Download Pathogen Recognition by the Innate Immune System

International Reviews of Immunology, 30:16–34, 2011
C Informa Healthcare USA, Inc.
Copyright ISSN: 0883-0185 print / 1563-5244 online
DOI: 10.3109/08830185.2010.529976
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by the Innate Immune
System
Himanshu Kumar,1 Taro Kawai,2 and Shizuo Akira2
1
Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka, Japan, and
Laboratory of Immunology, Indian Institute of Science Education and Research (IISER),
Bhopal, India; 2 Laboratory of Host Defense, WPI Immunology Frontier Research Center,
Osaka, Japan, and Department of Host Defense, Research Institute for Microbial Diseases,
Osaka University, Osaka, Japan
Microbial infection initiates complex interactions between the pathogen and the host. Pathogens
express several signature molecules, known as pathogen-associated molecular patterns (PAMPs),
which are essential for survival and pathogenicity. PAMPs are sensed by evolutionarily conserved,
germline-encoded host sensors known as pathogen recognition receptors (PRRs). Recognition
of PAMPs by PRRs rapidly triggers an array of anti-microbial immune responses through the induction of various inflammatory cytokines, chemokines and type I interferons. These responses
also initiate the development of pathogen-specific, long-lasting adaptive immunity through B and
T lymphocytes. Several families of PRRs, including Toll-like receptors (TLRs), RIG-I-like receptors
(RLRs), NOD-like receptors (NLRs), and DNA receptors (cytosolic sensors for DNA), are known to
play a crucial role in host defense. In this review, we comprehensively review the recent progress
in the field of PAMP recognition by PRRs and the signaling pathways activated by PRRs.
Keywords Innate immunity, Toll-like receptors, RIG-I-like receptors, NOD-like receptors
INTRODUCTION
Invasion of a host by pathogenic infectious agents triggers a battery of immune
responses through interactions between a diverse array of pathogen-borne virulence
factors and the immune surveillance mechanisms of the host. Host–pathogen interactions are generally initiated via host recognition of conserved molecular structures
known as pathogen-associated molecular patterns (PAMPs) [1] that are essential for
the life-cycle of the pathogen. However, these PAMPs are either absent or compartmentalized inside the host cell, and are sensed by the host’s germline encoded pattern
recognition receptors (PRRs), which are expressed on innate immune cells such as
dendritic cells, macrophages and neutrophils [2–5]. Effective sensing of PAMPs rapidly
induces host immune responses via the activation of complex signaling pathways that
culminate in the induction of inflammatory responses mediated by various cytokines
and chemokines, which subsequently facilitate the eradication of the pathogen [2–6].
The innate immune system is the primary, or early, barrier to infectious agents and
acts immediately. Furthermore, the innate immune system also mounts an effective
defense against infectious agents through the initiation of adaptive immunity, which
Address correspondence to Himanshu Kumar, Laboratory of Immunology, Department of
Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Transit
campus: ITI (Gas Rahat) building, Govindpura, Bhopal 460 023, India. E-mail:
[email protected]

Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

is long-lasting and has immunological memory. Adaptive immunity is mediated
via the generation of pathogen (antigen)-specific B and T lymphocytes through a
process of gene rearrangement [7, 8]. To date, several classes of PRRs, such as Toll-like
receptors (TLRs), RIG-I-like receptors (RLRs), NOD-like receptors (NLRs) and DNA
receptors (cytosolic sensors for DNA), have been discovered and characterized. These
PRRs are at the forefront of both extracellular and intracellular pathogen recognition
and sense various classes of molecules including proteins, lipids, carbohydrates and
nucleic acids [2–6]. In this review, we discuss recent progress in our understanding of
PAMP recognition and signaling through the various PRRs.
TLRs
TLRs are the most widely studied PRRs and are considered to be the primary sensors
of pathogens. The field of TLR immunobiology expanded rapidly after the discovery
of toll proteins in flies [9]. In humans, 10 TLR family members have been identified
(there are 12 in mice). TLR1 to 9 are conserved in both humans and mice. TLR10 is
expressed in humans but not in mice (because of a stop codon in the murine TLR10
gene), whereas TLR11 is expressed in mice, but not in humans. TLR10 in humans and
TLR12 and TLR13 in mice are not well characterized and their function remains unclear [2]. TLR1, 2, 4, 5 and 6 are primarily expressed on the cell surface and recognize
PAMPs derived from bacteria, fungi and protozoa, whereas TLR3, 7, 8 and 9 are exclusively expressed within endocytic compartments and primarily recognize nucleic acid
PAMPs derived from various viruses and bacteria [2, 3, 6]. TLRs are type I membrane
glycoproteins and consist of extracellular leucine rich repeats (LRRs) that are required
for PAMP recognition, and a cytoplasmic Toll/interleukin-1 receptor (TIR) domain, required for downstream signaling. The crystal structure of the extracellular recognition
domain of several TLRs bound to their agonist or antagonist PAMPs has been characterized. TLRs have a unique horseshoe, or “m” shaped architecture [10, 11]. TLR1
and TLR2 form stable heterodimers and the addition of Pam3CSK4 (a ligand for TLR1TLR2) activates downstream signaling. The TLR1-TLR2-Pam3CSK4 crystal shows that
two of the three hydrophobic lipid chains on Pam3CSK4 are submerged in the hydrophobic spaces within TLR2, with the remaining hydrophobic lipid chain penetrating into the hydrophobic space within TLR1 [12]. The crystal structure of TLR4 bound
to Lipid A (an agonist PAMP) or Eritoran (an antagonist PAMP) has also been reported.
Lipid A is composed of phosphorylated diglucosamine and six acyl chains, whereas Eritoran consists of phosphorylated diglucosamine and four acyl chains. Crystal structure studies suggest that five acyl chains of lipid A and four acyl chains of Eritoran are
submerged within the hydrophobic space of MD2 (myeloid differentiation factor-2), a
co-receptor for TLR4, and the remaining acyl chain of lipid A is submerged within the
hydrophobic space of TLR4. This facilitates the interaction between MD2 and TLR4
that is required for downstream signaling, which is not the case for Eritoran. Therefore, lipid A activates the TLR4 signaling pathway, but Eritoran does not [13, 14]. Furthermore, co-crystallization of TLR3 with dsRNA shows that the recognition domain of
TLR3 has a horseshoe-shaped solenoid structure and that dsRNA binds to the lateral
convex surface of the TLR3 ectodomain [15].
PAMPs RECOGNIZED BY TLRs
Rapid progress has been made not only in our understanding of the structure of TLRs
but also in revealing the complexity of TLR-mediated signaling and in the identification of PAMPs derived from microbial pathogens such as mycobacteria, bacteria,
viruses, fungi and parasites. The PAMPs recognized by the various TLRs are shown in
C Informa Healthcare USA, Inc.
Copyright 
H. Kumar et al.
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
TABLE I TLR Ligands and Cellular Location
TLR and
(co-receptors)
Cellular
localization
TLR1/2
TLR2 (Dectin-1,
C-type lectin)
Cell surface
Cell surface
TLR3
Endosome
TLR4 (MD2, CD14,
LBP)
Cell surface
TLR5
TLR6/2 (CD36)
TLR7
Cell surface
Cell surface
Endolysosome
TLR8 (only in
human)
TLR9
Endolysosome
TLR11 (only in
mouse)
Cell surface
Endolysosome
TLR ligands
Triacyl lipopeptides
Peptidoglycan, lipoarabinomannan, hemagglutinin,
phospholipomannan, glycosylphosphophatidyl
inositol mucin, zymosan
ssRNA virus, dsRNA virus, respiratory syncytial virus,
murine cytomegalovirus
Lipopolysaccride, mannan, glycoinositolphospholipids,
envelope and fusion proteins from mammary tumor
virus and respiratory syncytial virus, respectively,
endogenous oxidized phospholipids produced after
H5N1 avian influenza virus infection, pneumolysin
from streptococcus pneumonia, paclitaxel.
Flagellin from flagellated bacteria
Diacyl lipopeptides from mycoplasma), lipoteichoic acid
ssRNA viruses, purine analog compounds
(imidazoquinolines). RNA from bacteria from group B
streptococcus
ssRNA from RNA virus, purine analog compounds
(imidazoquinolines).
dsDNA viruses herpes simplex virus and murine
cytomegalovirus, CpG motifs from bacteria and
viruses, hemozoin malaria parasite
Uropathogenic bacteria, profillin-like molecule from
Toxoplasma gondii
Table I and have been discussed in great detail in several recent reviews [2, 3, 6]. Several of the bacterial, viral, fungal and parasite PAMPs sensed by TLRs are described
below.
BACTERIAL PAMPs SENSED BY TLRs
Of the TLRs, TLR1, 2, 4, 5, 6, 7, and 9 are primarily dedicated to the recognition of
various bacterial components. LPS is a major cell wall component of gram-negative
bacteria and is primarily sensed by TLR4 complexed with another molecule known as
MD2 [16, 17]. Another essential major component of gram-positive bacteria is peptidoglycan, which is sensed by TLR2 [18]. Mycobacteria, another class of bacteria rich in
lipoarabinomannan (LAM), are also sensed by TLR2 [19]. TLR2 (in conjugation with
TLR1 or TLR6) senses diacyl or triacyl lipopeptides on bacteria, mycobacteria and mycoplasma [6, 20]. TLR5 and TLR9 sense the flagellin protein expressed by flagellated
bacteria and bacterial/viral genomic DNA rich in unmethylated CpG, respectively [6,
20].Group B streptococci, which reside in the phagosome, are recognized by TLR7 [21].
Also, bacterial RNA produced in the lysosomal compartment is likely to act as a PAMP
for TLR7 [21]. Recognition of PAMPs by TLR1, TLR2, TLR4, TLR5 and TLR6 primarily
induces the production of inflammatory cytokines, whereas TLR7 and TLR9 induce
type I interferons.
VIRAL PAMPs SENSED BY TLRs
Nucleic acids (single stranded (ss)/double stranded (ds) RNA or ss/dsDNA) derived
from viruses are recognized by several TLRs. DNA from herpes simplex virus (HSV),
murine cytomegalovirus (MCMV), as well as CpG motifs containing synthetic oligonucleotides that contain unmethylated CpG DNA, are sensed by TLR9, which induces
the production of type I interferons, most likely through plasmacytoid dendritic cells
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

(pDCs) [2, 3, 6, 20]. RNA from RNA viruses is sensed by TLR7 and TLR8 (the function of
murine TLR8 is not known). In addition, several synthetic antiviral compounds, such
as R848, imiquimod and loxoribine, are also sensed by TLR7 and TLR8. Furthermore,
the synthetic analog of dsRNA, known as poly IC, is sensed by TLR3 which also activate
adaptive immunity when used as an vaccine adjuvant [22–24]. Another PAMP derived
from viruses is a coat protein. The coat proteins of respiratory syncytial virus (RSV) and
mouse mammary tumor virus (MMTV) are sensed by TLR4. However, in vivo studies
show that TLR2 and TLR6 play an essential role in controlling RSV infection. The coat
proteins of other viruses, such as the Measles virus hemagglutinin protein, are also
sensed by TLR2, as is Vaccinia virus. Notably, this recognition induces the production
of type I interferons by inflammatory monocytes [2, 3, 6, 20].
FUNGAL PAMPs SENSED BY TLRs
Several fungi, such as Candida albicans and Aspergillus fumigatus, are sensed by
several TLRs and induce inflammatory responses. However, this recognition requires
additional receptors such as dectins, CD14, mannose receptors, and DC-SIGN. βglucans are the primary component of the majority of fungal cell walls, including those
of baker’s yeast and some pathogenic fungi such as Candida albicans. These β-glucans
are recognized by TLR2 in association with dectin-1. Glucuronoxylomannans, another
fungal component sensed by CD14 and TLR4, also induce inflammatory responses [2,
3, 6, 20, 25].
PROTOZOAL PAMPs SENSED BY TLRs
Protozoal infections are a serious problem in developing countries and cause
diseases such as Toxoplasmosis (Toxoplasma gondii), malaria (Plasmodium
species), leishmaniasis (Leishmania species), and sleeping sickness (Trypanosoma
brucei). Unsaturated alkylacylglycerol and lipophosphoglycan (LPG) from Trypanosoma species and Leishmania species, respectively, are recognized by TLR2,
and glycoinositolphospholipids and glycosylphosphatidylinositol anchors from
Trypanosoma species, P. falciparum and T. gondii are recognized by both TLR2 and
TLR4. The profilin-like protein of T. gondii is sensed by murine TLR11. The genomic
DNA and hematin crystals of Trypanosoma and Plasmodium species, respectively,
are sensed by TLR9 [2, 3, 6, 20].
TLR SIGNALING
TLR signaling is primarily meditated via the recruitment of different TIR domaincontaining adaptor molecules such as MyD88, TRIF (TICAM-1), TIRAP (Mal), and
TRAM to the TIR domains of the different TLRs [2, 3, 6, 20]. Recruitment of these adaptor molecules activates various transcription factors such as NF-κB, IRF3/7, and MAP
kinases to induce the production of pro-inflammatory cytokines and type I interferons (Fig. 1). All TLRs, except for TLR3, recruit MyD88 and initiate MyD88-dependent
signaling to activate NF-κB and MAP kinases to induce proinflammatory cytokines in
macrophages and cDCs. In addition to MyD88, TLR1, TLR2, TLR4 and TLR6 recruit
TIRAP to initiate MyD88-dependent signaling. TLR3 and TLR4 recruit TRIF and initiate TRIF-dependent signaling to activate NF-κB and IRF3 to induce production of
pro-inflammatory cytokines and type I interferons. TLR4 recruits TRIF via an additional adaptor molecule, TRAM. TLR4 activates both MyD88- and TRIF-dependent
signaling via recruitment of all four adaptors. TLR4 first recruits TIRAP, which facilitates the recruitment of MyD88 to initiate the first phase of NF-κB and MAPK
C Informa Healthcare USA, Inc.
Copyright Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.

H. Kumar et al.
FIGURE 1 PRRs-mediated signaling.
Toll-like receptor (TLR) signaling. Recognition of PAMPs by plasma membrane-localized TLRs,
such as TLR4, TLR5, TLR11, and TLR2 (TLR2 forms a heterodimer with TLR1 or TLR6 to form a
functional receptor complex) and endosomal-localized TLRs, such as TLR3, TLR7, and TLR9, activates TLR signaling pathways. Endosomal-localized TLRs are transported to the endosomal compartment via the ER-localized protein, UNC93B. All TLRs, except TLR3, recruit MyD88 and activate MyD88-dependent signaling. TLR1, 2, 4, and 6 recruit the additional adaptor molecule, TIRAP,
for the recruitment of MyD88. TLR3 recruits TRIF and activates TRIF-dependent signaling. TLR4
also activates TRIF-dependent signaling through an additional adaptor molecule, TRAM. In cDCs,
MyD88-dependent signaling is initiated through the recruitment and activation of various signaling
molecules, such as IRAK family proteins, TRAF6, and TAK1 which, in turn, activate the IKK complex. The active IKK complex activates NF-κB subunits to initiate the transcription of inflammatory
cytokine genes. In pDCs, the TLR7 and TLR9-mediated signaling pathways activate NF-κB via an
MyD88-dependent signaling pathway in the same manner as for cDCs. In addition, stimulation with
TLR7 and TLR9 ligands induces MyD88-dependent type I interferon production through a direct interaction between MyD88 and IRF7 via IRAK family proteins and phosphorylated IRF7. Phosphorylated IRF7 translocates to the nucleus and initiates the transcription of type I interferons. cDCs
stimulated with TLR3 PAMPs activate the TRIF-dependent signaling pathway through recruitment
of TRIF to induce transcription of inflammatory cytokines and type I interferons through the IKK
complex and TBK1/IKKi, respectively, via the activation of NF-κB and IRF3/IRF7.
RIG-I-like receptor (RLR) signaling. Recognition of PAMPs by cytosolic sensors, such as RIG-I and
Mda5, activates signaling through the mitochondria-localized adaptor protein IPS-1 leading to the
activation of NF-κB and IRF3/IRF7 through the IKK complex and TBK1/IKKi, respectively, which
results in the production of inflammatory cytokines and type I interferons. LGP2, another member
of the RLR family, potentiates the RIG-I- and MDA5-mediated signaling pathways.
Cytosolic DNA sensor-dependent signaling. PAMPs in the cytoplasm of cells are sensed by cytosolic
DNA sensors, or DAI, which activate NF-κB and IRF3/IRF7 via the IKK complex and TBK1/IKKi, respectively, and the ER-localized protein, STING. Recognition of DNA by AIM2 also induces the maturation of proIL-1β to IL-1β through an inflammasome complex consisting of ASC and caspase-1.
Nod-like receptor (NLR) signaling. Recognition of PAMPs by NOD1 and NOD2 initiates the recruitment of RICK, which activates NF-κB via the IKK complex. Another member of the NLR family constitutes the inflammasome. The inflammasome is a multi-protein complex required for the maturation or activation of pro-IL-1 family cytokine to its bioactive IL-1 family cytokine. Activation of
the inflammasome requires two steps. First, NF-κB-dependent up-regulation of the pro-forms of
the cytokine and, second, conversion of the inactive form of the cytokine to a bioactive form by the
inflammasome.
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

activation. For TRIF-dependent signaling, TLR4 is trafficked to the endosome via
dynamin-dependent endocytosis and forms a complex with TRAM and TRIF. This
complex initiates the TRIF-dependent signaling required for IRF3 activation, which
induces type I interferon and this signaling pathway activates second-phase of NFκB and MAPK activation for the induction of inflammatory cytokines [26]. In cDCs,
UNC93B1 (a protein localized to the endoplasmic reticulum (ER)) plays a critical role
in the transportation of endosome-localized TLRs, such as TLR3, TLR7, and TLR9.
Mice with a mutation in this protein show complete abrogation of all cytokine production after stimulation with their respective PAMPs [27–29].
MyD88-DEPENDENT SIGNALING PATHWAYS
Stimulation of macrophages and DCs with TLR PAMPs initiates MyD88-dependent
signaling via recruitment of IRAK-family signaling proteins (Fig. 1) [2, 3, 6, 20]. First,
IRAK4 is activated and recruited by MyD88. Then, IRAK1 and IRAK2 are sequentially activated and recruited to form an active signaling complex which interacts with
TRAF6 (an E3 ligase required for Lys63 (K63)-linked poly-ubiquitination). Recently,
the crystal structure of the MyD88-IRAK4-IRAK2 complex was reported and shows a
left-handed helical oligomeric signaling complex, which consists of six, four, and four
molecules of MyD88, IRAK4, and the IRAK2 death domain, respectively [30]. MyD88
then recruits IRAK4 and this complex recruits the IRAK4 substrates, IRAK2 or IRAK1.
Formation of this signaling complex facilitates the phosphorylation of all these kinases, resulting in the activation of downstream signaling molecules. TRAF6, along
with E2 ubiquitin-conjugating enzymes, such as Ubc13 and Uev1A, ubiquitinates both
itself and IRAK1 to activate TAK1 [31]. Activated TAK1 then activates NF-κB and MAP
kinases to initiate the transcription and translation of various proinflammatory cytokines, chemokines, interferons, and other TLR-inducible genes. TLR4-mediated signaling also recruits TRAF3 to the MyD88 multiprotein complex, where it undergoes
K48-linked ubiquitination and degradation. This results in TAK1 activation and subsequent induction of inflammatory cytokines [32].
Of the TLR inducible-genes, several (IkBz, IkB-NS, ATF3, C/EBP, and the zincfinger proteins Zc3h12a and tristetraprolin) have been characterized [33–38]. IκBζ
and C/EBPd positively regulate the expression of IL-6 and IL-12p40. In contrast, IκBNS and ATF3 negatively regulate NF-κB-driven proinflammatory cytokines, such as
IL-6, IL-12p40, and TNFα. The zinc finger protein, Zc3h12a, consists of a CCCH-type
zinc-finger domain and an RNase domain and is involved in IL-6 mRNA and IL-12p40
mRNA degradation. Stimulation with TLR PAMPs induces large amounts of IL-6 and
IL-12p40 in macrophages lacking Zc3h12a compared with wild-type cells. Furthermore, mice lacking Zc3h112a show elevated serum immunoglobulins and autoantibody production. Another protein, tristetraprolin, which regulates the degradation of
TNFα mRNA by removing the poly(A) tail, plays a critical role in the development of
autoimmune arthritis.
In pDCs, MyD88 is required for the production of both proinflammatory cytokines
and type I interferons. In pDCs stimulated with TLR7 and TLR9 PAMPs, MyD88 recruits various signaling proteins, such as IRAK4, TRAF6, TRAF3, IRAK1, and IKKa,
which phosphorylate IRF7 to initiate the transcription of type I interferons. Other proteins, such as osteopontin (a protein induced after stimulation with TLR9), phosphoinositol 3 kinase (PI3K), mTOR (downstream of PI3K), and p70S6K, also play critical
roles in IRF7 activation [2, 3, 6, 20].
pDCs and cDCs stimulated with CpG (a TLR9 PAMP) are transported to the endolysosome, where TLR9 is cleaved by cathepsins B, K, and L and an asparagine endopeptidase. This cleaved form triggers TLR9-mediated induction of proinflammatory cytokines and type I interferons. Stimulation with TLR7 PAMPs also requires
C Informa Healthcare USA, Inc.
Copyright 
H. Kumar et al.
acidification of the endolysosomal compartment; however, it remains unclear
whether TLR7 needs to be cleaved for PAMP recognition [39–43].
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
TRIF-DEPENDENT SIGNALING PATHWAYS
Macrophages and DCs stimulated with TLR3 and TLR4 PAMPs trigger TRIFdependent signaling, which leads to the production of proinflammatory cytokines
and type I interferons via activation of NF-κB, MAP kinases and IRF3 (Fig. 1) [2, 3,
6, 20]. TRIF-dependent signaling is initiated through the recruitment of TRAF6 and
RIP1 to the distinct domain of TRIF. The interaction of TRAF6 with TRIF (N-terminal
TRAF-binding domain) activates TAK1 via mechanisms similar to those in the MyD88dependent pathway. However, TRIF interacts with RIP1 and undergoes K63-linked
polyubiquitination. RIP1 also interacts with TRADD, and this multiprotein complex
is required for NF-κB activation. TRIF recruits non-canonical IKKs, such as TBK1 and
IKKi (IKK), via TRAF3 to phosphorylate IFR3. Phosphorylated IFR3 translocates to
the nucleus and initiates the transcription of type I interferons. TRAF3 plays a critical
role in the regulation of both MyD88-dependent and TRIF-dependent signaling because TRAF3 degradation via K48-linked ubiquitination activates MyD88-dependent
signaling and suppresses TRIF-dependent signaling (and vice versa). Furthermore,
NRDP1, a RING-containing E3 ligase, regulates both MyD88-dependent and TRIFdependent signaling via its interaction with TBK1. K63-linked ubiquitination activates
TBK1 and suppresses the MyD88-mediated pathway. This suggests that cells have
mechanisms for regulating both signaling pathways to avoid injurious effects due to
overproduction of inflammatory cytokines during microbial infection.
RIG-I-LIKE RECEPTORS
The RLR family consists of three members, namely, RIG-I, MDA5, and LGP2. These
sensors recognize the RNA from RNA viruses in the cytoplasm of infected cells and induce inflammatory cytokines and type I interferons. Inflammatory cytokines primarily
initiate and co-ordinate various innate immune responses through recruitment of professional immune cells such as macrophages and dendritic cells [3, 6, 44]. Type I interferons consist of several structurally related IFN-α proteins and a single IFN-β protein,
which can bind directly to infected cells in an autocrine or paracrine manner through a
common receptor and initiate the transcription of several interferon-stimulated genes
(ISGs). Type I interferons, together with ISGs, induce an antiviral state in all infected
and healthy cells by altering various cellular processes. This inhibits viral replication,
induces apoptosis in infected cells, increases the lytic capacity of natural killer cells,
up-regulates the expression of MHC class I molecules and activates various components of the adaptive immune response.
STRUCTURE OF RLRs
RIG-I and MDA5 contain N-terminal tandem CARDs that are essential for downstream
signaling. LGP2 lacks the CARD domain, suggesting a negative regulatory role for
LGP2 in RIG-I- and MDA5-mediated signaling [3, 6, 44, 45]. However, genetic studies
show that LGP2 acts as a positive regulator of RIG-I- and MDA5-mediated signaling
[46]. RIG-I contains a repressor domain (RD), which is required for the regulation of
RIG-I-dependent downstream signaling. All three members contain an intermediate
DExD/H-box RNA helicase domain, which is required for ligand recognition or binding. This domain also contains ATPase activity and mice lacking ATPase activity (due
to a point mutation) in the LGP2 molecule do not produce type I interferons upon
International Reviews of Immunology
Pathogen Recognition by Innate Immunity
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
TABLE II

RLR Ligands and Cellular Location
RLRs
Cellular
localization
RIG-I
Cytoplasm
MDA5
Cytoplasm
RIG-I and
MDA5
Cytoplasm
Ligand and RNA viruses recognized by sensors
Short double-stranded RNA (up to 1 kb) with triphosphate or
monophosphate at 5 end; short length of poly IC, Newcastle
disease virus (negative-sense, single strand); Sendai virus
(negative-sense, single strand); vesicular stomatitis virus
(negative-sense, single strand); respiratory syncytial virus
(negative-sense, single strand); influenza A virus
(negative-sense, single strand); Ebola virus (negative-sense,
single strand); Japanese encephalitis virus (positive-sense,
single strand); hepatitis C virus (positive-sense, single strand)
Long length of poly IC, encephalomyocarditis virus
(positive-sense, single strand); mengovirus (positive-sense,
single strand); Theiler’s virus (positive-sense, single strand);
poliovirus (positive-sense, single strand)
Reovirus (double strand); dengue virus (positive-sense, single
strand); West Nile virus (positive-sense, single strand)
viral infection, suggesting that the ATPase activity of RLR members may be essential
for antiviral responses [46].
PAMPs OR VIRUSES RECOGNIZED BY RLR
RIG-I mainly recognizes members of paramyxoviridae family of viruses such as Newcastle Disease Virus (NDV) and Vesicular stomatitis virus (VSV). RIG-I-deficient cells
show reduced production of inflammatory cytokines and type I interferons [47]. In
addition, RIG-I recognizes members of the flaviviridae family, such as Japanese Encephalitis Virus (JEV) and Hepatitis C Virus (HCV) (Table II). MDA5 recognizes members of the picornaviridae family, such as the Polio Virus and encephalomyocarditis
virus (EMCV) (Table II) [48, 49]. RIG-I also recognizes enzymatically synthesized RNA
in vitro. It was thought that single-stranded RNAs bearing a 5 triphosphate were the
only essential component for this recognition [50, 51]; however, recent studies suggest that, during the enzymatic synthesis of RNA, a secondary structure for double
stranded RNA is generated, which acts as a RIG-I ligand [52, 53]. Chemically synthesized single-stranded RNA bearing a 5 triphosphate cannot induce inflammatory cytokines and type I interferons, whereas chemically synthesized double-stranded RNA
can, irrespective of whether there is a triphosphate or monophosphate group at the 5
end [54, 55].
MDA5 also recognizes the synthetic double stranded RNA analog, poly IC, when
this molecule is introduced into the cell [48]. Interestingly, enzymatically shortened
poly IC is preferentially recognized by RIG-I, rather than by MDA5, suggesting that
RIG-I and MDA5 recognize different lengths of double stranded RNA. Extrapolation
of these results may provide a possible clue for the differential recognition of viruses.
Furthermore, some viruses, such as dengue virus and West Nile Virus, require recognition by both RIG-I and MDA5 to generate a robust innate immune response [55].
The third member of the RLR family, LGP2, was considered as a negative regulator
of RIG-I- and MDA5-mediated signaling [56–58]. However, in vivo studies using LGP2deficient mice and mice harboring an inactive ATPase in the DExD/H-box RNA helicase domain show that LGP2 acts as a positive regulator of RIG-I- and MDA5-mediated
signaling after infection by RIG-I- and MDA5-specific RNA viruses. This suggests that
C Informa Healthcare USA, Inc.
Copyright 
H. Kumar et al.
LGP2 might facilitate the accessibility of viral RNA by RIG-I or MDA5 to induce robust
responses [46].
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
RLR SIGNALING
Viral infection is initiated either through direct introduction of viral nucleic acids
(PAMPs) or through the receptor mediated endocytosis and subsequent liberation of
viral nucleic acids (PAMPs) into the cytoplasm of the host cells [3, 6, 44, 45]. In the
cytoplasm, RIG-I and MDA5, along with LGP2, sense the viral RNA, which probably
leads to conformational changes within these sensors exposing the CARD domains
of RIG-I and MDA5, which then interact with the CARD-containing adaptor protein,
IPS-1 (also known as MAVS, Cardif, and VISA) [59–64]. IPS-1 localizes to the mitochondria, a process important for downstream signaling [60]. Recently, it has been shown
that IPS-1 is also localized on peroxisomes, and that peroxisomal IPS-1 and mitochondrial IPS-1 are required for robust antiviral responses. Peroxisomal IPS-1 induces
early responses through the induction of interferon-stimulating genes (ISGs) via the
transcription factor, IRF1, whereas mitochondrial IPS-1 induces delayed responses
through induction of ISGs and type I interferons via IRF3 [65]. Upon recruitment of
RIG-I and MDA5, IPS-1 activates the IKK-related kinase, TBK1/IKKi, which activates
IRF3/IRF7 and the subsequent transcription of type I interferons via TRAF3. IPS-1 also
activates NF-κB through recruitment of TRADD, FADD, caspase-8, and caspase-10 [59,
66]. Recently, an IPS-1-interacting protein, EYA4, was found to enhance interferon induction upon NDV and VSV infection [67]. EYA4 has phosphatase activity for phosphotyrosine and phosphothreonine and this activity is required for antiviral responses
(Fig. 1).
IPS-1 is negatively regulated by an NLR family protein known as NLRX1, which is
localized in mitochondria. NLRX1 interacts with IPS-1 at the outer membrane and inhibits IPS-1-mediated antiviral responses [68]. Furthermore, IPS-1 is also negatively
regulated by the autophagy-related proteins, Atg5 and Atg12. MEF and DCs lacking
autophagosome components, such as Atg5 and Atg12, show enhanced production of
type I interferons after RNA virus infection because malfunctioning mitochondria and
the IPS-1 associated with these mitochondria lead to the production of reactive oxygen species (ROS) [69]. Enhanced ROS production increases the production of type I
interferons.
The initial recognition by RIG-I is positively regulated by TRIM25 and RNF135 (a E3
ubiquitin ligase) via K63-linked ubiquitination [70, 71]. However, K48-linked ubiquitination of RIG-I by RNF125 leads to the down regulation of RIG-I-mediated signaling
[72]. Recently, the mechanism underlying the activation of RIG-I was reported. The
CARDs within RIG-I require K63-linked ubiquitination in the presence of RNA and
ATP. Furthermore, free K63-linked ubiquitin chains activate RIG-I-dependent downstream signaling, suggesting that free ubiquitin chains are the endogenous ligands of
RIG-I [73].
TLR INDEPENDENT DNA RECOGNITION
Introduction of DNA, plasmid DNA (used for DNA vaccines), or DNA from dying cells
into immune or non-immune cells, or infection with DNA viruses or pathogenic bacteria such as Listeria monocytogenes and Legionella pneumophila, induces the production of TLR9-independent type I interferons [3, 6, 74–76]. This indicates that cells
possess an additional sensor(s) for DNA. Studies show that induction of type I interferons in response to DNA requires TBK1/IKKi. DAI (also known as DLM1 and
ZBP1) is a cytoplasmic DNA sensor. In vitro studies, show that DAI is essential for type
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

I interferon production via TBK1/IKKi [77]; however, genetic studies show that DAI is
not essential for type I interferon production after the introduction of DNA, suggesting
that cells possess an unidentified DNA sensor [78].
Recently, the mechanism for poly dA:dT-induced type I interferon production was
elucidated by two independent groups [79, 80]. The results show that poly dA:dT introduced into cells is first transcribed into RNA by polymerase III, and this RNA has a
double stranded conformation. This dsRNA is then sensed by RIG-I, which activates
the RIG-I-IPS-1 signaling axis to induce type I interferons [79, 80]. However, introduction of poly dA:dT into RIG-I-deficient cells results only in a marginal reduction in type
I interferon production suggesting that cells requires other DNA sensors for poly dA:dT
recognition in addition to RIG-I, which senses the secondary metabolic products derived from the introduced DNA. Furthermore, another ER-localized protein, STING
(also known as TMEM173, ERIS, or MITA), was identified by functional screening for
IFN-β promoter activators [81–83]. STING interacts with TBK1 and induces type I interferon production after stimulation by DNA and RNA. However, STING does not interact directly with DNA, suggesting that STING acts downstream of an unidentified
DNA sensor. STING-deficient mice are highly susceptible to the DNA virus, HSV, and
the RNA virus, VSV, suggesting a role for STING in innate immune defense against various viruses [84]. Recently, ATG9a was implicated in the regulation of STING-mediated
TBK1 activation (Fig. 1). Cells lacking ATG9a show increased activation of TBK1 and
production of type I interferons by promoting the assembly of STING with TBK1 [85].
NLRs
NOD-like receptors (NLRs) are a family of molecules that sense a wide range of ligands
within the cytoplasm of cells. This family comprises 23 members in humans and approximately 34 in mice. Among NLRs member functions of several NLR members are
well characterized [3, 6, 86–88]. These sensors comprise three domains: the C-terminal
domain consists of several (LRRs) and is thought to be involved in the recognition of
microbial PAMPs, or endogeneous host molecules; the N-terminal domain consists
of a death effector domain (DED), a Pyrin domain (PYD), a CARD, baculovirus inhibitor repeats (BIRs) and an acidic domain (which is required for homotypic interactions with downstream signaling proteins); and an intermediate domain consisting
of nucleotide-binding and oligomerization (NACHT) domains, which are required for
ligand-induced, ATP-dependent oligomerization of the sensors and formation of active receptor complexes for activation of downstream signaling. Upon recognition of
PAMPs, these sensors either activate NF-κB or MAP kinases to induce the production
of inflammatory cytokines, or activate a multiprotein-complex, the “inflammasome,”
which either initiates the proteolytic cleavage (or maturation) of various caspases resulting in the maturation and production of inflammatory cytokines, such as IL-1β
and IL-18, or initiates cell death.
NOD1 AND NOD2
NOD1 and NOD2 (also known as CARD4 and CARD15, respectively) comprise Cterminal LRRs, a central oligomerization domain and an N-terminal domain containing either one (NOD1) or two (NOD2) CARDs. These proteins are mainly expressed
in the cytosol of various cells. However, expression on the plasma membrane has also
been reported [89, 90]. NOD1 and NOD2 recognize peptidoglycans, a major component of bacterial cell walls. NOD1 and NOD2 recognize iE-DAP and MDP, respectively
[91]; however, evidence for the direct recognition of these PAMPs is lacking. NOD1 and
NOD2 also recognize various pathogenic microbial pathogens (Table III) [6]. NOD2
C Informa Healthcare USA, Inc.
Copyright 
H. Kumar et al.
TABLE III NLR Ligands and Cellular Location
NLRs
Cellular
localization
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
NOD1 (CARD4) Cytoplasm
NOD2
(CARD15)
Cytoplasm
NLRP1 (NALP1) Cytoplasm
NLRP3 (NALP3, Cytoplasm
CIAS1 and
Cryopyrin)
NLRC4 (IPAF,
CLAN)
Cytoplasm
Ligand or pathogen
γ -D-glutamyl-meso-diaminopimelic acid (iE-DAP)
(a dipeptide) from Bacillus subtilis, Listeria
monocytogenes, entropathogen (Escherichia coli),
Shigella Flexneri, Pseudomonas aeruginosa,
Chlamydia pneumoniae, Campylobacter jejuni
and Helicobacter pylori
Muramyl dipeptide (MDP) from Streptococcus
pneumonia, Mycobacterium tuberculosis, Listeria
monocytogenes, Salmonella typhimurium,
Shigella Flexneri and Staphylococcus aureus
Muramyl dipeptide (MDP) is recognized by human
NLRP1, lethal toxin from Bacillus anthracis is
recognized by mouse NLRP1b
Crystals (uric acid, calcium pyrophosphade
dehydrate), extracellular ATP, fibrillar amyloid-β
peptide, hyaluronan, pollutants (silica and
asbestos), bacterial and viral RNA, poly IC,
antiviral compound (R837 and R848), toxins
(nigericin and maitotoxin), UV light, skin irritant
(picryl chloride and 2,4-dinitrofluorobenzene),
vaccine adjuvant (alum), fungi (Candida albican
and Saccharomyces cerevisiae), β-glucan,
bacteria (Listeria monocytogenes and
Staphylococcus aureus), Viruses (Sendai virus,
adenovirus and influenza virus)
Shigella flexneri, Salmonella typhimurium,
Pseudomonas aeruginosa, Legionella
pneumophila, Flagellin delivered into the
macrophages (In addition to NLRC4, NAIP5
recognize flagellin. Furthermore, TLR5 also
recognizes flagellin on surface of cells to induce
proinflammatory cytokine through NFκB and
MAP kinases)
is also important for defense against pathogenic protozoal parasites, such as Toxoplasma gondii [92]. PAMP recognition initiates oligomerization of these sensors, which
subsequently recruit a CARD-containing adaptor protein known as RIP2 (RICK) via
CARD-CARD interactions, and activate NF-κB and MAP kinases to induce the transcription of inflammatory cytokines (Fig. 1) [89, 90]. In humans, NOD1 and NOD2
variants have been reported; NOD1 variants are associated with elevated levels of IgE,
and a propensity toward asthma and atopic eczema [93, 94]. NOD2 variants are associated with chronic inflammation of the intestine, and these patients are susceptible
to Crohn’s disease [95, 96].
NLRC5
Another member of the NLR family, NLRC5 (also known as NOD27), has been recently characterized. NLRC5 mRNA and protein expression are induced by stimulation with IFN-γ , LPS, poly IC and viral infection of myeloid and lymphoid cells
lineages. This protein comprises a CARD and an LRR domain and is localized in the
cytoplasm and/or nucleus [97–99]. In vitro studies show that NLRC5 regulates antiviral
innate and adaptive immune responses through regulation of inflammatory cytokines
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

and/or type I interferons and transcriptional regulation of MHC class I molecules in
lymphoid and epithelial cell lines, respectively [97–101]. NLRC5 regulates antiviral innate responses through its association with IKK-α and IKK-β and inhibits their activation, thereby serving as a negative regulator of NF-κB activation. Moreover, NLRC5
interacts with RIG-I and MDA5 and suppresses both NF-κB and IRF3 activation [97]. In
contrast, another study showed that NLRC5 overexpression induces IFN-β promoter
activation and enhances RIG-I- and MDA5-mediated antiviral responses [97–99]. In
addition, overexpression of NLRC5 induces caspase-1-dependent maturation of IL-1
family cytokines [102]. However, in vivo studies of NLRC5-deficient mice suggest that
NLRC5 is not necessary for NF-κB- or IRF3-mediated production of inflammatory cytokines and type I interferons by various cell types including macrophages and DCs.
Moreover, both NLRC5-deficient and wild-type mice intra-peritoneally challenged
with poly IC show comparable levels of inflammatory cytokine and type I interferon
production [102]. Collectively, in vivo studies suggest that NLRC5 is not essential for
inflammatory cytokine and type I interferon production. However, NLRC5 may form
a protein complex, the inflammasome, with caspase-1 and this inflammasome may
sense some unknown pathogen or host ligand and induce the maturation of IL-1 family cytokines. One possible explanation for the differences between in vitro and in vivo
studies may be species differences.
INFLAMMASOMES
Stimulation of immune cells, such as macrophages and dendritic cells, with microbial PAMPs initiates the assembly of a protein complex known as the inflammasome,
which is composed of NLR members (e.g., NLRP3, NLRC4, NLRP1), non-NLR proteins,
AIM2 and ASC [6, 88, 103, 104]. This protein complex associates with an inactive form
of caspase-1 (procaspase-1) and promotes its proteolytic activation to yield caspase1, which, in turn, promotes proteolysis of the zymogan form of IL-1 family cytokines
(Fig. 1).
THE NLRP3 INFLAMMASOME
The NLRP3 inflammasome is the most widely studied inflammasome and, to date, numerous PAMPs from all classes of pathogens (viruses, bacteria, and fungi) and host
DAMPs (DAMPs [danger-associated molecular patterns] comprise molecules, such as
heat shock proteins and BCL2, which are derived from necrotic or traumatized host
cells and sensed by PRRs that induce inflammatory cytokines) have been reported (Table III), which activate the NLRP3 inflammasome [6, 103, 104]. In addition to PAMPs
and DAMPs, environmental pollutants, such as silica and asbestos are also reported
to activate the NLRP3 inflammasome. Although NLRP3 inflammasome biology has
rapidly expanded, the mechanism by which biochemically diverse ligands are sensed
by NLRP3 remains unknown. Furthermore, it is also unclear whether NLRP3 senses
ligands directly or indirectly. The NLRP3 inflammasome is composed of NLRP3, ASC,
and procaspase-1. Stimulation of cells with appropriate ligands induces oligomerization of NLRP3, which promotes the clustering of ASC with NLRP3 via a pyrin domain
(PYD)-PYD interaction. The CARD of ASC and the CARD of procaspase-1 then interact to induce catalysis of procaspase-1 to yield caspase-1, consisting of a p10/p20
tetramer, which catalyzes the proteolysis of pro IL-1β (inactive) to IL-1β (active). Several models of NLRP3 activation have been proposed including ATP-induced efflux
of potassium ions via P2X7 ion channels and pannexin-1, ROS induction, and lysosomal destabilization after phagocytosis of several crystalline and insoluble ligands (e.g.,
silica and amyloid-β), which leads to disruption of lysosomal membranes and the
C Informa Healthcare USA, Inc.
Copyright Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.

H. Kumar et al.
release of lysosomal proteins that activate the NLRP3 inflammasome [6, 88, 103, 104].
In addition, several studies in which mice were challenged with antigen and alum (a
ligand for the NLRP3 inflammasome) suggest the involvement of the NLRP3 inflammasome in the regulation of adaptive immunity [105–107]; however, inconsistencies
in the results were reported, which may be due to differences in the methods used and
the immunization protocol. Therefore, it is difficult to establish the involvement of the
NLRP3 inflammasome in adaptive immunity when alum is used as an adjuvant. Recently, several reports showed that the pathogenic fungus, Candida, and baker’s yeast
(Saccharomyces) induced IL-1β via NLRP3, ASC and caspase-1, and further studies
revealed that β-glucan, a major component of fungal cell walls, activates the NLRP3
inflammasome [108–115]. In addition, β-glucan-induced antibody responses are dependent upon the NLRP3 inflammasome. However, the IL-1β signaling pathway is not
essential for antibody responses [111]. On other hand, when β-glucan is used as an adjuvant, T cell responses in both NLRP3-deficient and wild-type mice are comparable.
Collectively these observations suggest that the NLRP3 inflammasome plays a pivotal
role in antibody production by B cells, which is independent of IL-1β or TLR signaling.
VIRUS-MEDIATED IL-1β PRODUCTION AND INNATE HOST DEFENSE
The influenza A virus also induces IL-1β production through activation of inflammasomes composed of NLRP3, ASC, and caspase-1; however, the requirement for
NLRP3 in inflammasome-induced IL-1β production remains controversial [116–120].
One group showed that the requirement for NLRP3 is cell-type specific, whereas other
groups showed that all cells require NLRP3. However, in vivo studies reveal that ASCand caspase-1-deficient mice are more susceptible to the influenza A virus infection
than wild-type mice or NLRP3-deficient mice after challenge with sub-lethal doses
of the virus. Influenza virus-specific adaptive immunity has also been demonstrated;
however, the results of these studies are dissimilar and the possible explanation for
these differences may be the different titers of virus used [116–120]. More recently, the
mechanism underlying influenza A virus-induced inflammasome activation was reported and showed that the M2 protein of the influenza virus, a proton-selective ion
channel, is required for inflammasome activation and viral pathogenesis [121].
THE NLRC4 INFLAMMASOME
The NLRC4 inflammasome is mainly composed of CARD-containing NLRC4 [122]
(also known as IPAF) and procaspase-1, and is activated via direct interaction with
the CARDs of caspase-1 and NLRC4 to induce pyroptosis through caspase-1 activation [123]. However, several studies suggest that ASC is also required for NLRC4 inflammasome activation and that ASC potentiates caspase-1 activation. These studies
suggest that other PYD-containing NLR members may be involved in the formation
of the NLRC4 inflammasome. The NLRC4 inflammasome is also involved in Shigella
flexneri-induced cell death, which is independent of ASC [124, 125]. Infection with Legionella pneumophila, Salmonella typhimurium, Pseudomonas aeruginosa, or Shigella
flexneri [125, 128] suggests that a type III or type IV secretion system (this secretion system makes pores in host cells and introduces virulence factors into the cells to activate
various effector responses, such as caspase-1 activation and cell death) is essential for
the activation of the NLRC4 inflammasome. Another study showed that another NLR
family member, NAIP5, is required for the recognition and replication of Legionella
pneumophila [129]. Moreover, NAIP5 recognizes the C-terminal portion of flagellin.
International Reviews of Immunology
Pathogen Recognition by Innate Immunity

Introduction of flagellin into the cytoplasm of cells is necessary for the activation of
the NLRC4 inflammasome (which is independent of TLR5).
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
THE NLRP1 INFLAMMASOME
The human NLRP1 inflammasome senses MDP and comprises NLRP1, ASC, and
caspase-1 [130]. ASC is not a necessary component, but the presence of ASC potentiates caspase-1 activation [130]. Three paralogs of NLRP1 have been identified in the
mouse genome, namely NLRP1a, NLRP1b, and NLRP1c. NLRP1b senses lethal toxins
from Bacillus anthracis, which plays an important role in pathogenesis [131].
THE AIM2 INFLAMMASOME
Introduction of DNA into cells, or infection with DNA viruses, induces the production
of IL-1β via the AIM2 inflammasome. AIM2 is a HIN-200 family, PYD-containing protein and is a cytoplasmic DNA sensor that directly senses DNA and induces proteolytic
activation of caspase-1. This results in the production and maturation of IL-1β via the
PYD-PYD-mediated interaction between AIM2 and ASC [132–138]. Recently, the in
vivo function of AIM2 was demonstrated by two independent groups that generated
AIM2-deficient mice and showed that AIM2 is critical for caspase-1 activation, production of IL-1β and IL-18, and pyroptosis (induced cell death) after infection with
Francisella tularensis, Vaccinia virus and MCMV. In addition, AIM2 plays a role after
Listeria infection. AIM2-deficient mice also have a higher mortality compared with
wild-type mice after infection with MCMV and Francisella [139–142].
CONCLUSION
In this review, we have extensively discussed the ligands, PRRs express on/in the cell
surface, cellular vesicles, or cytoplasm and the signaling pathways activated by TLRs,
RLRs, NLRs, and DNA receptors. However, most studies were performed either with
a pure ligand, or model laboratory pathogens, using mouse models. Therefore, these
studies may not reflect the true picture of host–pathogen interactions in the context of human disease. To resolve these issues, further studies using human immune
cells challenged with clinical isolates of pathogens will provide deep insight into the
host–pathogen interactions involved in various infectious disease conditions. In addition, it is noted that pathogens consist of multiple ligands, which may activate multiple signaling pathways, and that this may lead to the crosstalk between various signaling pathways resulting in a wide range of innate immune responses. Therefore, we
need to extend our present knowledge of innate immune immunobiology by stimulating immune cells with multiple ligands to understand the net outcome of innate
immune responses and their influence on the development of adaptive immunity. To
date, human studies suggest that TLRs, RLRs, NLRs, and DNA sensors are not sufficient
to mount protective immune responses against a wide range of infectious agents, suggesting that unidentified PRRs play a key role in defense against an array of pathogens.
Therefore, the identification and characterization of new PRRs is needed. Collectively,
these studies will be important not only for the basic understanding of host–pathogen
interactions, but also for the development of various therapeutic strategies and better
adjuvants for existing and new vaccines.
C Informa Healthcare USA, Inc.
Copyright 
H. Kumar et al.
ACKNOWLEDGMENTS
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
H.K. was, in part, supported by Kishimoto foundation fellowships from the WPI and
the Immunology Frontier Research Center, Osaka University, Osaka, Japan and the
Japan Society for the Promotion of Science (JSPS) from the government of Japan.
Declaration of Interest
The authors have no conflicts of interest to declare. The authors alone are responsible
for the content and writing of the paper.
REFERENCES
[1] Janeway Jr. CA, Medzhitov R. Innate immune recognition. Annu Rev Immunol 2002;20:197–216.
[2] Kawai T, Akira S. The role of pattern-recognition receptors in innate immunity: Update on Toll-like
receptors. Nat Immunol 2010;11:373–384.
[3] Takeuchi O, Akira S. Pattern recognition receptors and inflammation. Cell 2010;140:805–820.
[4] Medzhitov R. Recognition of microorganisms and activation of the immune response. Nature
2007;449:819–826.
[5] Blasius AL, Beutler B. Intracellular Toll-like receptors. Immunity 2010;32:305–315.
[6] Kumar H, Kawai T, Akira S. Pathogen recognition in the innate immune response. Biochem J
2009;420:1–16.
[7] Hoebe K, Janssen E, Beutler B. The interface between innate and adaptive immunity. Nat Immunol
2004;5:971–974.
[8] Iwasaki A, Medzhitov R. Regulation of adaptive immunity by the innate immune system. Science
2010;327:291–295.
[9] Lemaitre B, Nicolas E, Michaut L, et al. The dorsoventral regulatory gene cassette spatzle/toll/cactus
controls the potent antifungal response in drosophila adults. Cell 1996;86:973–983.
[10] Jin MS, Lee JO. Structures of the Toll-like receptor family and its ligand complexes. Immunity
2008;29:182–191.
[11] Carpenter S, O’Neill LA. Recent insights into the structure of Toll-like receptors and posttranslational modifications of their associated signalling proteins. Biochem J 2009;422:1–10.
[12] Jin MS, Kim SE, Heo JY, et al. Crystal structure of the TLR1-TLR2 heterodimer induced by binding
of a tri-acylated lipopeptide. Cell 2007;130:1071–1082.
[13] Kim HM, Park BS, Kim JI, et al. Crystal structure of the TLR4-MD-2 complex with bound endotoxin
antagonist eritoran. Cell 2007;130:906–917.
[14] Park BS, Song DH, Kim HM, et al. The structural basis of lipopolysaccharide recognition by the
TLR4-MD-2 complex. Nature 2009;458:1191–1195.
[15] Liu L, Botos I, Wang Y, et al. Structural basis of Toll-like receptor 3 signaling with double-stranded
RNA. Science 2008;320:379–381.
[16] Poltorak A, He X, Smirnova I, et al. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice:
Mutations in Tlr4 gene. Science 1998;282:2085–2088.
[17] Hoshino K, Takeuchi O, Kawai T, et al. Cutting edge: Toll-like receptor 4 (tlr4)-deficient mice
are hyporesponsive to lipopolysaccharide: Evidence for TLR4 as the lps gene product. J Immunol
1999;162:3749–3752.
[18] Schwandner R, Dziarski R, Wesche H, et al. Peptidoglycan- and lipoteichoic acid-induced cell activation is mediated by Toll-like receptor 2. J Biol Chem 1999;274:17406–17409.
[19] Underhill DM, Ozinsky A, Smith KD, Aderem A. Toll-like receptor-2 mediates mycobacteriainduced proinflammatory signaling in macrophages. Proc Natl Acad Sci U S A 1999;96:14459–14463.
[20] Kumar H, Kawai T, Akira S. Toll-like receptors and innate immunity. Biochem Biophys Res Commun
2009;388:621–625.
[21] Mancuso G, Gambuzza M, Midiri A, et al. Bacterial recognition by TLR7 in the lysosomes of conventional dendritic cells. Nat Immunol 2009;10:587–594.
[22] Kumar H, Koyama S, Ishii KJ, et al. Cutting edge: Cooperation of IPS-1- and TRIF-dependent
pathways in poly IC-enhanced antibody production and cytotoxic T cell responses. J Immunol
2008;180:683–687.
[23] Longhi MP, Trumpfheller C, Idoyaga J, et al. Dendritic cells require a systemic type I interferon response to mature and induce CD4+ Th1 immunity with poly IC as adjuvant. J Exp Med
2009;206:1589–1602.
[24] Miyake T, Kumagai Y, Kato H, et al. Poly I:C-induced activation of NK cells by CD8 alpha +dendritic
cells via the IPS-1 and TRIF-dependent pathways. J Immunol 2009;183:2522–2528.
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

[25] Willment JA, Brown GD. C-type lectin receptors in antifungal immunity. Trends Microbiol
2008;16:27–32.
[26] Kagan JC, Su T, Horng T, et al. TRAM couples endocytosis of Toll-like receptor 4 to the induction of
interferon-beta. Nat Immunol 2008;9:361–368.
[27] Tabeta K, Hoebe K, Janssen EM, et al. The UNC93b1 mutation 3d disrupts exogenous antigen presentation and signaling via Toll-like receptors 3, 7 and 9. Nat Immunol 2006;7:156–164.
[28] Kim YM, Brinkmann MM, Paquet ME, Ploegh HL. UNC93b1 delivers nucleotide sensing Toll-like
receptors to endolysosomes. Nature 2008;452:234–238.
[29] Brinkmann MM, Spooner E, Hoebe K, et al. The interaction between the ER membrane protein
UNC93b and TLR3, 7, and 9 is crucial for TLR signaling. J Cell Biol 2007;177:265–275.
[30] Lin SC, Lo YC, Wu H. Helical assembly in the MyD88-IRAK4- IRAK2 complex in TLR/IL-1R signaling.
Nature 2010;465:885–890.
[31] Yamamoto M, Okamoto T, Takeda K, et al. Key function for the UNC13 E2 ubiquitin conjugating
enzyme in immune receptor signaling. Nat Immunol 2006;7:962–970.
[32] Tseng PH, Matsuzawa A, Zhang W, et al. Different modes of ubiquitination of the adaptor TRAF3 selectively activate the expression of type I interferons and proinflammatory cytokines. Nat Immunol
2010;11:70–75.
[33] Yamamoto M, Yamazaki S, Uematsu S, et al. Regulation of Toll/IL-1-receptor mediated gene expression by the inducible nuclear protein Iκbζ . Nature 2004;430:218–222.
[34] Kuwata H, Matsumoto M, Atarashi K, et al. IκBNS inhibits induction of a subset of toll-like receptordependent genes and limits inflammation. Immunity 2006;24:41–51.
[35] Gilchrist M, Thorsson V, Li B, et al. Systems biology approaches identify ATF3 as a negative regulator
of Toll-like receptor 4. Nature 2006;441:173–178.
[36] Litvak V, Ramsey SA, Rust AG, et al. Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol 2009;10:437–
443.
[37] Matsushita K, Takeuchi O, Standley DM, et al. Zc3h12a is an RNase essential for controlling immune
responses by regulating mRNA decay. Nature 2009;458:1185–1190.
[38] Carrick DM, Lai WS, Blackshear PJ. The tandem CCCH zinc finger protein tristetraprolin and its
relevance to cytokine mRNA turnover and arthritis. Arthritis Res Ther 2004;6:248–264.
[39] Ewald SE, Lee BL, Lau L, et al. The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptor. Nature 2008;456:658–662.
[40] Park B, Brinkmann MM, Spooner E, et al. Proteolytic cleavage in an endolysosomal compartment
is required for activation of Toll-like receptor 9. Nat Immunol 2008;9:1407–1414.
[41] Asagiri M, Hirai T, Kunigami T, et al. Cathepsin K-dependent Toll-like receptor 9 signaling revealed
in experimental arthritis. Science 2008;319:624–627.
[42] Matsumoto F, Saitoh S, Fukui R, et al. Cathepsins are required for Toll-like receptor 9 responses.
Biochem Biophys Res Commun 2008;367:693–699.
[43] Sepulveda FE, Maschalidi S, Colisson R, et al. Critical role for asparagine endopeptidase in endocytic toll-like receptor signaling in dendritic cells. Immunity 2009;31:737–748.
[44] Wilkins C, Gale Jr. M. Recognition of viruses by cytoplasmic sensors. Curr Opin Immunol
2010;22:41–47.
[45] Yoneyama M, Fujita T. Structural mechanism of RNA recognition by the RIG-I-like receptors. Immunity 2008;29:178–181.
[46] Satoh T, Kato H, Kumagai Y, et al. LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses. Proc Natl Acad Sci U S A 2010;107:1512–1517.
[47] Kato H, Sato S, Yoneyama M, et al. Cell type-specific involvement of RIG-I in antiviral response.
Immunity 2005;23:19–28.
[48] Kato H, Takeuchi O, Sato S, et al. Differential roles of MDA5 and RIG-I helicases in the recognition
of RNA viruses. Nature 2006;441:101–105.
[49] Loo YM, Fornek J, Crochet N, et al. Distinct RIG-I and MDA5 signaling by RNA viruses in innate
immunity. J Virol 2008;82:335–345.
[50] Hornung V, Ellegast J, Kim S, et al. 5’-triphosphate RNA is the ligand for RIG-I. Science
2006;314:994–997.
[51] Pichlmair A, Schulz O, Tan CP, et al. RIG-I-mediated antiviral responses to single stranded RNA
bearing 5’-phosphates. Science 2006;314:997–1001.
[52] Schlee M, Roth A, Hornung V, et al. Recognition of 5’ triphosphate by RIG-I helicase requires
short blunt double-stranded RNA as contained in panhandle of negative strand virus. Immunity
2009;31:25–34.
[53] Schmidt A, Schwerd T, Hamm W, et al. 5’-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I. Proc Natl Acad Sci U S A 2009;106:12067–12072.
C Informa Healthcare USA, Inc.
Copyright Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.

H. Kumar et al.
[54] Takahasi K, Kumeta H, Tsuduki N, et al. Solution structures of cytosolic RNA sensor MDA5 and LGP2
C-terminal domains: Identification of the rna recognition loop in RIG-I-like receptors. J Biol Chem
2009;284:17465–17474.
[55] Kato H, Takeuchi O, Mikamo-Satoh E, et al. Length-dependent recognition of double-stranded ribonucleic acids by Retinoic acid-inducible gene-I and Melanoma differentiation-associated gene
5. J Exp Med 2008;205:1601–1610.
[56] Rothenfusser S, Goutagny N, DiPerna G, et al. The RNA helicase LGP2 inhibits TLR-independent
sensing of viral replication by Retinoic acid-inducible gene-I. J Immunol 2005;175:5260–5268.
[57] Yoneyama M, Kikuchi M, Matsumoto K, et al. Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity. J Immunol 2005;175:2851–2858.
[58] Saito T, Hirai R, Loo YM, et al. Regulation of innate antiviral defenses through a shared repressor
domain in RIG-I and LGP2. Proc Natl Acad Sci U S A 2007;104:582–587.
[59] Kawai T, Takahashi K, Sato S, et al. IPS-1, an adaptor triggering RIG-I and MDA5-mediated type I
interferon induction. Nat Immunol 2005;6:981–988.
[60] Seth RB, Sun L, Ea CK, Chen ZJ. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-κ and IRF3. Cell 2005;122:669–682.
[61] Meylan E, Curran J, Hofmann K, et al. Cardif is an adaptor protein in the RIG-I antiviral pathway
and is targeted by Hepatitis C virus. Nature 2005;437:1167–1172.
[62] Xu LG, Wang YY, Han KJ, et al. VISA is an adapter protein required for virus triggered IFN-beta
signaling. Mol Cell 2005;19:727–740.
[63] Kumar H, Kawai T, Kato H, et al. Essential role of IPS-1 in innate immune responses against RNA
viruses. J Exp Med 2006;203:1795–1803.
[64] Sun Q, Sun L, Liu HH, et al. The specific and essential role of MAVS in antiviral innate immune
responses. Immunity 2006;24:633–642.
[65] Dixit E, Boulant S, Zhang Y, et al. Peroxisomes are signaling platforms for antiviral innate immunity.
Cell 2010;141:668–681.
[66] Takahashi K, Kawai T, Kumar H, et al. Roles of caspase-8 and caspase-10 in innate immune responses to double-stranded RNA. J Immunol 2006;176:4520–4524.
[67] Okabe Y, Sano T, Nagata S. Regulation of the innate immune response by threonine-phosphatase
of eyes absent. Nature 2009;460:520–524.
[68] Moore CB, Bergstralh DT, Duncan JA, et al. NLRX1 is a regulator of mitochondrial antiviral immunity. Nature 2008;451:573–577.
[69] Jounai N, Takeshita F, Kobiyama K, et al. The Atg5 Atg12 conjugate associates with innate antiviral
immune responses. Proc Natl Acad Sci U S A 2007;104:14050–14055.
[70] Gack MU, Shin YC, JooCH, et al. TRIM25 ring-finger E3 ubiquitin ligase is essential for RIG-Imediated antiviral activity. Nature 2007;446:916–920.
[71] Pichlmair A, Schulz O, Tan CP, et al. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J Virol 2009;83:10761–10769.
[72] Arimoto K, Takahashi H, Hishiki T, et al. Negative regulation of the RIG-I signaling by the ubiquitin
ligase RNF125. Proc Natl Acad Sci U S A 2007;104:7500–7505.
[73] Zeng W, Sun L, Jiang X, et al. Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell 2010;141:315–330.
[74] Takeshita F, Ishii KJ. Intracellular DNA sensors in immunity. Curr Opin Immunol 2008;20:383–388.
[75] IshiiKJ, Coban C, Kato H, et al. A toll-like receptor-independent antiviral response induced by
double-stranded B-form DNA. Nat Immunol 2006;7:40–48.
[76] Stetson DB, Medzhitov R. Recognition of cytosolic DNA activates an IRF3-dependent innate immune response. Immunity 2006;24:93–103.
[77] Takaoka A, Wang Z, Choi MK, et al. DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator
of innate immune response. Nature 2007;448:501–505.
[78] Ishii KJ, Kawagoe T, Koyama S, et al. Tank-binding kinase-1 delineates innate and adaptive immune
responses to DNA vaccines. Nature 2008;451:725–729.
[79] Ablasser A, Bauernfeind F, Hartmann G, et al. RIG-I-dependent sensing of poly (dA:dT)
through the induction of an RNA polymerase III-transcribed RNA intermediate. Nat Immunol
2009;10:1065–1072.
[80] Chiu YH, Macmillan JB, Chen ZJ. RNA polymerase III detects cytosolic DNA and induces type I
interferons through the RIG-I pathway. Cell 2009;138:576–591.
[81] Ishikawa H, Barber GN. Sting is an endoplasmic reticulum adaptor that facilitates innate immune
signaling. Nature 2008;455:674–678.
[82] Zhong B, Yang Y, Li S, et al. The adaptor protein MITA links virus-sensing receptors to IRF3 transcription factor activation. Immunity 2008;29:538–550.
[83] Sun W, Li Y, Chen L, et al. ERIS, an endoplasmic reticulum IFN stimulator, activates innate immune
signaling through dimerization. Proc Natl Acad Sci U S A 2009;106:8653–8658.
International Reviews of Immunology
Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.
Pathogen Recognition by Innate Immunity

[84] Ishikawa H, Ma Z, Barber GN. STING regulates intracellular DNA-mediated, type I interferondependent innate immunity. Nature 2009;461:788–792.
[85] Saitoh T, Fujita N, Hayashi T, et al. ATG9a controls dsDNA-driven dynamic translocation of sting
and the innate immune response. Proc Natl Acad Sci U S A 2009;106:20842–20846.
[86] Shaw MH, Reimer T, Kim YG, Nunez G. Nod-like receptors (NLRs): Bona fide intracellular microbial
sensors. Curr Opin Immunol 2008;20:377–382.
[87] Kanneganti TD, Lamkanfi M, Nunez G. Intracellular Nod-like receptors in host defense and disease.
Immunity 2007;27:549–559.
[88] Franchi L, Warner N, Viani K, Nunez G. Function of Nod-like receptors in microbial recognition and
host defense. Immunol Rev 2009;227:106–128.
[89] Kufer TA, Kremmer E, Adam AC, et al. The pattern-recognition molecule NOD1 is localized at the
plasma membrane at sites of bacterial interaction. Cell Microbiol 2008;10:477–486.
[90] Barnich N, Aguirre JE, Reinecker HC, et al. Membrane recruitment of NOD2 in intestinal epithelial
cells is essential for nuclear factor-{kappa}b activation in muramyl dipeptide recognition. J Cell
Biol 2005;170:21–26.
[91] McDonald C, Inohara N, Nunez G. Peptidoglycan signaling in innate immunity and inflammatory
disease. J Biol Chem 2005;280:20177–20180.
[92] Shaw MH, Reimer T, Sanchez-Valdepenas C, et al. T cell-intrinsic role of NOD2 in promoting type
1 immunity to Toxoplasma gondii. Nat Immunol 2009;10:1267–1274.
[93] Hysi P, Kabesch M, Moffatt MF, et al. Nod1 variation, immunoglobulin E and asthma. Hum Mol
Genet 2005;14:935–941.
[94] Weidinger S, Klopp N, Rummler L, et al. Association of nod1 polymorphisms with atopic eczema
and related phenotypes. J Allergy Clin Immunol 2005;116:177–184.
[95] Ogura Y, Bonen DK, Inohara N, et al. A frameshift mutation in NOD2 associated with susceptibility
to Crohn’s disease. Nature 2001;411:603–606.
[96] Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with
susceptibility to Crohn’s disease. Nature 2001;411:599–603.
[97] Cui J, Zhu L, Xia X, et al. NLRC5 negatively regulates the NFκB and type I interferon signaling pathways. Cell 2010;141:483–496.
[98] Kuenzel S, Till A, Winkler M, et al. The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses. J Immunol 2010;184:1990–
2000.
[99] Neerincx A, LautzK,Menning M, et al. A role for the human nucleotide-binding domain,
leucine-rich repeat-containing family member NLRC5 in antiviral responses. J Biol Chem
2010;285:26223–26232.
[100] Benko S, Magalhaes JG, Philpott DJ, Girardin SE. NLRC5 limits the activation of inflammatory pathways. J Immunol 2010;185:1681–1691.
[101] Meissner TB, Li A, Biswas A, et al. NLR family member NLRC5 is a transcriptional regulator of MHC
class I genes. Proc Natl Acad Sci U S A 2010;107:13794–13799.
[102] Kumar H, Pandey S, Zou J, et al. NLRC5 Deficiency Does Not Influence Cytokine Induction by Virus
and Bacteria Infection. J Immunol doi:10.4049/jimmunol.1002094.
[103] Franchi L, Eigenbrod T, Munoz-Planillo R, Nunez G. The inflammasome: A caspase-1activation platform that regulates immune responses and disease pathogenesis. Nat Immunol
2009;10:241–247.
[104] Schroder K, Tschopp J. The inflammasomes. Cell 2010;140:821–832.
[105] Williams A, Flavell RA, Eisenbarth SC. The role of Nod-like receptors in shaping adaptive immunity.
Curr Opin Immunol 2010;22:34–40.
[106] Eisenbarth SC, Colegio OR, O’Connor W, et al. Crucial role for the NALP3 inflammasome in the
immunostimulatory properties of aluminium adjuvants. Nature 2008;453:1122–1126.
[107] Franchi L, Nunez G. The NALP3 inflammasome is critical for aluminium hydroxide mediated IL1beta secretion but dispensable for adjuvant activity. Eur J Immunol 2008;38:2085–2089.
[108] Gross O, Poeck H, Bscheider M, et al. Syk kinase signalling couples to the NALP3 inflammasome for
anti-fungal host defence. Nature 2009;459:433–436.
[109] Hise AG, Tomalka J, Ganesan S, et al. An essential role for the NALP3 inflammasome in host defense
against the human fungal pathogen candida albicans. Cell Host Microbe 2009;5:487–497.
[110] Lamkanfi M, Malireddi RK, Kanneganti TD. Fungal zymosan and mannan activate the cryopyrin
inflammasome. J Biol Chem 2009;284:20574–20581.
[111] Kumar H, Kumagai Y, Tsuchida T, et al. Involvement of the NALP3 inflammasome in innate and humoral adaptive immune responses to fungal β-glucan. J Immunol 2009;183:8061–
8067.
[112] Joly S, Ma N, Sadler JJ, et al. Cutting edge: Candida albicans hyphae formation triggers activation of
the NALP3 inflammasome. J Immunol 2009;183:3578–3581.
C Informa Healthcare USA, Inc.
Copyright Int Rev Immunol Downloaded from informahealthcare.com by Helmholtz Zentrum fuer Infektionsforschung GmbH -Bibliothek- on 10/15/13
For personal use only.

H. Kumar et al.
[113] Said-Sadier N, Padilla E, Langsley G, Ojcius DM. Aspergillus fumigatus stimulates the NALP3 inflammasome through a pathway requiring ROS production and the syk tyrosine kinase. PLoS One
2010;5:e10008.
[114] PoeckH, Ruland J. Syk kinase signaling and the NALP3 inflammasome in antifungal immunity. J
Mol Med 2010;88:745–752.
[115] Poeck H, J. Ruland J. ITAM receptor signaling and the NALP3 inflammasome in antifungal immunity. J Clin Immunol 2010;30:496–501.
[116] Ichinohe T, Lee HK, Ogura Y, et al. Inflammasome recognition of influenza virus is essential for
adaptive immune responses. J Exp Med 2009;206:79–87.
[117] Allen IC, Scull MA, Moore CB, et al. The NALP3 inflammasome mediates in vivo innate immunity
to influenza a virus through recognition of viral RNA. Immunity 2009;30:556–565.
[118] Thomas PG, Dash P, Aldridge Jr. JR, et al. The intracellular sensor NALP3 mediates key innate and
healing responses to influenza a virus via the regulation of caspase-1. Immunity 2009;30:566–575.
[119] Cilloniz C, Shinya K, Peng X, et al. Lethal influenza virus infection in macaques is associated with
early dysregulation of inflammatory related genes. PLoS Pathog 2009;5:e1000604.
[120] Owen DM, Gale Jr. M. Fighting the flu with inflammasome signaling. Immunity 2009;30:476–478.
[121] Ichinohe T, Pang IK, Iwasaki A. Influenza virus activates inflammasomes via its intracellular M2 ion
channel. Nat Immunol 2010;11:404–410.
[122] Poyet JL, Srinivasula SM, Tnani M, et al. Identification of IPAF, a human caspase-1-activating protein
related to APAF-1. J Biol Chem 2001;276:28309–28313.
[123] Fink SL, Cookson BT. Caspase-1-dependent pore formation during pyroptosis leads to osmotic lysis
of infected host macrophages. Cell Microbiol 2006;8:1812–1825.
[124] Suzuki T, Franchi L, Toma C, et al. Differential regulation of caspase-1 activation, pyroptosis, and
autophagy via IPAF and ASC in shigella-infected macrophages. PLoS Pathog 2007;3:e111.
[125] Suzuki T, Nunez G. A role for Nod-like receptors in autophagy induced by shigella infection. Autophagy 2008;4:73–75.
[126] Amer A, Franchi L, Kanneganti TD, et al. Regulation of legionella phagosome maturation and infection through flagellin and host IPAF. J Biol Chem 2006;281:35217–35223.
[127] Franchi L, Amer A, Body-Malapel M, et al. Cytosolic flagellin requires IPAF for activation of caspase1 and interleukin 1β in salmonella-infected macrophages. Nat Immunol 2006;7:576–582.
[128] Miao EA, Ernst RK, Dors M, et al. Pseudomonas aeruginosa activates caspase 1 through IPAF. Proc
Natl Acad Sci U S A 2008;105:2562–2567.
[129] Wright EK, Goodart SA, Growney JD, et al. NAIP5 affects host susceptibility to the intracellular
pathogen legionella pneumophila. Curr Biol 2003;13:27–36.
[130] Faustin B, Lartigue L, Bruey JM, et al. Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation. Mol Cell 2007;25:713–724.
[131] Boyden ED, Dietrich WF. NALP1b controls mouse macrophage susceptibility to anthrax lethal toxin.
Nat Genet 2006;38:240–244.
[132] Roberts TL, Idris A, Dunn JA, et al. HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA. Science 2009;323:1057–1060.
[133] Hornung V, Ablasser A, Charrel-Dennis M, et al. AIM2 recognizes cytosolic dsDNA and forms a
caspase-1-activating inflammasome with ASC. Nature 2009;458:514–518.
[134] Fernandes-Alnemri T, Yu JW, Datta P, et al. AIM2 activates the inflammasome and cell death in
response to cytoplasmic DNA. Nature 2009;458:509–513.
[135] Burckstummer T, Baumann C, Bluml S, et al. An orthogonal proteomic-genomic screen identifies
AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat Immunol 2009;10:266–272.
[136] Tsuchiya K, Hara H, Kawamura I, et al. Involvement of Absent in melanoma 2 in inflammasome
activation in macrophages infected with listeria monocytogenes. J Immunol 2010;185:1186–1195.
[137] Wu J, Fernandes-Alnemri T, Alnemri ES. Involvement of the AIM2, NLRC4, and NLRP3 inflammasomes in caspase-1 activation by listeria monocytogenes. J Clin Immunol 2010;30:693–702.
[138] Sauer JD, Witte CE, Zemansky J, et al. Listeria monocytogenes triggers AIM2-mediated pyroptosis
upon infrequent bacteriolysis in the macrophage cytosol. Cell Host Microbe 2010;7:412–419.
[139] Rathinam VA, Jiang Z, Waggoner SN, et al. The AIM2 inflammasome is essential for host defense
against cytosolic bacteria and DNA viruses. Nat Immunol 2010;11:395–402.
[140] Fernandes-Alnemri T, Yu JW, Juliana C, et al. The AIM2 inflammasome is critical for innate immunity to Francisella tularensis. Nat Immunol 2010;11:385–393.
[141] Jones JW, Kayagaki N, Broz P, et al. Absent in melanoma 2 is required for innate immune recognition
of Francisella tularensis. Proc Natl Acad Sci U S A 2010;107:9771–9776.
[142] Warren SE, Armstrong A, Hamilton MK, et al. Cutting edge: Cytosolic bacterial DNA activates the
inflammasome via AIM2. J Immunol 2010;185:818–821.
International Reviews of Immunology