide modifications reveals that the structural motif responsible for HTLV-I RNA dimerization forms a trinucleotide RNA loop, unlike any previously characterized retroviral dimerization motif. Molecular modeling demonstrates that this can be formed by an unusual C:synG base pair closing the loop. Comparative phylogeny indicates that such a motif may also exist in other deltaretroviruses.

Polymorphisms in ovine PrP at amino acid residues 141 and 154 are associated with susceptibility to ovine prion disease: Leu141Arg154 with classical scrapie and Phe141Arg154 and Leu141His154 with atypical scrapie. Classical scrapie is naturally transmissible between sheep, whereas this may not be the case with atypical scrapie. Critical amino acid residues will determine the range or stability of structural changes within the ovine prion protein or its functional interaction with potential cofactors, during conversion of PrPC to PrPSc in these different forms of scrapie disease. Here we computationally identified that regions of ovine PrP, including those near amino acid residues 141 and 154, displayed more conservation than expected based on local structural environment. Molecular dynamics simulations showed these conserved regions of ovine PrP displayed genotypic differences in conformational repertoire and amino acid side-chain interactions. Significantly, Leu141Arg154 PrP adopted an extended beta sheet arrangement in the N-terminal palindromic region more frequently than the Phe141Arg154 and Leu141His154 variants. We supported these computational observations experimentally using circular dichroism spectroscopy and immunobiochemical studies on ovine recombinant PrP. Collectively, our observations show amino acid residues 141 and 154 influence secondary structure and conformational change in ovine PrP that may correlate with different forms of scrapie.

Highlights • We have studied the interaction between NOD2 and CARD9. • The NACHT domain and CARD–NACHT linker of NOD2 are crucial for the interaction. • The CARD domains of NOD2 and CARD9 do not directly interact., NOD2 activation by muramyl dipeptide causes a proinflammatory immune response in which the adaptor protein CARD9 works synergistically with NOD2 to drive p38 and c-Jun N-terminal kinase (JNK) signalling. To date the nature of the interaction between NOD2 and CARD9 remains undetermined. Here we show that this interaction is not mediated by the CARDs of NOD2 and CARD9 as previously suggested, but that NOD2 possesses two interaction sites for CARD9; one in the CARD–NACHT linker and one in the NACHT itself., Structured summary of protein interactions NOD2 physically interacts with CARD9 by anti tag coimmunoprecipitation (View interaction)

We have previously mapped the sequences required for dimerisation of the 5′ leader of the human T-cell leukaemia virus type-1 (HTLV-1) genome. The smallest sequence necessary and sufficient for dimer formation, in vitro, was ascertained to be a 37 nucleotide (nt) region downstream of the splice donor and just upstream of the primer binding site. Deletion of a 32 base-pair sequence encompassing this region within the provirus was associated with a minor decrease in infectivity of the virus in an in vitro system. To further map and help elucidate the nature of the dimer linkage, we used RNA and DNA oligonucleotide competition assays to define the nucleotides involved. These experiments revealed that a 14 nt sequence containing a potential stem loop structure, formed from a palindromic sequence, is important for dimer formation. This was confirmed by the ability of this RNA sequence to form heterodimers with larger RNA transcripts from the same region, while sequences lacking this motif could not. RNA transcripts containing the reverse sequence, the same nucleotides in a random arrangement, and complementary DNA oligos, all failed to form heterodimers with the 14 nt sequence. The primary dimer initiation site of HTLV-1 has thus been located to a 14 nt palindrome containing sequence, and dimerisation is shown to be dependent on specific sense–sense RNA interactions.

Dramatic advances in our understanding of the ultrastructure of the inflammasome and the molecular interactions involved in its assembly have recently been made. The adaptor protein ASC has been proposed to display prion-like activity that results in the formation of filamentous structures in the cell. These filamentouos structures can subsequently become inflammatory themselves if released into the extracellular space and then phagocytosed. Various groups have now utilised a variety of microscopy and structural approaches in order to visualise components of, and indeed the entire, inflammasome in both endogenous and overexpression systems. In this brief review we draw upon these new pieces of work to describe how our understanding of the global structure of the inflammasome has progressed in light of these new observations. In particular we begin by providing an initial perspective on the possible formation of small circular, wheel-like, oligomers resembling apoptosomes. We then address the current view that inflammasomes result from the formation of a much larger complex which may involve polymeric filaments. We discuss how these developments fit with recent theories of inflammatory signalling, what questions these advances raise, and propose key areas for further investigation.

Background Activation and signal transduction in the Nucleotide binding, leucine-rich repeat containing receptor (NLR) family needs to be tightly regulated in order to control the inflammatory response to exogenous and endogenous danger signals. Phosphorylation is a common cellular mechanism of regulation that has recently been shown to be important in signalling in another family of cytoplasmic pattern recognition receptors, the RIG-I like receptors. In addition, single nucleotide polymorphisms can alter receptor activity, potentially leading to dysfunction and/or a predisposition to inflammatory barrier diseases. Findings We have computationally analysed the N-terminus of NOD1 and found seven theoretical phosphorylation sites in, or immediately before, the NOD1 Caspase Activation Domain (CARD). Two of these, serine 7 and tyrosine 49 are also found as rare polymorphisms in the African-American population and European-American populations respectively. Mutating serine 7 to either an aspartic acid or an asparagine to mimic the potential impact of phosphorylation or the polymorphism respectively did not affect the response of NOD1 to ligand-mediated NFκB signalling. Conclusions The NOD1 polymorphism S7N does not interfere with receptor function in response to ligand stimulation.

Amino acids with functional or key structural roles display higher degrees of conservation through evolution. The comparative analysis of protein sequences from multiple species and/or between homologous proteins can be highly informative in the identification of key structural and functional residues. Residues which in turn provide insight into the molecular mechanisms of protein function. We have explored the genomic and amino acid conservation of the prototypic innate immune genes NOD1 and NOD2. NOD1 orthologs were found in all vertebrate species analyzed, whilst NOD2 was absent from the genomes of avian, reptilian and amphibian species. Evolutionary trace analysis was used to identify highly conserved regions of NOD1 and NOD2 across multiple species. Consistent with the known functions of NOD1 and NOD2 highly conserved patches were identified that matched the Walker A and B motifs and provided interaction surfaces for the adaptor protein RIP2. Other patches of high conservation reflect key structural functions as predicted by homology models. In addition, the pattern of residue conservation within the leucine-rich repeat (LRR) region of NOD1 and NOD2 is indicative of a conserved mechanism of ligand recognition involving the concave surface of the LRRs.

Multiple chemically and biologically diverse stimuli activate the NLRP3 inflammasome, but the precise mechanism for activation remains to be determined (Davis et al., 2011xDavis, B.K., Wen, H., and Ting, J.P.-Y. Annu. Rev. Immunol. 2011; 29: 707–735Crossref | PubMed | Scopus (433)See all ReferencesDavis et al., 2011). Cellular perturbation and homeostatic destabilization also activate NLRP3. Consistent with this, in the September 2012 issue of Immunity, Compan et al. (2012)xCompan, V., Baroja-Mazo, A., Lopez-Castejon, G., Gomez, A.I., Martinez, C.M., Angosto, D., Montero, M.T., Herranz, A.S., Bazan, E., Reimers, D. et al. Immunity. 2012; 37: 487–500Abstract | Full Text | Full Text PDF | PubMed | Scopus (67)See all ReferencesCompan et al. (2012) presented data suggesting that the NLRP3 inflammasome is activated by cell swelling. Cell swelling followed by a restorative reduction in volume resulted in caspase-1 activation in murine bone-marrow-derived macrophages and macrophages from the teleost fish Sparus aurata (gilthead seabream) (Figure 2 in Compan et al., 2012xCompan, V., Baroja-Mazo, A., Lopez-Castejon, G., Gomez, A.I., Martinez, C.M., Angosto, D., Montero, M.T., Herranz, A.S., Bazan, E., Reimers, D. et al. Immunity. 2012; 37: 487–500Abstract | Full Text | Full Text PDF | PubMed | Scopus (67)See all ReferencesCompan et al., 2012). Murine cells lacking NLRP3 (or ASC or caspase-1) did not process interleukin-1β in response to cell swelling, leading to the conclusion that the NLRP3 inflammasome mediates the cellular response to cell swelling and that this is evolutionarily conserved from fish to mammals.Various NLR-specific expansions have been identified in fish. Generally they cannot be identified as full orthologs of specific mammalian NLRs. However, a number show greatest similarity to the NACHT domain of NLRC3 (Huang et al., 2008xHuang, S., Yuan, S., Guo, L., Yu, Y., Li, J., Wu, T., Liu, T., Yang, M., Wu, K., Liu, H. et al. Genome Res. 2008; 18: 1112–1126Crossref | PubMed | Scopus (166)See all ReferencesHuang et al., 2008; Laing et al., 2008xLaing, K.J., Purcell, M.K., Winton, J.R., and Hansen, J.D. BMC Evol. Biol. 2008; 8: 42Crossref | PubMed | Scopus (90)See all ReferencesLaing et al., 2008). To date there are, to our knowledge, no published reports of direct NLRP3 orthologs in fish.We have consequently performed a detailed search of the currently available fish genome assemblies in ENSEMBL for evidence of NLRP3 orthologs. These encompassed Takifugu rubripes (fugu), Xiphophorus maculatus (platyfish), Gasterosteus aculeatus (stickleback), Gadus morhua (cod), Latimeria chalumnae (coelacanth), Tetraodon nigroviridis (tetraodon), Oreochromis niloticus (tilapia), and Danio rerio (zebrafish).BLASTP searches with the amino acid sequence of human NLRP3 (NCBI accession number NP_004886.3) identified a gene on zebrafish chromosome 17 (ENSEMBL gene ID ENSDARG00000090946) that, upon reciprocal BLASTP analysis against the nonredundant human protein database, returned NLRP3 as the most significant hit. However, the domain organization of the zebrafish protein differs from that of mammalian NLRP3, consisting of an NTPase domain, leucine-rich repeats, and a C-terminal PRY-SPRY domain. Homology searches failed to identify a specific N-terminal effector domain. Hence it is questionable whether this protein can be described as a true NLRP3 ortholog. Importantly, we were unable to identify any other putative NLRP3 orthologs in the other fish genomes with human NLRP3, or indeed the supposed zebrafish NLRP3, as search terms. Instead, NLR expansions with greatest similarity to the NLRC3 NTPase were returned as hits. All the fish, except the tetraodon, possessed clear orthologs of ASC.It is plausible that NLRP3-like functionality is provided by a fish-specific NLR expansion, such as NLR-B, the NACHT of which phylogentically clusters with the mammalian NLRPs (Laing et al., 2008xLaing, K.J., Purcell, M.K., Winton, J.R., and Hansen, J.D. BMC Evol. Biol. 2008; 8: 42Crossref | PubMed | Scopus (90)See all ReferencesLaing et al., 2008). However, Sparus aurata macrophages do not respond to classical NLRP3 activators including ATP, nigericin, alum crystals, and monosodium urate crystals (Figure 2E in Compan et al., 2012xCompan, V., Baroja-Mazo, A., Lopez-Castejon, G., Gomez, A.I., Martinez, C.M., Angosto, D., Montero, M.T., Herranz, A.S., Bazan, E., Reimers, D. et al. Immunity. 2012; 37: 487–500Abstract | Full Text | Full Text PDF | PubMed | Scopus (67)See all ReferencesCompan et al., 2012), suggesting that this may not be the case. The absence of direct NLRP3 orthologs and the lack of classical NLRP3 activity in the teleost indicate that reconsideration of the evolutionary and mechanistic basis for the observed inflammatory response to cell swelling is needed.

For the first time there is now clear biochemical and biophysical evidence indicating that members of the nucleotide-binding domain and leucine-rich repeat containing (NLR) family can be activated as a result of direct interaction between the receptor and ligand. NLRX1 leucine-rich repeats bind to RNA; murine NAIP (NLR family, apoptosis inhibitory protein) 5 binds flagellin directly; and NOD (nucleotide-binding oligomerization domain containing) 1 and NOD2 may interact directly with fragments of peptidoglycan. It remains to be seen if NLRP3 has a specific ligand, but progress has been made in addressing its mechanism of activation, with cellular imbalances and mitochondrial dysfunction being important. This review updates our understanding of NLR activation in light of these recent advances and their impact on the NLR research.

Our bodies are under constant attack from pathogens. Despite this continual bombardment, under normal circumstances we remain healthy for most of our lives. This protection against infectious and harmful agents is provided by our immune system. The immune system can be broken into two elements: adaptive immunity and innate immunity. Adaptive immunity is a specific response targeted against particular pathogens through, for example, cytotoxic T cells and antibody production. The adaptive immune system has the potential to raise a defence against any invading pathogen. However, this is a relatively slow and energy expensive process. Innate immunity in contrast provides a non-specific response against any pathogen via a variety of components and processes. These include: barrier functions, complement, natural killer (NK) cells, antimicrobial peptides, mucosal secretions, pattern recognition receptors (PRRs) and the commensal micro-organisms. Innate immunity is responsible for clearing the majority of pathogen exposures that would result in infection before the adaptive system is even involved. This chapter will focus upon the role of one particular arm of the innate immune response to infectious diseases – Pattern Recognition Receptors. It will broadly address the mechanisms by which PRRs recognise the pathogens, the effects this has and the types if response it has. It will also bring in examples of evasion strategies used by pathogens to avoid detection and touch on the impact of polymorphisms in the receptors. Finally we will discuss the role of PRRs in a key defence against infectious diseases, vaccination.

TLRs are critical pattern recognition receptors that recognize bacterial and viral pathogen-associated molecular patterns leading to innate and adaptive immune responses. TLRs signal via homotypic interactions between their cytoplasmic Toll/IL-1R (TIR) domains and TIR domain-containing adaptor proteins. Over the course of evolution, viruses have developed various immune evasion strategies, one of which involves inhibiting TLR signaling pathways to avoid immune detection. Thus, vaccinia virus encodes the A46 protein, which binds to multiple TIR-domain containing proteins, ultimately preventing TLRs from signaling. We have identified an 11-aa–long peptide from A46 (termed viral inhibitor peptide of TLR4, or VIPER), which, when fused to a cell-penetrating delivery sequence, potently inhibits TLR4-mediated responses. VIPER was TLR4 specific, being inert toward other TLR pathways, and was active in murine and human cells and in vivo, where it inhibited LPS-induced IL-12p40 secretion. VIPER also prevented TLR4-mediated MAPK and transcription factor activation, suggesting it acted close to the TLR4 complex. Indeed, VIPER directly interacted with the TLR4 adaptor proteins MyD88 adaptor-like (Mal) and TRIF-related adaptor molecule (TRAM). Viral proteins target host proteins using evolutionary optimized binding surfaces. Thus, VIPER possibly represents a surface domain of A46 that specifically inhibits TLR4 by masking critical binding sites on Mal and TRAM. Apart from its potential therapeutic and experimental use in suppressing TLR4 function, identification of VIPER’s specific binding sites on TRAM and Mal may reveal novel therapeutic target sites. Overall, we demonstrate for the first time disruption of a specific TLR signaling pathway by a short virally derived peptide.

TLR4 is the primary sensor of LPS. In this study, we describe for the first time TLR4 interactor with leucine-rich repeats (TRIL), which is a novel component of the TLR4 complex. TRIL is expressed in a number of tissues, most prominently in the brain but also in the spinal cord, lung, kidney, and ovary. TRIL is composed of a signal sequence, 13 leucine-rich repeats, a fibronectin domain, and a single transmembrane spanning region. TRIL is induced by LPS in the human astrocytoma cell line U373, in murine brain following i.p. injection, and in human PBMC. Endogenous TRIL interacts with TLR4 and this interaction is greatly enhanced following LPS stimulation. TRIL also interacts with the TLR4 ligand LPS. Furthermore, U373 cells stably overexpressing TRIL display enhanced cytokine production in response to LPS. Finally, knockdown of TRIL using small interfering RNA attenuates LPS signaling and cytokine production in cell lines, human PBMC, and primary murine mixed glial cells. These results demonstrate that TRIL is a novel component of the TLR4 complex which may have particular relevance for the functional role of TLR4 in the brain.

The Toll-like receptors and NOD-like receptors are key families in the innate immune response. The specific detection of activating ligand facilitates receptor interactions, the formation of multiprotein signalling complexes and initiation of signal transduction cascades. This process can trigger the upregulation of proinflammatory mediators, apoptosis, and modulation of other immune defences. Recently, significant advances have been made in the identification of new activating ligands and the determination of the molecular basis of ligand recognition within these receptor families. Understanding these processes provides information essential to the development of new vaccine adjuvants and the treatment of infectious diseases, inflammatory disorders and, potentially, cancer.