Innate immunity: sensing and signalling

Eicke Latz and Katherine A. Fitzgerald

In response to microbial products, distinct families of pattern-recognition receptors
initiate intracellular signalling events that lead to complex immune responses designed
to eliminate invading pathogens. These include receptors that recognize conserved
molecular patterns derived from bacteria, viruses, protozoa and fungi (the TLRs), receptors
that sense fungi (the CLRs), and receptors in the cytosol that sense viral nucleic acids (the
RLRs and DAI) or bacterial products (the NLRs). The NLRs also sense endogenous products
released by dying cells. These receptors, with the exception of the NALP proteins of the
NLR family, recruit adaptor molecules, which in turn create multi-protein platforms to
which additional kinases, transcription factors and possibly other molecules are recruited.
These events ultimately lead to the expression of genes that encode key factors that
regulate the immune response. Some of these factors require additional processing, which
is carried out by members of the NLR family. Given the rapidity at which such interactions
have been described, here, we attempt to summarize our current understanding of these
events in an effort to provide a framework for future studies.

Innate immune receptors

RIG-I TLR3 TLR4 TLR2 TLR5 NALP3 NOD1 NOD2 NALP1 Dectin-1 RLRs and DAI. The cytoplasm contains proteins that sense DNA or RNA
5′-triphosphate RNA dsRNA (viruses) LPS (Gram-negative bacteria) LTA (bacteria) and BLP (bacteria) Flagellin (Gram-negative bacteria) Low intracellular K+ concentration, ATP, iE-DAP MDP MDP β-glucans (yeast) derived from invading viruses. RNA is recognized by the RLR family of
(paramyxoviruses, polyI:C GIPLs (Trypanosoma cruzi) LPS (Porphyromonas gingivalis) TNP, MSU crystals, CPPD crystals, R848 Curdlan (Agrobacterium biobar) proteins, which consists of at least two members, RIG-I and MDA5. LGP2,
F-protein (RSV) Zymosan (yeast) TLR11 Nigericin (Streptomyces hygroscopicus) NALP1b T-cell ligand?
orthomyxoviruses and a related family member (not depicted), may act as a negative regulator
TLR7 and TLR8 Env (MMTV) AraLAM (Mycobacterium spp.) Profilin (Toxoplasma gondii) Aerolysin (Aeromonas hydrophila) Lethal toxin (Bacillus anthracis)
rhabdoviruses) Dectin-2 of these receptors by sequestering RNA. RIG-I recognizes 5′-triphosphate
ssRNA (viruses) Pam2CSK4 and Pam3CSK4 Uropathogenic Escherichia coli (?) Maitotoxin (marine dinoflagellates) IPAF Zymosan (yeast) RNAs, whereas MDA5 is thought to sense dsRNA. The E3-ubiquitin ligase
MDA5 Imidazoquinolines (R848, R837 Gramicidin (Bacillus brevis) Flagellin (Gram-negative bacteria)
dsRNA? (picornaviruses) and Gardiquimod) Alpha toxin (Staphylococcus aureus) TRIM25 induces ubiquitylation of RIG-I, which is essential for RIG-I
TLR1, TLR2, FcγRIII
Nucleoside analogues (Loxoribine) LBP ? (Listeria monocytogenes) FcγRIII Immunoglobulin Fc fragment function.
TLR4 TLR6 TLR5 TLR11 The RLRs contain CARD domains that recruit IPS1 (also known as
DAI RNA–immunoglobulin complexes MAIRI (CD16)
LPS
dsDNA (viruses and bacteria) TREM1 CARDIF, MAVS or VISA), which is an adaptor molecule that is tethered
TLR9 Dectin-1 Dectin-2 to the mitochondria. IPS1 associates with the E3-ubiquitin ligase TRAF3
MD2 LRR
CpG DNA (viruses and bacteria) CD14 and activates the IKK-related kinases TBK1 and IKKε, which
DNA–immunoglobulin complexes phosphorylate and activate IRF3 and IRF7, the key regulators of type I
FcRγ DAP12 IFN gene transcription in most cell types. IKKg, TANK, NAP1 and
Cytoplasm TIR domain SINTBAD form a complex with these kinases. IPS1 also induces NF-κB
TRIF MyD88 ITAM P SYK P P P P activation through FADD and caspase-8 and/or caspase-10, and
Mitochondrion MDA5 P P P activates the MAPKs p38 and JNK. Cells also contain DNA sensors in the
TRAM MAL cytoplasm. One such protein DAI (also known as ZBP1) binds dsDNA
TRIM25 NALP3
Ub IPS1 and activates IRF3 through TBK1.
NOD1 or TLR4 TLR4
β2 integrins TLRs. The TLRs are type I transmembrane receptors found on the plasma
NOD2 CD14
IPS1 TLR3 TLR7, MD2 membrane or in endosomal compartments. Upon ligand binding, they
TLR8, ASC
RIG-I TLR9 recruit adaptor molecules through TIR–TIR interactions. Signalling by
IL-1β Myristoylation TLR5, TLR7, TLR8, TLR9 and TLR11 relies solely on MyD88, whereas TLR1,
Pro-caspase-1
Endosome NOD TLR2 and TLR6 also recruit MAL (also known as TIRAP). TLR3 signals
NALP3 CARD9 PtdIns(4,5)P2
inflammasome Proteolytic P independently of MyD88 and MAL through TRIF (also known as TICAM1).
TRAF3 PKCε TLR4 uses MAL and TRAM to recruit MyD88 and TRIF. MAL is targeted to
RIP1 cleavage
PI5K ARF6
RIP2 CARD9 CARD9
BCL-10 the plasma membrane through a PtdIns(4,5)P2-binding domain, whereas
Proteolytic TRIF
TRAM is anchored though myristoylation at its N-terminus. PKCε
DAI FADD IRAK2, cleavage TRAM MAL MyD88
Pro-caspase-8 Active regulates TRAM function (see TLR4 inset). Signalling through these
TAK1 IRAK4 caspase-1 MALT1 adaptors leads to either NF-κB or IRF3 activation.
TAB2 NLRs IRAK2 and IRAK4, activated by MyD88, are crucial for NF-κB activation.
TAK1 NALP1 They enable the recruitment and activation of TRAF6, which activates
TANK NAP1 TRAF6 TAB3
CARD TAK1 through K63-linked polyubiquitylation. TAK1 in turn activates the
SINTBAD Caspase-8 Caspase-5
IRAK1 IRAK1 IRAK1 Pro-IL-1β IKK complex, which phosphorylates IκB and targets it for ubiquitylation
IKKγ FIIND
TAB2 NALP3 IPAF NAIP and subsequent degradation by the proteasome. NF-κB is then released,
IKKα IKKβ TAK1 translocates to the nucleus and regulates the expression of its target
TBK1 TAB3 IKKγ LRR
TRAF6 TRAF6 TRAF3 TRAF6 IKKα IKKβ MAPKK genes, which include pro-inflammatory cytokines. TAK1 also controls
MAPKK IKKε IKKγ
NAD activation of the MAPK pathway. TRIF activates NF-κB through RIP1,
MAPKK and activates IRF3 through TRAF3, which associates with TBK1 and IKKε
P IκB P IκB NACHT leading to type I IFN gene transcription.
p38 JNK IRF7 IRF3 p50 p65 IRF5 IRF5 IRF7 IRF1 P NFAT p50 p65 p38 JNK ASC TLR7, TLR8 and TLR9 activate NF-κB as well as IRF1, IRF5 and IRF7
p38 JNK
PYD BIR through MyD88. In plasmacytoid DCs IRF7 is a crucial factor for IFN
production, whereas IRF1 and IRF5 control the IFN response in
P P P P P P P P P P P P NFAT P P conventional DCs. IKKa is thought to have a role in IRF7 activation
ATF2 JUN IRF7 IRF3 IRF3 IRF3 p50 p65 ATF2 JUN IRF5 IRF5 IRF7 IRF1 p50 p65 ATF2 JUN
P P P P P P P P P P P P P P in plasmacytoid DCs. IRF5 is activated downstream of most, if not all,
Caspase-1
NF-κB the TLRs through MyD88 and IRAK1 and in this case regulates pro-
inflammatory cytokine production.

Nucleus
Type I IFNs
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Pro-inflammatory
cytokines
including pro-IL-1β
Abbreviations
AraLAM, non-mannose-capped lipoarrabinomannan; ASC, apoptosis-
associated speck-like protein containing a CARD; ATF2, activating
transcription factor 2; BCL-10, B-cell lymphoma 10; BIR, baculoviral IAP
repeat; CARD, caspase-recruitment domain; CLR, C-type lectin receptor;
CPPD, calcium pyrophosphate dihydrate; DAI, DNA-dependent activator of
IRFs; DC, dendritic cell; dsDNA, double-stranded DNA; FADD, FAS-associated
via death domain; FcγR, Fc receptor for IgG; FcR, Fc receptor; FIIND,
function-to-find domain; GIPL, glycoinositolphospholipid; IκB, inhibitor of
NF-κB; iE-DAP, γ‑d‑glutamyl-meso-diaminopimelic acid; IFN, interferon;
IKK, IκB kinase; IL, interleukin; IPAF, ICE-protease activating factor; IPS1,
IFNB-promoter stimulator 1; IRAK, IL-1 receptor-associated kinase; IRF, IFN-
regulatory factor; ITAM, immunoreceptor tyrosine-based activation motif;
JNK, JUN N‑terminal kinase; LBP, LPS-binding protein; LPS, lipopolysaccharide;
LRR, leucine-rich repeat; LTA, lipoteichoic acid; MAL, MyD88-adaptor-like
protein; MALT1, mucosa-associated-lymphoid-tissue lymphoma-translocation
gene 1; MAPK, mitogen-activated protein kinase; MAPKK, MAPK kinase;
Type I IFNs
MDA5, melanoma differentiation-associated gene 5; MDP, muramyl dipeptide;
MMTV, mouse mammary tumour virus; MSU, monosodium urate; MyD88,
myeloid differentiation primary-response gene 88; NACHT, domain present
in NAIP, CIITA, HET‑E and TP1; NAIP, neuronal apoptosis inhibitory protein;
NALP, NACHT-, LRR- and PYD-domain-containing protein; NAP1; NAK-
associated protein 1; NFAT, nuclear factor of activated T cells; NF-κB, nuclear
factor-κB; NLR, nucleotide-binding domain LRR-containing family; NOD,
nucleotide-binding oligomerization domain; Pam2CSK4, Pam2Cys-Ser-Lys-
Lys-Lys-Lys; PGN, peptidoglycan; PI5K, phosphoinositide 5-kinase; PKC,
protein kinase C; polyI:C, polyinosinic–polycytidylic acid; PtdIns(4,5)P2,
phosphatidylinositol-4,5-bisphosphate; PYD, pyrin domain; RIG-I, retinoic-
acid-inducible gene I; RIP, receptor-interacting protein; RLH, RIG-I-like RNA
helicases; RLR, RIG-I-like receptor; RSV, respiratory syncytial virus;
SINTBAD, similar to NAP1 TBK1 adaptor; ssRNA, single-stranded RNA;
SYK, spleen tyrosine kinase; TAB, TAK1-binding protein 1; TAK, TGFβ-
activated kinase; TANK, TRAF-family-member-associated NF-κB activator;
TBK, TANK-binding kinase; TIR, Toll/IL-1 receptor; TLR, Toll-like receptor;
Pro-inflammatory
cytokines
TNP, trinitrophenyl; TRAF, TNF-receptor-associated factor; TRAM, TRIF-
related adaptor molecule; TREM, triggering receptor expressed on myeloid
cells; TRIF, TIR-domain-containing adaptor protein inducing IFNβ; TRIM25,
tripartite-motif-containing 25; Ub, ubiquitin.
Affiliations
Eicke Latz and Katherine Fitzgerald are at the Division of Infectious
Diseases & Immunology, University of Massachusetts Medical School,
364 Plantation Street, Worcester, Massachusetts 01605, USA.
e-mails: eicke.latz@umassmed.edu; kate.fitzgerald@umassmed.edu
Edited by Olive Leavy; copy edited by Marta Tufet;
designed by Simon Bradbrook.
© 2008 Nature Publishing Group.
http://www.nature.com/nri/poster/innate
NLRs. This large receptor family of more than 20 proteins in humans
contains NOD1, NOD2, NALPs, IPAF and NAIP. The NOD proteins
recognize different moieties of bacterial PGN and activate NF-κB through
RIP2 (also known as RICK) and MAPK through CARD9. NALPs and IPAF
form multimolecular complexes termed ‘inflammasomes’ following their
activation. NALP3 recruits the adaptor molecule ASC that in turn recruits
pro-caspase-1, which is activated by autocatalytic cleavage. Cleaved
caspase-1 catalyses proteolytic processing of pro‑IL‑1β (and pro-IL-18,
not shown) into the active cytokines that are then released.
CLRs. Activation of members of the CLR protein family can induce the
production of pro-inflammatory cytokines, promote phagocytosis and
elicit a respiratory burst. SYK interacts with phosphotyrosines within
ITAMs in dectin-1 or in associated signalling chains to initiate a CARD9-
dependent activation of the BCL-10–MALT1 complex. This complex can
subsequently initiate NF-κB signalling through the activation of the IKK
complex. TREM proteins also associate with adaptor proteins that
contain ITAMs to initiate CARD9 signalling. The CLRs trigger MAPK
activation and in the case of dectin-1 activate NFAT in myeloid cells to
regulate pro-inflammatory cytokine production.