Degradation triggers the alarm

Inflammasomes are multiprotein complexes that orchestrate proinflammatory cytokine secretion and cell death. Proteases such as anthrax lethal factor can activate an inflammasome known as NLRP1B, but the mechanism for this activation has been unclear. Chui et al. used genome-wide knockout screens to show that proteolysis of NLRP1B by lethal factor induces proteasomal degradation of the amino-terminal domains of NLRP1B and eventual cell death. Sandstrom et al. found that degradation of the amino-terminal domains of NLRP1B resulted in the release of a carboxyl-terminal fragment that activates caspase-1. This process, called “functional degradation,” allows the immune system to detect pathogen-associated activities, much as it recognizes pathogen-associated antigens.
Science, this issue p. 82, p. eaau1330

Structured Abstract


Detection of pathogens by the innate immune system is an essential first step in successful host defense against infection. Pathogens are typically detected by germline-encoded innate immune receptors that bind directly to pathogen-derived ligands. Here, we describe a distinct mechanism of pathogen-sensing mediated by an immune sensor protein called NLRP1B. NLRP1B is not known to bind directly to a pathogen ligand but instead appears to detect the enzymatic activity of lethal factor (LF), a protease toxin produced by the anthrax bacterium, Bacillus anthracis. LF was previously shown to cleave NLRP1B at its N terminus, leading to activation of a multiprotein complex called an inflammasome. Inflammasomes initiate immune responses by activating a proinflammatory protease called caspase-1. However, the mechanism by which cleavage of NLRP1 results in inflammasome assembly was unknown.


NLRP1B is a member of the nucleotide-binding domain leucine-rich repeat (NLR) protein superfamily. Unlike other NLRs, NLRP1B encodes a C-terminal function-to-find domain (FIIND) followed by a caspase activation and recruitment domain (CARD). The FIIND undergoes constitutive autoproteolytic processing, which cleaves NLRP1B into two separate polypeptides, which nevertheless remain noncovalently associated. The functional importance of this distinctive protein architecture has been a long-standing mystery. Also unexplained is the prior observation that NLRP1B activation requires the activity of the proteasome. We therefore sought a mechanism that explains how N-terminal cleavage by LF, FIIND autoprocessing, and the proteasome cooperate to initiate NLRP1B inflammasome formation.


We found that N-terminal cleavage of NLRP1B by LF protease results in destabilization of NLRP1B and its degradation by the proteasome. Paradoxically, NLRP1B inflammasome activation inversely correlated with the stability of the NLRP1B protein after protease cleavage: Proteasome inhibitors stabilized cleaved NLRP1B and prevented NLRP1B inflammasome activation. Indeed, we found that targeted degradation of NLRP1B induced inflammasome activation, even in the absence of protease cleavage, indicating that proteasomal degradation is not only necessary but also sufficient for NLRP1B inflammasome activation. FIIND autoprocessing was required for NLRP1B activation regardless of whether activation occurred via LF cleavage or targeted degradation. To explain these observations, we hypothesized that the function of the proteasome during NLRP1B activation is to degrade the N-terminal domains of NLRP1B, leading to release of a bioactive C-terminal CARD-containing fragment. Consistent with this model, we found that the C-terminal CARD-containing fragment of NLRP1B is sufficient to self-assemble, recruit caspase-1, and form a functional inflammasome. LF protease treatment resulted in specific degradation of the N-terminal domains of NLRP1B, whereas the liberated C-terminal domain associated with inflammasome puncta in cells. We refer to this proteasome-dependent mechanism of NLRP1B inflammasome activation as functional degradation. Similar conclusions were reached independently by Bachovchin and colleagues (this issue).
The functional degradation model raised the possibility that NLRP1B could sense not only proteases but also any pathogen effector that induced proteasomal degradation of NLRP1B. In accord with this prediction, we identified IpaH7.8, an E3 ubiquitin ligase secreted by the pathogen Shigella flexneri, as another activator of NLRP1B. IpaH7.8 directly and specifically ubiquitylates NLRP1B, leading to NLRP1B degradation and inflammasome activation in Shigella-infected macrophages.


We speculate that functional degradation may also explain the activation of other FIIND-containing proteins, such as CARD8 and PIDD1. More broadly, our results reveal a mechanism, distinct from recognition of pathogen-associated ligands, by which hosts can initiate protective immune responses via detection of diverse pathogen-associated activities.
Diverse pathogen enzymes activate the NLRP1B inflammasome by functional degradation.
NLRP1B autoprocesses within the FIIND to generate two noncovalently associated fragments. Cleavage of NLRP1B by anthrax LF, or ubiquitylation by Shigella IpaH7.8, results in proteasome-mediated degradation of NLRP1B, leading to release of the bioactive C-terminal fragment and inflammasome assembly. LRR, leucine-rich repeat; NBD, nucleotide binding domain; Nt, N terminus; Ub, ubiquitylation.


Inflammasomes are multiprotein platforms that initiate innate immunity by recruitment and activation of caspase-1. The NLRP1B inflammasome is activated upon direct cleavage by the anthrax lethal toxin protease. However, the mechanism by which cleavage results in NLRP1B activation is unknown. In this study, we find that cleavage results in proteasome-mediated degradation of the amino-terminal domains of NLRP1B, liberating a carboxyl-terminal fragment that is a potent caspase-1 activator. Proteasome-mediated degradation of NLRP1B is both necessary and sufficient for NLRP1B activation. Consistent with our functional degradation model, we identify IpaH7.8, a Shigella flexneri ubiquitin ligase secreted effector, as an enzyme that induces NLRP1B degradation and activation. Our results provide a unified mechanism for NLRP1B activation by diverse pathogen-encoded enzymatic activities.

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Supplementary Material


Figs. S1 to S7


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Volume 364 | Issue 6435
5 April 2019

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We are grateful to J. Chavarría-Smith for discussions and for laying the experimental foundations for this work. We thank P. R. Beatty and UC Berkeley undergraduates in the MCB150L course for help with generating the 2A12 monoclonal antibody; the Rape laboratory for guidance with ubiquitylation assays; J. Mogridge for the AKR/J Nlrp1b allele construct (21); A. Holland for the AID and TIR1 constructs; the Bachovchin laboratory for the HEK and RAW cell lines and for sharing results before submission; G. Barton, J. Chavarría-Smith, H. Darwin, M. Dorrington, and J. Tenthorey for comments on the manuscript; and members of the Vance and Barton laboratories for discussions. Funding: R.E.V. is an HHMI Investigator and is supported by NIH AI075039 and AI063302. P.S.M. is supported by a Jane Coffin Childs Memorial Fund postdoctoral fellowship. C.F.L. is a Brit d’Arbeloff MGH Research Scholar and is supported by NIH AI064285. Author contributions: Conceptualization, A.S., P.S.M., and R.E.V.; Methodology, A.S., P.S.M., and R.E.V.; Investigation, A.S., P.S.M., L.G., and E.W.M.; Resources, A.S., P.S.M., L.G., C.F.L., and R.E.V; Writing – Original Draft, A.S., P.S.M., and R.E.V.; Writing – Review & Editing, A.S., P.S.M., C.F.L., and R.E.V.; Visualization, A.S. and P.S.M.; Supervision, A.S., P.S.M., C.F.L., and R.E.V. Competing interests: A patent related to this work has been submitted by R.E.V., A.S., and P.S.M. R.E.V. is a scientific advisory board member for Metchnikoff Therapeutics, Inc. Data and materials availability: All data are available in the main text or the supplementary materials.



Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA.
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
Patrick S. Mitchell*
Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA.
Lisa Goers
Department of Microbiology, Harvard Medical School, Boston, MA, USA.
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA.
Department of Microbiology, Harvard Medical School, Boston, MA, USA.
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA.
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.

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These authors contributed equally to this work.
Corresponding author. Email: [email protected]

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