Structure and functional characterization of the RNA-binding element of the NLRX1 innate immune modulator

Innate Immunity Never "NODs" Off: NLRs Regulate the Host Anti-Viral Immune Response

A robust innate immune response is essential in combating viral pathogens. However, it is equally critical to quell overzealous immune signaling to limit collateral damage and enable inflammation resolution. Pattern recognition receptors are critical regulators of these processes. The cytosolic nucleotide-binding domain leucine-rich repeat (NLR; NOD-like receptor) family of pattern recognition receptors plays essential roles in the sensing of viral pathogen-associated molecular patterns and is best characterized for itsr pro-inflammatory biological functions. Specifically, these include the formation of multi-protein complexes, defined as inflammasomes or NODosomes that regulate the production of IL-1beta, IL-18, and pyroptosis, or the induction of NF-ΚB signaling. While these biological effects are inherently pro-inflammatory, it is also important to recognize that other NLR family members conversely function to negatively regulate inflammation through modulating signaling initiated by other families of pattern recognition receptors. Mechanistically, these unique NLRs also form multiprotein complexes that act to attenuate a variety of biological signaling pathways, such as the inhibition of NF-ΚB. This inhibition facilitates inflammation resolution and functions to restore cellular homeostasis. Despite extensive characterization of individual NLR family members, the mechanisms of immune system regulation are highly nuanced and remain enigmatic. This is especially true for non-inflammasome-forming, regulatory NLRs. Here, we discuss recent findings associated with NLR family members that play essential roles in the host immune response to viruses and mechanisms by which these pattern recognition receptors may function to regulate antiviral immunity.

Insights into the structure of NLR family member X1: Paving the way for innovative drug discovery

Nucleotide-binding oligomerization domain, leucine rich repeat containing X1 (NLRX1) is a negative regulator of the nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway, with a significant role in the context of inflammation. Altered expression of NLRX1 is prevalent in inflammatory diseases leading to interest in NLRX1 as a drug target. There is a lack of structural information available for NLRX1 as only the leucine-rich repeat domain of NLRX1 has been crystallised. This lack of structural data limits progress in understanding function and potential druggability of NLRX1. We have modelled full-length NLRX1 by combining experimental, homology modelled and AlphaFold2 structures. The full-length model of NLRX1 was used to explore protein dynamics, mutational tolerance and potential functions. We identified a new RNA binding site in the previously uncharacterized N-terminus, which served as a basis to model protein-RNA complexes. The structure of the adenosine triphosphate (ATP) binding domain revealed a potential catalytic functionality for the protein as a member of the ATPase Associated with Diverse Cellular Activity family of proteins. Finally, we investigated the interactions of NLRX1 with small molecule activators in development, revealing a binding site that has not previously been discussed in literature. The model generated here will help to catalyse efforts towards creating new drug molecules to target NLRX1 and may be used to inform further studies on functionality of NLRX1.

Porcine NLRC3 specially binds short dsDNA to regulate cGAS activation

Host immune system has evolved multiple sensors to detect pathogenic and damaged DNA, where precise regulation is critical for distinguishing self from non-self. Our previous studies showed that NLRC3 is an inhibitory nucleic acid sensor that binds to viral DNA and thereby unleashing STING activation. In this study, we demonstrate that human NLRC3 favors long dsDNA, while porcine NLRC3 shows an affinity for shorter dsDNA. Mechanistically, a conserved arginine residue within the leucine-rich repeats of primates NLRC3 forms a structural bridge facilitating the binding of long dsDNA. Conversely, a glycine residue that replaces the arginine in non-primates disrupts this bridge. Furthermore, porcine NLRC3 negatively regulates type I interferon by interacting with cyclic GMP-AMP synthase (cGAS) to inhibit its DNA binding, thereby preventing cGAS activation. These results reveal an unrecognized mechanism by which a species-specific amino acid variation of NLRC3 influences nucleic acid recognition, providing insights into the evolution of innate immunity to pathogens.

Focus on negatively regulated NLRs in inflammation and cancer

Nucleotide-binding and oligomerization structural domain (NOD)-like receptors (NLRs) play an important role in innate immunity as cytoplasmic pattern recognition receptors (PRRs). Over the past decade, considerable progress has been made in understanding the mechanisms by which NLR family members regulate immune system function, particularly the formation of inflammasome and downstream inflammatory signals. However, recent studies have shown that some members of the NLRs, including Nlrp12, NLRX1, and NLRC3, are important in the negative regulation of inflammatory signaling and are involved in the development of various diseases, including inflammatory diseases and cancer. Based on this, in this review, we first summarize the interactions between canonical and non-canonical nuclear factor-κB (NF-κB) signaling pathways that are mainly involved in NLRs, then highlight the mechanisms by which the above NLRs negatively regulate inflammatory signaling responses as well as their roles in tumor progression, and finally summarize the synthetic and natural derivatives with therapeutic effects on these NLRs, which are considered as potential therapeutic agents for overcoming inflammatory diseases.

Natural selection directing molecular evolution in vertebrate viral sensors

Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.

A zebrafish NLRX1 isoform downregulates fish IFN responses by targeting the adaptor STING

In mammals, NLRX1 is a unique member of the nucleotide-binding domain and leucine-rich repeat (NLR) family showing an ability to negatively regulate IFN antiviral immunity. Intron-containing genes, including NLRX1, have more than one transcript due to alternative splicing; however, little is known about the function of its splicing variants. Here, we identified a transcript variant of NLRX1 in zebrafish (Danio rerio), termed NLRX1-tv4, as a negative regulator of fish IFN response. Zebrafish NLRX1-tv4 was slightly induced by viral infection, with an expression pattern similar to the full-length NLRX1. Despite the lack of an N-terminal domain that exists in the full-length NLRX1, overexpression of NLRX1-tv4 still impaired fish IFN antiviral response and promoted viral replication in fish cells, similar to the full-length NLRX1. Mechanistically, NLRX1-tv4 targeted STING for proteasome-dependent protein degradation by recruiting an E3 ubiquitin ligase RNF5 to drive the K48-linked ubiquitination, eventually downregulating the IFN antiviral response. Mapping of NLRX1-tv4 domains showed that its N-terminal and C-terminal regions exhibited a similar potential to inhibit STING-mediated IFN antiviral response. Our findings reveal that like the full-length NLRX1, zebrafish NLRX-tv4 functions as an inhibitor to shape fish IFN antiviral response.IMPORTANCEIn this study, we demonstrate that a transcript variant of zebrafish NLRX1, termed NLRX1-tv4, downregulates fish IFN response and promotes virus replication by targeting STING for protein degradation and impairing the interaction of STING and TBK1 and that its N- and C-terminus exhibit a similar inhibitory potential. Our results are helpful in clarifying the current contradictory understanding of structure and function of vertebrate NLRX1s.

Molecular characterization of a novel mitochondrial NOD-like receptor X1 in chicken that negatively regulates IFN-β expression via STING

NOD-like receptor X1 (NLRX1) is known for its unique mitochondrial localization and plays a negative role in innate immunity. The initial characterization and function of chicken NLRX1 remain unclear. Here, chicken mitochondrial-targeted NLRX1 (chNLRX1) protein was identified. It had relatively conserved domains, a unique N-terminal "X" mitochondrial-targeting domain (MT) and 2 highly conserved motifs at positions 510-520 and 412-421. Furthermore, chNLRX1 had a unique 53aa N-terminus-MT consistent with its localization to mitochondria. Additionally, chNLRX1 was observed to reduce the DNA sensing adaptor stimulator of interferon genes (STING)-induced IFN-β by attenuating the STING-TANK-binding kinase 1 (TBK1) interaction, which is a requisite for the STING-TBK1-IFN-β signaling pathway. These results suggested that chNLRX1 negatively regulated type-I interferon production via STING in host innate immunity.

The NLR gene family: from discovery to present day

The mammalian NLR gene family was first reported over 20 years ago, although several genes that were later grouped into the family were already known at that time. Although it is widely known that NLRs include inflammasome receptors and/or sensors that promote the maturation of caspase 1, IL-1β, IL-18 and gasdermin D to drive inflammation and cell death, the other functions of NLR family members are less well appreciated by the scientific community. Examples include MHC class II transactivator (CIITA), a master transcriptional activator of MHC class II genes, which was the first mammalian NBD-LRR-containing protein to be identified, and NLRC5, which regulates the expression of MHC class I genes. Other NLRs govern key inflammatory signalling pathways or interferon responses, and several NLR family members serve as negative regulators of innate immune responses. Multiple NLRs regulate the balance of cell death, cell survival, autophagy, mitophagy and even cellular metabolism. Perhaps the least discussed group of NLRs are those with functions in the mammalian reproductive system. The focus of this Review is to provide a synopsis of the NLR family, including both the intensively studied and the underappreciated members. We focus on the function, structure and disease relevance of NLRs and highlight issues that have received less attention in the NLR field. We hope this may serve as an impetus for future research on the conventional and non-conventional roles of NLRs within and beyond the immune system.

Genome-wide identification, phylogenetic relationships and expression patterns of the NOD-like receptor (NLR) gene family in flounder (Paralichthys olivaceus)

NOD-like receptors (NLRs) are one of the pattern recognition receptors which have been widely known for identifying pathogens and regulating innate immunity in mammals, but the functions of the NLR gene family in teleost fish remain poorly understood. In this study, we conducted a comprehensive identification and analysis of the flounder (Paralichthys olivaceus) NLR gene family, including bioinformatics information, evolutionary relationships, gene structures, conserved motifs, domain composition, expression patterns and protein-protein interaction (PPI). We identified 22 NLRs in flounder (flNLRs) which were clustered into three subfamilies according to their domain organizations and phylogenetic features, i.e., NLR-A (6 members) resembling mammalian NODs, NLR-B (1 member) resembling mammalian NLRPs, and NLR-C (15 members) unique to teleost fish. All flNLRs shared a conserved NACHT domain including an N-terminal nucleotide-binding domain, a middle helical domain 1, and a winged helix domain. Gene structure analysis displayed that flNLRs were significantly different, with exon numbers from 1 to 52. Conserved domain analysis showed that the N-terminus of flNLRs possessed different characteristics of the domains including CARD domain, PYRIN domain, RING domain, and fish-specific FISNA domain, and the C-terminus of seven NLR-C members contained an extra B30.2 domain, named NLRC-B30.2 group. Notably, flNLRs were expressed in all nine tested tissues, showing higher expressions in the systemic and mucosal immune tissues (e.g., kidney, spleen, hindgut, gills, skin, liver) in healthy flounder, and significant responses to intraperitoneal injection and immersion immunization of inactivated Vibrio anguillarum in mucosal tissues, especially the NLR-C members. In addition, PPI analysis demonstrated that some flNLRs of NLR-A and NLR-C shared the same interacting proteins such as RIPK2, TRAF6, MAVS, CASP, ASC, and ATG5, suggesting they might play crucial roles in host defense, antiviral innate immunity, inflammation, apoptosis and autophagy. This study for the first time characterized the NLR gene family of flounder at the genome-wide level, and the results provided a better understanding of the evolution of the NLR gene family and their immune functions in innate immunity in fish.

Immunometabolic rewiring of tubular epithelial cells in kidney disease

Kidney tubular epithelial cells (TECs) have a crucial role in the damage and repair response to acute and chronic injury. To adequately respond to constant changes in the environment, TECs have considerable bioenergetic needs, which are supported by metabolic pathways. Although little is known about TEC metabolism, a number of ground-breaking studies have shown that defective glucose metabolism or fatty acid oxidation in the kidney has a key role in the response to kidney injury. Imbalanced use of these metabolic pathways can predispose TECs to apoptosis and dedifferentiation, and contribute to lipotoxicity and kidney injury. The accumulation of lipids and aberrant metabolic adaptations of TECs during kidney disease can also be driven by receptors of the innate immune system. Similar to their actions in innate immune cells, pattern recognition receptors regulate the metabolic rewiring of TECs, causing cellular dysfunction and lipid accumulation. TECs should therefore be considered a specialized cell type - like cells of the innate immune system - that is subject to regulation by immunometabolism. Targeting energy metabolism in TECs could represent a strategy for metabolically reprogramming the kidney and promoting kidney repair.

Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor

Mitochondria regulate steroid hormone synthesis, and in turn sex hormones regulate mitochondrial function for maintaining cellular homeostasis and controlling inflammation. This crosstalk can explain sex differences observed in several pathologies such as in metabolic or inflammatory disorders. Nod-like receptor X1 (NLRX1) is a mitochondria-associated innate receptor that could modulate metabolic functions and attenuates inflammatory responses. Here, we showed that in an infectious model with the human protozoan parasite, Leishmania guyanensis, NLRX1 attenuated inflammation in females but not in male mice. Analysis of infected female and male bone marrow derived macrophages showed both sex- and genotype-specific differences in both inflammatory and metabolic profiles with increased type I interferon production, mitochondrial respiration, and glycolytic rate in Nlrx1-deficient female BMDMs in comparison to wild-type cells, while no differences were observed between males. Transcriptomics of female and male BMDMs revealed an altered steroid hormone signaling in Nlrx1-deficient cells, and a “masculinization” of Nlrx1-deficient female BMDMs. Thus, our findings suggest that NLRX1 prevents uncontrolled inflammation and metabolism in females and therefore may contribute to the sex differences observed in infectious and inflammatory diseases.

The All-Encompassing Importance of Innate Immunity

In their AAI President’s Addresses reproduced in this issue, Jeremy M. Boss, Ph.D. (AAI ’94; AAI President 2019–2020) and Jenny P.-Y. Ting, Ph.D. (AAI ’97; AAI President 2020–2021) welcomed attendees to the AAI annual meeting, Virtual IMMUNOLOGY2021™. Due to the SARS-CoV-2 pandemic and the cancellation of IMMUNOLOGY2020™, Dr. Boss and Dr. Ting each presented their respective President’s Address to open the meeting.

Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations

Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.

Impact of intracellular innate immune receptors on immunometabolism

Immunometabolism, which is the metabolic reprogramming of anaerobic glycolysis, oxidative phosphorylation, and metabolite synthesis upon immune cell activation, has gained importance as a regulator of the homeostasis, activation, proliferation, and differentiation of innate and adaptive immune cell subsets that function as key factors in immunity. Metabolic changes in epithelial and other stromal cells in response to different stimulatory signals are also crucial in infection, inflammation, cancer, autoimmune diseases, and metabolic disorders. The crosstalk between the PI3K-AKT-mTOR and LKB1-AMPK signaling pathways is critical for modulating both immune and nonimmune cell metabolism. The bidirectional interaction between immune cells and metabolism is a topic of intense study. Toll-like receptors (TLRs), cytokine receptors, and T and B cell receptors have been shown to activate multiple downstream metabolic pathways. However, how intracellular innate immune sensors/receptors intersect with metabolic pathways is less well understood. The goal of this review is to examine the link between immunometabolism and the functions of several intracellular innate immune sensors or receptors, such as nucleotide-binding and leucine-rich repeat-containing receptors (NLRs, or NOD-like receptors), absent in melanoma 2 (AIM2)-like receptors (ALRs), and the cyclic dinucleotide receptor stimulator of interferon genes (STING). We will focus on recent advances and describe the impact of these intracellular innate immune receptors on multiple metabolic pathways. Whenever appropriate, this review will provide a brief contextual connection to pathogenic infections, autoimmune diseases, cancers, metabolic disorders, and/or inflammatory bowel diseases.

Innate Immune Responses and Pulmonary Diseases

Innate immunity is the first defense line of the host against various infectious pathogens, environmental insults, and other stimuli causing cell damages. Upon stimulation, pattern recognition receptors (PRRs) act as sensors to activate innate immune responses, containing NF-κB signaling, IFN response, and inflammasome activation. Toll-like receptors (TLRs), retinoic acid-inducible gene I-like receptors (RLRs), NOD-like receptors (NLRs), and other nucleic acid sensors are involved in innate immune responses. The activation of innate immune responses can facilitate the host to eliminate pathogens and maintain tissue homeostasis. However, the activity of innate immune responses needs to be tightly controlled to ensure the optimal intensity and duration of activation under various contexts. Uncontrolled innate immune responses can lead to various disorders associated with aberrant inflammatory response, including pulmonary diseases such as COPD, asthma, and COVID-19. In this chapter, we will have a broad overview of how innate immune responses function and the regulation and activation of innate immune response at molecular levels as well as their contribution to various pulmonary diseases. A better understanding of such association between innate immune responses and pulmonary diseases may provide potential therapeutic strategies.

Characterization and expression analysis of mitochondrial localization molecule: NOD-like receptor X1 (Nlrx1) in mucosal tissues of turbot (Scophthalmus maximus) following bacterial challenge

The NOD-like receptor X1 (NLRX1) is a member of highly conserved nucleotide-binding domain (NBD)- and leucine-rich-repeat (LRR)-containing family (known as NLR), that localizes to the mitochondrial outer membrane and regulate the innate immunity by interacting with mitochondrial antiviral-signaling protein (MAVS). As one of cytoplasmic PRRs, NLRX1 plays key roles for pathogen recognition, autophagy and regulating of subsequent immune signaling pathways. In this study, we identified the nlrx1 in turbot as well as its expression profiles in mucosal surfaces following bacterial infection. In our results, the full-length nlrx1 transcript consists of an open reading frame (ORF) of 4,886 bp encoding the putative peptide of 966 amino acids. The phylogenetic analysis revealed the SmNlrx1 showed the closest relationship to Cynoglossus semilaevis. In addition, the Nlrx1 mRNA expression could be detected in all the examined tissues, with the most abundant expression level in head kidney, and the lowest expression level in liver. Moreover, Nlrx1 showed similar expression patterns following Vibrio anguillarum and Streptococcus iniae infection, that were both significantly up-regulated following challenge, especially post S. iniae challenge. Finally, fluorescence microscopy unveiled that the SmNlrx1 localized to mitochondria in HEK293T by N-terminal mitochondrial targeting sequence. Characterization of Nlrx1 might have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity and will probably contribute to the development of novel intervention strategies for farming turbot.

A crucial residue in the hydrophobic core of the solenoid structure of leucine rich repeats

Leucine rich repeats (LRRs) with 20-30 residues form a super helix arrangement. Individual LRRs are separated into a highly conserved segment with a highly conserved (HCS) and a variable segment (VS). In LRRs short β-strands in HCS stack in parallel, while VS adopts various secondary structures. Among eleven classes recognized, only RI-like, Cysteine-containing (CC), and GALA classes adopt an α-helix. However, the repeat unit lengths are usually different from each other. We performed some analyses based on the atomic coordinates in the known LRR structures. In the VS consensuses of the three classes, position 8 in the VS part is, in common, occupied by conserved aliphatic residue adopting an α-helix. This aliphatic residue is near to the two conserved hydrophobic residues at position 4 (in the center of β-strands) in two adjacent HCS parts. The conserved aliphatic residue plays a crucial role to preserve two parallel β-strands.

The emerging roles of NOD-like receptors in antiviral innate immune signaling pathways

Viral infection triggers host pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns or danger-associated molecular patterns to initiate antiviral innate immune responses. NOD-like receptors (NLRs) are a subgroup of cytosolic PRRs. While substantial advances have been made over the past decade, recent studies have unveiled NLRs' emerging roles in the antiviral innate immune signaling pathways. However, the underlying mechanisms have not been fully understood. Here we present a detailed updated overview and novel insights into NLRs' functions in the antiviral innate immune signaling pathways, including TLR, RLR, and cyclic GMP-AMP synthase-stimulator of interferon genes signaling pathways, and highlight discrepancies in the reported findings and current challenges to future studies. A better understanding of this interplay's underlying molecular mechanisms is very important to provide scientific and theoretical bases for regulating antiviral innate immunity.

Focusing on the Cell Type Specific Regulatory Actions of NLRX1

Cells utilize a diverse repertoire of cell surface and intracellular receptors to detect exogenous or endogenous danger signals and even the changes of their microenvironment. However, some cytosolic NOD-like receptors (NLR), including NLRX1, serve more functions than just being general pattern recognition receptors. The dynamic translocation between the cytosol and the mitochondria allows NLRX1 to interact with many molecules and thereby to control multiple cellular functions. As a regulatory NLR, NLRX1 fine-tunes inflammatory signaling cascades, regulates mitochondria-associated functions, and controls metabolism, autophagy and cell death. Nevertheless, literature data are inconsistent and often contradictory regarding its effects on individual cellular functions. One plausible explanation might be that the regulatory effects of NLRX1 are highly cell type specific and the features of NLRX1 mediated regulation might be determined by the unique functional activity or metabolic profile of the given cell type. Here we review the cell type specific actions of NLRX1 with a special focus on cells of the immune system. NLRX1 has already emerged as a potential therapeutic target in numerous immune-related diseases, thus we aim to highlight which regulatory properties of NLRX1 are manifested in disease-associated dominant immune cells that presumably offer promising therapeutic solutions to treat these disorders.

NLR in eXile: Emerging roles of NLRX1 in immunity and human disease

NLRX1 is a member of the NOD-like receptor family, a set of pattern recognition receptors associated with innate immunity. Interestingly, NLRX1 exists in somewhat of an exile from its NLR counterparts with unique features that mediate atypical functions compared with traditional NOD-like receptors (NLRs). Aside from a mitochondrial targeting sequence, the N-terminal region is yet to be characterized. Mitochondrially located, NLRX1 sits within a subgroup of regulatory NLRs responsible for negatively regulating cellular inflammatory signalling. As well as modulating pathogen response, emerging evidence is implicating NLRX1 as a central homeostatic gatekeeper between mitochondrial biology and immunological response. More recently, NLRX1 has been implicated in a wide range of disease, both pathogen-driven and otherwise. Emerging links of NLRX1 in cancer biology, autoimmunity and other inflammatory conditions are raising the potential of targeting NLRX1 therapeutically, with recent studies in inflammatory bowel disease showing great promise. Within this review, we address the unique features of NLRX1, its roles in innate immune signalling and its involvement in a range of inflammatory, metabolic and oncology disease indications with a focus on areas that could benefit from therapeutic targeting of NLRX1.

The Next Generation of Pattern Recognition Receptor Agonists: Improving Response Rates in Cancer Immunotherapy

The recent success of checkpoint blocking antibodies has sparked a revolution in cancer immunotherapy. Checkpoint inhibition activates the adaptive immune system leading to durable responses across a range of tumor types, although this response is limited to patient populations with pre-existing tumor-infiltrating T cells. Strategies to stimulate the immune system to prime an antitumor response are of intense interest and several groups are now working to develop agents to activate the Pattern Recognition Receptors (PRRs), proteins which detect pathogenic and damageassociated molecules and respond by activating the innate immune response. Although early efforts focused on the Toll-like Receptor (TLR) family of membrane-bound PRRs, TLR activation has been associated with both pro- and antitumor effects. Nonetheless, TLR agonists have been deployed as potential anticancer agents in a range of clinical trials. More recently, the cytosolic PRR Stimulator of IFN Genes (STING) has attracted attention as another promising target for anticancer drug development, with early clinical data beginning to emerge. Besides STING, several other cytosolic PRR targets have likewise captured the interest of the drug discovery community, including the RIG-Ilike Receptors (RLRs) and NOD-like Receptors (NLRs). In this review, we describe the outlook for activators of PRRs as anticancer therapeutic agents and contrast the earlier generation of TLR agonists with the emerging focus on cytosolic PRR activators, both as single agents and in combination with other cancer immunotherapies.

Behind the Scenes: Nod-Like Receptor X1 Controls Inflammation and Metabolism

Regulatory Nod-like receptors (NLRs) are a subgroup of the cytosolic NLR family of pathogen recognition receptors (PRRs). These receptors can tune the innate immune responses triggered by the activation of other PRRs by either augmenting or attenuating the activated pro-inflammatory signaling cascades. Nod-like receptor X1 (NLRX1) is the only known mitochondria-associated negative regulatory NLR. NLRX1 attenuates several inflammatory pathways and modulates cellular processes such as autophagy and mitochondrial function following infection or injury. Using both in vitro expression and in vivo experimental models, NLRX1 is extensively described in the context of anti-viral signaling and host-defense against invading pathogens. More recently, NLRX1 has also gained interest in the field of cancer and metabolism where NLRX1 functions to attenuate overzealous inflammation in various inflammatory and autoimmune diseases. However, the exact function of this novel receptor is still under debate and many, often contradictory, mechanisms of action together with cellular localizations have been proposed. Thus, a better understanding of the underlying mechanism is crucial for future research and development of novel therapeutical approaches. Here, we summarize the current findings on NLRX1 and discuss its role in both infectious and inflammatory context.

NLRX1 is a key regulator of immune signaling during invasive pulmonary aspergillosis

Aspergillus fumigatus is an opportunistic fungal pathogen of immunocompromised patient populations. Mortality is thought to be context-specific and occurs via both enhanced fungal growth and immunopathogenesis. NLRX1 is a negative regulator of immune signaling and metabolic pathways implicated in host responses to microbes, cancers, and autoimmune diseases. Our study indicates loss of Nlrx1 results in enhanced fungal burden, pulmonary inflammation, immune cell recruitment, and mortality across immuno-suppressed and immuno-competent models of IPA using two clinically derived isolates (AF293, CEA10). We observed that the heightened mortality is due to enhanced recruitment of CD103+ dendritic cells (DCs) that produce elevated amounts of IL-4 resulting in a detrimental Th2-mediated immune response. Adoptive transfer of Nlrx1-/- CD103+ DCs in neutropenic NRG mice results in enhanced mortality that can be ablated using IL-4 neutralizing antibodies. In vitro analysis of CD103+ DCs indicates loss of Nlrx1 results in enhanced IL-4 production via elevated activation of the JNK/JunB pathways. Interestingly, loss of Nlrx1 also results in enhanced recruitment of monocytes and neutrophils. Chimeras of irradiated Nlrx1-/- mice reconstituted with wild type bone marrow have enhanced neutrophil recruitment and survival during models of IPA. This enhanced immune cell recruitment in the absence of Nlrx1 is mediated by excessive production of CXCL8/IL-8 family of chemokines and IL-6 via early and enhanced activation of P38 in response to A. fumigatus conidia as shown in BEAS-2B airway epithelial cells. In summary, our results point strongly towards the cell-specific and contextual function of Nlrx1 during invasive pulmonary aspergillosis and may lead to novel therapeutics to reduce Th2 responses by CD103+ DCs or heightened recruitment of neutrophils.

Fungal infections are mitigated and controlled in part by a robust immune response and generation of reactive oxygen species. In certain instances, the immune response may become harmful to the host. Nlrx1 is a known negative regulator of inflammatory aspects of the immune system in response to viruses, bacteria, and cancers. In this study we describe the novel importance of Nlrx1 in controlling and fighting fungal infections in two different host cell populations through two distinct mechanisms. Nlrx1 may function as a future target to mitigate inflammation and immunopathogenesis during fungal pulmonary infection as well as enhance beneficial neutrophil recruitment.

Distinct and Orchestrated Functions of RNA Sensors in Innate Immunity

Faithful maintenance of immune homeostasis relies on the capacity of the cellular immune surveillance machinery to recognize "nonself", such as the presence of pathogenic RNA. Several families of pattern-recognition receptors exist that detect immunostimulatory RNA and then induce cytokine-mediated antiviral and proinflammatory responses. Here, we review the distinct features of bona fide RNA sensors, Toll-like receptors and retinoic-acid inducible gene-I (RIG-I)-like receptors in particular, with a focus on their functional specificity imposed by cell-type-dependent expression, subcellular localization, and ligand preference. Furthermore, we highlight recent advances on the roles of nucleotide-binding oligomerization domain (NOD)-like receptors and DEAD-box or DEAH-box RNA helicases in an orchestrated RNA-sensing network and also discuss the relevance of RNA sensor polymorphisms in human disease.

LRR domain of NLRX1 protein delivery by dNP2 inhibits T cell functions and alleviates autoimmune encephalomyelitis

Multiple sclerosis (MS) is a demyelinating inflammatory disease of the central nervous system (CNS), which is a chronic progressive disease and is caused by uncontrolled activation of myelin antigen specific T cells. It has high unmet medical needs due to the difficulty of efficient drug delivery into the CNS to control tissue inflammation. In this study, we demonstrate that a fusion protein of NOD-like receptor family member X1 (NLRX1) and blood brain barrier (BBB)-permeable peptide, dNP2 ameliorates experimental autoimmune encephalomyelitis (EAE). Methods: We purified recombinant LRR or NBD regions of NLRX1 protein conjugated with dNP2. To examine intracellular delivery efficiency of the recombinant protein, we incubated the proteins with Jurkat T cells or murine splenic T cells and their delivery efficiency was analyzed by flow cytometry. To investigate the therapeutic efficacy in an EAE model, we injected the recombinant protein into mice with 3 different treatment schemes e.g., prevention, semi-therapeutic, and therapeutic. To analyze their functional roles in T cells, we treated MACS-sorted naïve CD4 T cells with the proteins during their activation and differentiation into Th1, Th17, and Treg cells. Results: dNP2-LRR protein treatment showed significantly higher delivery efficiency than TAT-LRR or LRR alone in Jurkat T cells and mouse splenic T cells. In all three treatment schemes of EAE experiments, dNP2-LRR administration showed ameliorated tissue inflammation and disease severity with reduced number of infiltrating T cells producing inflammatory cytokines such as IFNγ. In addition, dNP2-LRR inhibited T cell activation, cytokine production, and Th1 differentiation. Conclusion: These results suggest that dNP2-LRR is a novel agent, which regulates effector T cell functions and could be a promising molecule for the treatment of CNS autoimmune diseases such as multiple sclerosis.

Avian Pattern Recognition Receptor Sensing and Signaling

Pattern recognition receptors (PRRs) are a class of immune sensors that play a critical role in detecting and responding to several conserved patterns of microorganisms. As such, they play a major role in the maintenance of immune homeostasis and anti-microbial defense. Fundamental knowledge pertaining to the discovery of PRR functions and their ligands continue to advance the understanding of immune system and disease resistance, which led to the rational design and/or application of various PRR ligands as vaccine adjuvants. In addition, the conserved nature of many PRRs throughout the animal kingdom has enabled the utilization of the comparative genomics approach in PRR identification and the study of evolution, structural features, and functions in many animal species including avian. In the present review, we focused on PRR sensing and signaling functions in the avian species, domestic chicken, mallard, and domestic goose. In addition to summarizing recent advances in the understanding of avian PRR functions, the present review utilized a comparative biology approach to identify additional PRRs, whose functions have been well studied in mammalians but await functional characterization in avian.

NLRP6 self-assembles into a linear molecular platform following LPS binding and ATP stimulation

NOD-like receptors (NLRs) localize in the cytosol to recognize intracellular pathogen products and initialize the innate immune response. However, the ligands and ligand specificity of many NLRs remain unclear. One such NLR, NLRP6, plays an important role in maintaining intestinal homeostasis and protecting against various intestinal diseases such as colitis and intestinal tumorigenesis. Here, we show that the major component of the outer membrane of gram-negative bacteria, lipopolysaccharide (LPS), binds NLRP6 directly and induces global conformational change and dimerization. Following stimulation by ATP, the NLRP6 homodimer can further assemble into a linear molecular platform, and ASC is recruited to form higher molecular structures, indicative of a step-by-step activation mechanism. Our study sheds light on the mystery of LPS-induced inflammasome initiation, reveals the architecture and structural basis of potential pre-inflammasome, and suggests a novel molecular assembly pattern for immune receptors.

Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon

Immune suppression is a crucial component of immunoregulation and a subgroup of nucleotide-binding domain (NBD), leucine-rich repeat (LRR)-containing proteins (NLRs) attenuate innate immunity. How this inhibitory function is controlled is unknown. A key question is whether microbial ligands can regulate this inhibition. NLRC3 is a negative regulator that attenuates type I interferon (IFN-I) response by sequestering and attenuating stimulator of interferon genes (STING) activation. Here, we report that NLRC3 binds viral DNA and other nucleic acids through its LRR domain. DNA binding to NLRC3 increases its ATPase activity, and ATP-binding by NLRC3 diminishes its interaction with STING, thus licensing an IFN-I response. This work uncovers a mechanism wherein viral nucleic acid binding releases an inhibitory innate receptor from its target.

Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9

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PRRSV infection up-regulates NLRX1 expression.

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NLRX1 impairs PRRSV replication.

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NLRX1 suppresses the synthesis of viral subgenomic RNAs.

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NLRX1 interacts and colocalizes with the Nsp9 of PRRSV.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes one of the most economically important diseases of swine worldwide. Current antiviral strategies provide only limited protection. Nucleotide-binding oligomerization domain-like receptor (NLR) X1 is unique among NLR proteins in its functions as a pro-viral or antiviral factor to different viral infections. To date, the impact of NLRX1 on PRRSV infection remains unclear. In this study, we found that PRRSV infection promoted the expression of NLRX1 gene. In turn, ectopic expression of NLRX1 inhibited PRRSV replication in Marc-145 cells, whereas knockdown of NLRX1 enhanced PRRSV propagation in porcine alveolar macrophages (PAMs). Mechanistically, NLRX1 was revealed to impair intracellular viral subgenomic RNAs accumulation. Finally, Mutagenic analyses indicated that the LRR (leucine-rich repeats) domain of NLRX1 interacted with PRRSV Nonstructural Protein 9 (Nsp9) RdRp (RNA-dependent RNA Polymerase) domain and was necessary for antiviral activity. Thus, our study establishes the role of NLRX1 as a new host restriction factor in PRRSV infection.

Animal NLRs continue to inform plant NLR structure and function

Plant NLRs share many of the structural hallmarks of their animal counterparts. At a functional level, the central nucleotide-binding pocket appears to have binding and hydrolysis activities, similar to that of animal NLRs. The TIR domains of plant NLRs have been shown to self-associate, and there is emerging evidence that full-length plant NLRs may do so as well. It is therefore tempting to speculate that plant NLRs may form higher-order complexes similar to those of the mammalian inflammasome. Here we review the available knowledge on structure-function relationships in plant NLRs, focusing on how the information available on animal NLRs informs the mechanism of plant NLR function, and highlight the evidence that innate immunity signalling pathways in multicellular organisms often require the formation of higher-order protein complexes.

NLRX1 resides in mitochondrial RNA granules and regulates mitochondrial RNA processing and bioenergetic adaptation

The role of mitochondria is emerging in regulation of innate immunity, inflammation and cell death beyond its primary role in energy metabolism. Mitochondria act as molecular platform for immune adaptor protein complexes, which participate in innate immune signaling. The mitochondrial localized immune adaptors are widely expressed in non-immune cells, however their role in regulation of mitochondrial function and metabolic adaption is not well understood. NLRX1, a member of NOD family receptor proteins, localizes to mitochondria and is a negative regulator of anti-viral signaling. However, the submitochondrial localization of NLRX1 and its implication in regulation of mitochondrial functions remains elusive. Here, we confirm that NLRX1 translocates to mitochondrial matrix and associates with mitochondrial FASTKD5 (Fas-activated serine-threonine kinase family protein-5), a bonafide component of mitochondrial RNA granules (MRGs). The association of NLRX1 with FASTKD5 negatively regulates the processing of mitochondrial genome encoded transcripts for key components of complex-I and complex-IV, to modulate its activity and supercomplexes formation. The evidences, here, suggest an important role of NLRX1 in regulating the post-transcriptional processing of mitochondrial RNA, which may have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity.

Expression of pattern recognition receptors in porcine uterine epithelial cells in vivo and in culture

Preservation of a pathogen free uterine environment is critical for maintaining healthy swine herds with high reproductive performance. Considering that uterine epithelial cells are the most numerous and thus likely point of cellular contact for pathogens in the uterus, we hypothesize that these cells may be critical for activating the immune system to clear uterine infections. Although uterine epithelial cells have not been well characterized in pigs, studies in several other species have shown that these cells express several pattern recognition receptors (PRR) and thus may act as sentinels for the uterine immune response. To characterize PRR expression in the porcine uterine epithelia, we used laser-capture microdissection to isolate epithelial cells lining the porcine uterus to quantify in vivo mRNA expression levels for select PRRs. As well, primary uterine epithelial cells (UECs) were isolated, cultured, polarized and PRR expression was quantified. Immunohistofluorescence and immunofluorescence were used to determine subcellular localization of TLR3, TLR4 and TLR9 in both uterine tissue and in polarized primary UECs. Finally, polarized primary UECs were stimulated with ligands for TLR3, TLR4, TLR9 and NOD2 to determine their functional innate immune response. Uterine epithelial cells (in vivo and in vitro) were shown to express TLR1-7, TLR9, NOD1, NOD2, NLRP3, NLRP6, NLRX1, RIG1, MDA5 and LGP2. Subcellular localization of in vivo and polarized primary UECs exhibited TLR3 and TLR9 localized to the apical cell surface whereas TLR4 was localized to the intracellular space. Polarized primary UECs stimulated with TLR3, TLR4 and TLR9 ligands showed induced secretion of IL-6, IL-13 and IL-10, respectively indicating that these receptors were functional. These results indicate that pig uterine epithelial cells are functional innate immune cells that may act as sentinels to protect against uterine infection.

NLRX1 modulates differentially NLRP3 inflammasome activation and NF-κB signaling during Fusobacterium nucleatum infection

NOD-like receptors (NLRs) play a large role in regulation of host innate immunity, yet their role in periodontitis remains to be defined. NLRX1, a member of the NLR family that localizes to mitochondria, enhances mitochondrial ROS (mROS) generation. mROS can activate the NLRP3 inflammasome, yet the role of NLRX1 in NLRP3 inflammasome activation has not been examined. In this study, we revealed the mechanism by which NLRX1 positively regulates ATP-induced NLRP3 inflammasome activation through mROS in gingival epithelial cells (GECs). We found that depletion of NLRX1 by shRNA attenuated ATP-induced mROS generation and redistribution of the NLRP3 inflammasome adaptor protein, ASC. Furthermore, depletion of NLRX1 inhibited Fusobacterium nucleatum infection-activated caspase-1, suggesting that it also inhibits the NLRP3 inflammasome. Conversely, NLRX1 also acted as a negative regulator of NF-κB signaling and IL-8 expression. Thus, NLRX1 stimulates detection of the pathogen F. nucleatum via the inflammasome, while dampening cytokine production. We expect that commensals should not activate the inflammasome, and NLRX1 should decrease their ability to stimulate expression of pro-inflammatory cytokines such as IL-8. Therefore, NLRX1 may act as a potential switch with regards to anti-microbial responses in healthy or diseased states in the oral cavity.

NLRX1 promotes immediate IRF1-directed antiviral responses by limiting dsRNA-activated translational inhibition mediated by PKR

NLRX1 is unique among nucleotide-binding domain and leucine-rich repeat (NLR) proteins in its mitochondrial localization and capacity to negatively regulate MAVS- and STING-dependent antiviral innate immunity. However, some studies suggest a positive regulatory role for NLRX1 in inducing antiviral responses. We show that NLRX1 exerts opposing regulatory effects on virus activation of the transcription factors IRF1 and IRF3, potentially explaining these contradictory results. Whereas NLRX1 suppresses MAVS-mediated IRF3 activation, NLRX1 conversely facilitates virus-induced increases in IRF1 expression, thereby enhancing control of virus infection. NLRX1 has a minimal effect on NF-κB-mediated IRF1 transcription, and regulates IRF1 abundance post-transcriptionally by preventing translational shutdown mediated by the dsRNA-activated protein kinase PKR, thereby allowing virus-induced increases in IRF1 protein abundance.

Epithelial Cell Inflammasomes in Intestinal Immunity and Inflammation

Pattern recognition receptors (PRR), such as NOD-like receptors (NLRs), sense conserved microbial signatures, and host danger signals leading to the coordination of appropriate immune responses. Upon activation, a subset of NLR initiate the assembly of a multimeric protein complex known as the inflammasome, which processes pro-inflammatory cytokines and mediates a specialized form of cell death known as pyroptosis. The identification of inflammasome-associated genes as inflammatory bowel disease susceptibility genes implicates a role for the inflammasome in intestinal inflammation. Despite the fact that the functional importance of inflammasomes within immune cells has been well established, the contribution of inflammasome expression in non-hematopoietic cells remains comparatively understudied. Given that intestinal epithelial cells (IEC) act as a barrier between the host and the intestinal microbiota, inflammasome expression by these cells is likely important for intestinal immune homeostasis. Accumulating evidence suggests that the inflammasome plays a key role in shaping epithelial responses at the host-lumen interface with many inflammasome components highly expressed by IEC. Recent studies have exposed functional roles of IEC inflammasomes in mucosal immune defense, inflammation, and tumorigenesis. In this review, we present the main features of the predominant inflammasomes and their effector mechanisms contributing to intestinal homeostasis and inflammation. We also discuss existing controversies in the field and open questions related to their implications in disease. A comprehensive understanding of the molecular basis of intestinal inflammasome signaling could hold therapeutic potential for clinical translation.

The Scaffolding Protein IQGAP1 Interacts with NLRC3 and Inhibits Type I IFN Production

Sensing of cytosolic nucleotides is a critical initial step in the elaboration of type I IFN. One of several upstream receptors, cyclic GMP-AMP synthase, binds to cytosolic DNA and generates dicyclic nucleotides that act as secondary messengers. These secondary messengers bind directly to stimulator of IFN genes (STING). STING recruits TNFR-associated NF-κB kinase-binding kinase 1 which acts as a critical node that allows for efficient activation of IFN regulatory factors to drive the antiviral transcriptome. NLRC3 is a recently characterized nucleotide-binding domain, leucine-rich repeat containing protein (NLR) that negatively regulates the type I IFN pathway by inhibiting subcellular redistribution and effective signaling of STING, thus blunting the transcription of type I IFNs. NLRC3 is predominantly expressed in lymphoid and myeloid cells. IQGAP1 was identified as a putative interacting partner of NLRC3 through yeast two-hybrid screening. In this article, we show that IQGAP1 associates with NLRC3 and can disrupt the NLRC3-STING interaction in the cytosol of human epithelial cells. Furthermore, knockdown of IQGAP1 in THP1 and HeLa cells causes significantly more IFN-β production in response to cytosolic nucleic acids. This result phenocopies NLRC3-deficient macrophages and fibroblasts and short hairpin RNA knockdown of NLRC3 in THP1 cells. Our findings suggest that IQGAP1 is a novel regulator of type I IFN production, possibly via interacting with NLRC3 in human monocytic and epithelial cells.

Danger of frustrated sensors: Role of Toll-like receptors and NOD-like receptors in aseptic and septic inflammations around total hip replacements

The innate immune sensors, Toll-like receptors (TLRs) and nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), can recognize not only exogenous pathogen-associated molecular patterns (PAMPs), but also endogenous molecules created upon tissue injury, sterile inflammation, and degeneration. Endogenous ligands are called damage-associated molecular patterns (DAMPs), and include endogenous molecules released from activated and necrotic cells as well as damaged extracellular matrix. TLRs and NLRs can interact with various ligands derived from PAMPs and DAMPs, leading to activation and/or modulation of intracellular signalling pathways. Intensive research on the innate immune sensors, TLRs and NLRs, has brought new insights into the pathogenesis of not only various infectious and rheumatic diseases, but also aseptic foreign body granuloma and septic inflammation of failed total hip replacements (THRs). In this review, recent knowledge is summarized on the innate immune system, including TLRs and NLRs and their danger signals, with special reference to their possible role in the adverse local host response to THRs.

Translational potential of this article: A clear understanding of the roles of Toll-like receptors and NOD-like receptors in aseptic and septic loosening of joint replacements will facilitate potential strategies to mitigate these events, thereby extending the longevity of implants in humans.

Role of Innate Genes in HIV Replication

Cells use an elaborate innate immune surveillance and defense system against virus infections. Here, we discuss recent studies that reveal how HIV-1 is sensed by the innate immune system. Furthermore, we present mechanisms on the counteraction of HIV-1. We will provide an overview how HIV-1 actively utilizes host cellular factors to avoid sensing. Additionally, we will summarize effectors of the innate response that provide an antiviral cellular state. HIV-1 has evolved passive mechanism to avoid restriction and to regulate the innate response. We review in detail two prominent examples of these cellular factors: (i) NLRX1, a negative regulator of the innate response that HIV-1 actively usurps to block cytosolic innate sensing; (ii) SAMHD1, a restriction factor blocking the virus at the reverse transcription step that HIV-1 passively avoids to escape sensing.

Mutation screening of the LRIT3, CABP4, and GPR179 genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness

BACKGROUND

Schubert-Bornschein congenital stationary night blindness (CSNB) is a rare retinal disorder that may lead to severe visual impairment in patients. The aim of this study was to detect mutations in the LRIT3, CABP4, and GPR179 genes in Chinese patients with Schubert-Bornschein CSNB.

MATERIALS AND METHODS

A cohort of eight unrelated Chinese probands with Schubert-Bornschein CSNB was recruited for this study. Six of these probands were assessed in our previous study, in which we screened the NYX, CACNA1F, GRM6, and TRPM1 genes for mutations but identified none. The other two patients were newly recruited and had not been screened for mutations in these genes. Genomic DNA and clinical data were collected from the eight recruited families. Variants of the LRIT3, CABP4, and GPR179 genes were identified by Sanger sequencing. All of the identified variants were also assessed in 192 control individuals.

RESULTS

In this study, a novel compound heterozygous mutation, c.[1A>G]; [608G>T] (p.[0?]; p.[W203L]), was identified in the LRIT3 gene of a proband. These two mutations were not present in any of the 192 normal control individuals or in the other patients, and the missense mutation c.608G>T was predicted to be pathogenic. No mutations were identified in the CABP4 or GPR179 gene.

CONCLUSIONS

These results expand the mutational spectrum of LRIT3, thus potentially enriching our understanding of the molecular basis of complete CSNB. Additional genes that potentially contribute to incomplete CSNB remain to be identified in future studies.

Structure-informed insights for NLR functioning in plant immunity

To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.

NLR-regulated pathways in cancer: opportunities and obstacles for therapeutic interventions

NLRs (nucleotide-binding domain, leucine-rich repeat containing receptors) are pattern recognition receptors associated with immunity and inflammation in response to endogenous and exogenous pathogen and damage associated molecular patterns (PAMPs and DAMPs respectively). Dysregulated NLR function is associated with several diseases including cancers, metabolic diseases, autoimmune disorders and autoinflammatory syndromes. In the last decade, distinct cell and organ specific roles for NLRs have been identified however; their roles in cancer initiation, development and progression remain controversial. This review summarizes the emerging role of NLRs in cancer and their possible future as targets for cancer therapeutics.

Beyond the inflammasome: regulatory NOD-like receptor modulation of the host immune response following virus exposure

A complex interaction exists between elements of the host innate immune system and viral pathogens. It is essential that the host mount a robust immune response during viral infection and effectively resolve inflammation once the pathogen has been eliminated. Members of the nucleotide-binding domain leucine-rich repeat [NBD-LRR; known as NOD-like receptor (NLR)] family of cytosolic pattern-recognition receptors are essential components of these immunological processes and have diverse functions in the host antiviral immune response. NLRs can be subgrouped based on their general function. The inflammasome-forming subgroup of NLRs are the best-characterized family members, and several have been found to modulate the maturation of IL-1β and IL-18 following virus exposure. However, the members of the regulatory NLR subgroups are significantly less characterized. These NLRs uniquely function to modulate signalling pathways initiated by other families of pattern-recognition receptors, such as Toll-like receptors and/or Rig-I-like helicase receptors. Regulatory NLRs that augment pro-inflammatory pathways include nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and NOD2, which have been shown to form a multiprotein complex termed the NODosome that significantly modulates IFN and NF-κB signalling following viral infection. Conversely, a second subgroup of regulatory NLRs functions to negatively regulate inflammation. These inhibitory NLRs include NLRX1, NLRP12 and NLRC3, which have been shown to interact with TRAF molecules and various kinases to modulate diverse cellular processes. Targeting NLR signalling following infection with a virus represents a novel and promising therapeutic strategy. However, significant effort is still required to translate the current understanding of NLR biology into effective therapies.

Modeling-Enabled Characterization of Novel NLRX1 Ligands

Nucleotide-binding domain and leucine-rich repeat containing (NLR) family are intracellular sentinels of cytosolic homeostasis that orchestrate immune and inflammatory responses in infectious and immune-mediated diseases. NLRX1 is a mitochondrial-associated NOD-like receptor involved in the modulation of immune and metabolic responses. This study utilizes molecular docking approaches to investigate the structure of NLRX1 and experimentally assesses binding to naturally occurring compounds from several natural product and lipid databases. Screening of compound libraries predicts targeting of NLRX1 by conjugated trienes, polyketides, prenol lipids, sterol lipids, and coenzyme A-containing fatty acids for activating the NLRX1 pathway. The ligands of NLRX1 were identified by docking punicic acid (PUA), eleostearic acid (ESA), and docosahexaenoic acid (DHA) to the C-terminal fragment of the human NLRX1 (cNLRX1). Their binding and that of positive control RNA to cNLRX1 were experimentally determined by surface plasmon resonance (SPR) spectroscopy. In addition, the ligand binding sites of cNLRX1 were predicted in silico and validated experimentally. Target mutagenesis studies demonstrate that mutation of 4 critical residues ASP677, PHE680, PHE681, and GLU684 to alanine resulted in diminished affinity of PUA, ESA, and DHA to NLRX1. Consistent with the regulatory actions of NLRX1 on the NF-κB pathway, treatment of bone marrow derived macrophages (BMDM)s with PUA and DHA suppressed NF-κB activity in a NLRX1 dependent mechanism. In addition, a series of pre-clinical efficacy studies were performed using a mouse model of dextran sodium sulfate (DSS)-induced colitis. Our findings showed that the regulatory function of PUA on colitis is NLRX1 dependent. Thus, we identified novel small molecules that bind to NLRX1 and exert anti-inflammatory actions.

Mitochondrial Regulation of Inflammasome Activation in Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is characterized by enhanced chronic airway and lung inflammatory responses to noxious particles or gases. It is a major unmet medical need worldwide, and in Western society is strongly associated with exposure to cigarette smoke (CS). CS-induced inflammation is believed to be a key immune driver in the pathogenesis of COPD. Since the concept of inflammasomes was first introduced nearly a decade ago, these have been increasingly recognized as a central player in innate immune and inflammatory responses. In addition, studies have emerged demonstrating that mitochondrial innate immune signaling plays an important role in CS-induced inflammasome activation, pulmonary inflammation and tissue remodeling responses. Here, recent discoveries about inflammasome activation and mitochondrial biology and their role in COPD pathogenesis are reviewed. In addition, the current limitations of our understanding of this theme and future research directions are discussed.

Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

The NOD-like receptors (NLRs) and Toll-like receptors (TLRs) are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs) that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids). The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.

Intracellular detection of viral nucleic acids

Successful clearance of a microbial infection depends on the concerted action of both the innate and adaptive arms of the immune system. Accurate recognition of an invading pathogen is the first and most crucial step in eliciting effective antimicrobial defense mechanisms. In recent years, remarkable progress has been made towards understanding the molecular details of how the innate immune system recognizes microbial signatures, commonly called pathogen-associated molecular patterns (PAMPs). For viral pathogens, nucleic acids-both viral genomes and viral replication products-represent a major class of PAMPs that trigger antiviral host responses via activation of germline-encoded innate immune receptors. Here we summarize recent advances in intracellular innate sensing mechanisms of viral RNA and DNA.

How 'arm-twisting' by the inducer triggers activation of the MalT transcription factor, a typical signal transduction ATPase with numerous domains (STAND)

Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized by contacts with the arm, a domain that connects the NOD to the inducer-binding domain called the sensor. How the inducer triggers NOD opening remains unclear. Here, I pinpointed the NOD-arm interface of the MalT STAND transcription factor, and I generated a MalT variant in which this interface can be covalently locked on demand, thereby trapping the NOD in the closed state. By characterizing this locked variant, I found that the inducer is recognized in two steps: it first binds to the sole sensor with low affinity, which then triggers the recruitment of the arm to form a high-affinity arm-sensor inducer-binding site. Strikingly, this high-affinity binding step was incompatible with arm-NOD contacts maintaining the NOD closed. Through this toggling between two mutually exclusive states reminiscent of a single-pole double-throw switch, the arm couples inducer binding to NOD opening, shown here to precede nucleotide exchange. This scenario likely holds for other STANDs like mammalian NLR innate immunity receptors.