SUMMARY NLR genes mediate host immunity to various pathogenic stimuli. However, in vivo evidence for NLR involvement in viral sensing has not been widely investigated and remains controversial. As an ultimate test of the physiologic role of NLRP3 during RNA viral infection, this work explores the in vivo role of NLRP3 inflammasome components during influenza virus infection. Mice lacking Nlrp3, ASC, or Caspase-1, but not Nlrc4, exhibit dramatically increased mortality but reduced immune response following influenza virus exposure. Utilizing analogs of dsRNA (poly(I:C)) and ssRNA (ssRNA40), we demonstrate that NLRP3-mediated response can be activated by RNA species. Mechanistically, NLRP3 inflammasome activation by influenza virus is dependent upon lysosomal maturation and reactive oxygen species. Inhibition of ROS induction eliminated IL-1β production in animals during influenza infection. Together, these data place the NLRP3 inflammasome as an essential component in host defense against influenza infection through the sensing of viral RNA.

The RIG-like helicase (RLH) family of intracellular receptors detect viral nucleic acid and signal through the mitochondrial antiviral signalling adaptor MAVS (also known as Cardif, VISA and IPS-1) during a viral infection [1][2][3][4][5][6] . MAVS activation leads to the rapid production of antiviral cytokines, including type 1 interferons. Although MAVS is vital to antiviral immunity, its regulation from within the mitochondria remains unknown. Here we describe human NLRX1, a highly conserved nucleotide-binding domain (NBD)-and leucine-rich-repeat (LRR)-containing family member (known as NLR) that localizes to the mitochondrial outer membrane and interacts with MAVS. Expression of NLRX1 results in the potent inhibition of RLH-and MAVS-mediated interferon-b promoter activity and in the disruption of virus-induced RLH-MAVS interactions. Depletion of NLRX1 with small interference RNA promotes virus-induced type I interferon production and decreases viral replication. This work identifies NLRX1 as a check against mitochondrial antiviral responses and represents an intersection of three ancient cellular processes: NLR signalling, intracellular virus detection and the use of mitochondria as a platform for anti-pathogen signalling. This represents a conceptual advance, in that NLRX1 is a modulator of pathogen-associated molecular pattern receptors rather than a receptor, and identifies a key therapeutic target for enhancing antiviral responses.Mammalian members of the nucleotide-binding domain (NBD) and leucine-rich-repeat-containing (LRR) (known as NLR, see http://www.genenames.org/genefamily/nacht.html) family of proteins are indispensable for cellular responses to pathogens. This NBD-LRR protein structure is ancient and highly conserved, as shown by its initial identification among plant disease-resistance proteins 7-12 . Current dogma posits that NLRs function as cytoplasmic surveillance molecules that sense intracellular pathogen-associated molecular patterns (PAMPs), or as regulators of pathogen-initiated signalling cascades 13,14 . Viral PAMPs are detected by the cytoplasmic RLH receptors RIG-I (also known as DDX58) and MDA-5 (also known as IFIH1), which signal through the mitochondrial protein MAVS, resulting in the activation of interferon regulatory factor 3 (IRF3) and NF-kB and type-1 interferon transcription [1][2][3][4][5][6] . Abrogation of MAVS expression or function leads to reduced type 1 interferon production and antiviral protection 15 .To study the potential role of NLR proteins in regulating mitochondrial antiviral signalling, we used bioinformatics to identify NLRs localized to the mitochondria. We identified one putative mitochondrial NLR called NLRX1 (previously known as CLR11.3 and NOD9) 9,16 (Fig. 1a). The predicted peptide sequence and distinct domains of NLRX1 are shown in Supplementary Fig. 1. Consistent with the conserved motif structure of the NLR family, NLRX1 contains a central putative NBD and carboxy-terminal LRRs. The assignment of the amino-terminal effector domain to a subclass i...

SUMMARY The nucleotide-binding domain and leucine-rich repeat containing (NLR) proteins regulate innate immunity. Although the positive regulatory impact of NLRs is clear, their inhibitory roles are not well defined. We showed Nlrx1−/− mice exhibited increased expression of antiviral signaling molecules IFN-β, STAT2, OAS1 and IL-6 after influenza virus infection. Consistent with increased inflammation, Nlrx1−/− mice exhibited marked morbidity and histopathology. Infection of these mice with an influenza strain that carries a mutated NS-1 protein, which normally prevents IFN induction by interaction with RNA and the intracellular RNA sensor RIG-I, further exacerbated IL-6 and type I IFN signaling. NLRX1 also weakened cytokine responses to the 2009 H1N1 pandemic influenza virus in human cells. Mechanistically, Nlrx1 deletion led to constitutive interaction of MAVS and RIG-I. Additionally, an inhibitory function is identified for NLRX1 during LPS-activation of macrophages where the MAVS-RIG-I pathway was not involved. NLRX1 interacts with TRAF6 and inhibits NF-κB activation. Thus, NLRX1 functions as a checkpoint of overzealous inflammation.

SUMMARY The mitochondrial protein MAVS (also known as IPS-1, VISA, CARDIF) interacts with RLR (RIG-I-like receptors) to induce type 1 interferon (IFN-I) during viral infection. NLRX1 is a mitochondrial NLR (nucleotide-binding, leucine-rich repeats containing) protein that attenuates MAVS-RLR signaling. Using Nlrx1−/− cells we confirmed NLRX1 attenuated IFN-I production, but additionally promoted autophagy during viral infection. This dual function of NLRX1 paralleled the previously described functions of the autophagy-related proteins Atg5-Atg12, but NLRX1 did not associate with Atg5-Atg12. High throughput quantitative mass spectrometry and endogenous protein-protein interaction revealed an NLRX1-interacting partner, mitochondrial Tu translation elongation factor (TUFM). TUFM interacted with Atg5-Atg12 and Atg16L1, and has similar functions as NLRX1 by inhibiting RLR-induced IFN-I but promoting autophagy. In the absence of NLRX1, increased IFN-I and decreased autophagy provide an advantage for host defense against vesicular stomatitis virus. This study establishes a link between an NLR protein and the viral-induced autophagic machinery via an intermediary partner, TUFM.