Structural mechanisms in NLR inflammasome signaling

Highlights

• We discuss recent advances in understanding inflammasome formation and regulation.

• We compare the recent structure of NLRC4 to Apaf-1 and apoptosomes.

• NLRC4 autoinhibition and NLR oligomerization are discussed.

• The nature of NLRC4 and NLRP3/ASC/caspase-1 inflammasome assemblies is discussed.

• We discuss role and nature of PYD and CARD domains in inflammasomes.

Members of the NOD-like receptor (NLR) family mediate the innate immune response to a wide range of pathogens, tissue damage and other cellular stresses. They achieve modulation of these signals by forming oligomeric signaling platforms, which in analogy to the apoptosome are predicted to adopt a defined oligomeric architecture and will here be referred to as NLR oligomers. Once formed, oligomers of the NLR proteins NLRP3 or NLRC4 ‘recruit’ the adaptor protein ASC and the effector caspase-1, whereby NLRC4 can also directly interact with caspase-1. This results in large multi-protein assemblies, termed inflammasomes. Ultimately, the formation of these inflammasomes leads to the activation of caspase-1, which then processes the cytokines IL-1β and IL-18 triggering the immune response. Here we review new insights into NLR structure and implications on NLR oligomer formation as well as the nature of multi-protein inflammasomes. Of note, so dubbed ‘canonical inflammasomes’ [1] can also be triggered by the NLR NLRP1b and the non-NLR protein AIM2, however the most detailed mechanistic information at hand pertains to NLRC4 while NLRP3 represents the quintessential inflammasome trigger. Thus these two NLRs are mainly used as examples in this article.

Introduction

In humans the NLR protein family comprises 22 members [2, 3, 4], which are capable of sensing a plethora of pathogen-associated or damage-associated molecular patterns (DAMPs or PAMPs) [1, 5, 6]. Sensing these patterns ultimately leads to the oligomerization of initially auto-inhibited monomeric NLRs to form defined NLR oligomers [7] (Figure 1a). Of note, we specifically use the term ‘NLR oligomer’ in the following, since commonly the term inflammasome refers to large multi-protein assemblies also containing ASC and caspase-1 next to NLRs. This is as such different from ‘apoptosomes’ (see below), which commonly refer to the oligomeric form of the NLR relative Apaf-1 and its homologues such as CED4 [8••, 9].

Importantly, once formed, these NLR oligomers recruit or seed apoptosis-associated speck-like protein containing a CARD (ASC) and caspase-1 [10, 11] and as such represent the key regulatory trigger of inflammasome formation. The term (canonical) inflammasome commonly refers to multi-protein assemblies formed by the adaptor protein ASC and effector caspase-1 and the NLRs NLRP3 and NLRC4 as well as NLRP1b and the non-NLR protein AIM2 [1]. Hereby the NLR NLRC4 can also directly interact with and activate caspase-1, yet ASC leads to a stark amplification of this signal, which is outlined in later part of the manuscript.

In any case, NLR oligomerization is the key factor in triggering inflammasome formation. NLR oligomerization however is dependent on the transition of a monomeric NLR to an architecturally defined NLR oligomer. Thus, obtaining structural and mechanistic insight into this event is arguably the most crucial point to understand the regulation of inflammasome formation and, for example, to depict structural features for drug development leveraging this transition to combat aberrant inflammasome signaling in disease.

Although no high-resolution structure is available for such an NLR oligomer, a defined ring-like structure can be implied for NLR inflammasomes based on homologies to a closely related oligomer, the apoptosome [8••, 9, 12, 13]. In analogy to the apoptosome the NLR monomer-to-oligomer transition is strictly dependent on a conformational change of the monomeric NLR [14, 15••, 16•, 17]. This change occurs when the NLR senses PAMPs or DAMPs leading to an opening of the NLR that includes the reorientation of multiple domains and subsequently allows the NLR to oligomerize [1]. The recent structure of a monomeric NLR, NLRC4 [15^••] allowed the first detailed insights into NLR regulatory features as well as their implications on NLR oligomerization and is therefore at the heart of this review. The nature of the subsequent larger multi-protein inflammasome assemblies is less clear and will be discussed in the end of this review.