Viral RNA detection by RIG-I-like receptors
Introduction
In 2004, RLRs were identified as RNA sensors to trigger innate immune responses against viral infection [1]. Mammalian RLRs are composed of three family members; RIG-I (DDX58), MDA5 (IFIH1) and laboratory of genetics and physiology 2 (LGP2; DHX58), and all are expressed in the cytoplasm of ubiquitous types of cells [2]. These RLRs all share a DExD/H-box RNA helicase domain and a C-terminal domain (CTD), while RIG-I and MDA5, but not LGP2, have a N-terminal caspase recruitment domain (CARD), which is responsible for interacting with a downstream adaptor molecule, MAVS/IPS-1 (Figure 1). The C-terminal RNA helicase and CTD are implicated in the detection of viral RNA, and ATP-dependent conformational change allows CARDs to interact with MAVS/IPS-1. For RIG-I activation, conjugation of Lys63-linked ubiquitin chain (Ubs) by tripartite motif protein 25 (TRIM25) and/or association of unanchored Ubs with CARD are required [3]. A recent in vitro study revealed that MDA5 also interacts with unanchored Ubs [4]. The CARDs accumulated on the mitochondrial surface recruits signaling adaptors and kinases, including IκB kinase (IKK) family kinases, IKKα/β/γ, TBK1 and IKKɛ⋅ IKKα/β/γ activates NF-κB and TBK1 and IKKɛ activates IFN regulatory factor (IRF)-3 and 7. The activated NF-κB and IRF-3/7 can translocate into the nucleus, and interact with the promoter regions of target genes, including IFNs and inflammatory cytokines. Secreted IFNs transmit a signal via cognate receptors and induce the expression of hundreds of IFN-stimulated genes (ISGs), including, double-stranded RNA dependent protein kinase (PKR), 2′-5′-oligoadenylate synthetase (OAS) and RLRs, leading to the establishment of an antiviral state [5]. Here we review recent advances in our knowledge of the molecular machinery for RLR activation and RLR-mediated signal transduction.
Section snippets
RNA recognition and signal activation by RLRs
RIG-I is activated by infection by a variety of RNA viruses, such as influenza A virus (IAV), Newcastle disease virus, Sendai virus, vesicular stomatitis virus (VSV), measles virus (MV), and hepatitis C virus [2, 6]. The non-self signature of these viruses is a 5′-triphosphate (5′ppp)-containing short double-stranded (ds) structure with a complementary end and/or a poly-U/UC rich ds-stretch. Recently, it has been demonstrated that incoming 5′ppp-containing viral RNA with nucleocapsid proteins
Signal activation via aggregate formation of RLRs
Previously, it was suggested that dimerization or oligomerization of RLRs is required for signal activation [14]. Recent in vitro studies proposed a model in which RIG-I, MDA5 and MAVS/IPS-1 signal through multimolecular aggregates (Figure 2). RIG-I forms a complex with dsRNA in a 5′ppp and ATP-dependent, but also 2CARD-independent manner [30, 31]. Since sliding RIG-I on dsRNA was reported [32], ATP hydrolysis-driven translocation may allow RIG-I to form a beads-on-a-string complex on viral
Stress response and RLR signaling
Recent studies demonstrate that infection by various viruses induces the formation of stress granule (SG)-like aggregates, termed antiviral SG (avSG), in the cytoplasm [40]. In many cases, PKR is responsible for sensing viral infection and initiating avSG formation (Figure 2). An avSG contains RLRs and several antiviral molecules, including PKR and OAS as well as viral ribonucleoprotein complex (RNP) [41•]. Inhibition of the avSG formation impairs the virus-induced activation of IFN genes,
Regulation of RLRs-mediated signaling by ubiquitin chains
In vitro experiments showed that Lys-63-linked Ub chains are critical for the oligomerization of RIG-I and MDA5. However, the involvement of Lys63-Ubs has been controversial. Although the initial report indicated that ubiquitination of 2CARD at Lys172 by TRIM25 is required for RIG-I activation [3], subsequent studies have shown that RIG-I with Arg172 is fully active [43] and that the interaction between 2CARD and unanchored Ubs is important for the signaling-competent tetramer formation of
Regulation by phosphorylation of RLRs
It was suggested that RIG-I signaling is attenuated by phosphorylation at the 2CARD and CTD of RIG-I by protein kinase C (PKC) α/β and casein kinase II (CKII) respectively [55]. On the other hand, protein phosphatase 1 (PP1), PP1α and PP1γ, directly interact with and dephosphorylate RIG-I and MDA5 and virus-induced signaling [56••]. In the case of MDA5, phosphorylation at the Ser88 residue in 2CARD attenuates MDA5 signaling and it is dephosphorylated by PP1, suggesting a role for the
Concluding remarks
Recent advances in biochemical and structural analysis elegantly elucidates the molecular machinery underlying non-self RNA recognition and signal activation by RLRs and MAVS/IPS-1. Although RIG-I and MDA5 differentially recognize distinct RNA species, both induce filamentous aggregates on dsRNA and the relieved 2CARDs form an oligomer to interact with the prion-like aggregates of MAVS/IPS-1 CARDs. Furthermore, virus-induced SG-like aggregates might also be involved in some parts of these
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
This work was supported by grants from The Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, including Innovative Area “Infection competency” (No. 24115004 and 25115503), Scientific Research “A” (No. 23249023) and “B” (No. 26293101), The Ministry of Health, Labor and Welfare (MHLW) of Japan, the Uehara Memorial Foundation, the Mochida Memorial Foundation for Medical and Pharmaceutical Research, the Takeda Science Foundation and the Naito Foundation.
References (57)
- et al.
Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response
Immunity
(2012) - et al.
Pattern recognition receptors and inflammation
Cell
(2010) - et al.
Incoming RNA virus nucleocapsids containing a 5’-triphosphorylated genome activate RIG-I and antiviral signaling
Cell Host Microbe
(2013) - et al.
In vivo ligands of MDA5 and RIG-I in measles virus-infected cells
PLoS Pathog
(2014) - et al.
Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5
Cell
(2013) - et al.
Autoimmune disorders associated with gain of function of the intracellular sensor MDA5
Immunity
(2014) - et al.
Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity
J Immunol
(2005) - et al.
Functional characterization of domains of IPS-1 using an inducible oligomerization system
PLoS ONE
(2013) - et al.
A bicistronic MAVS transcript highlights a class of truncated variants in antiviral immunity
Cell
(2014) - et al.
ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon
EMBO Rep
(2013)
MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response
Cell
Structural basis for the prion-like MAVS filaments in antiviral innate immunity
eLife
Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
Proc Natl Acad Sci
MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA
EMBO J
A distinct role of Riplet-mediated K63-Linked polyubiquitination of the RIG-I repressor domain in human antiviral innate immune responses
PLoS Pathog
TRIM13 is a negative regulator of MDA5-mediated type I interferon production
J Virol
MAVS recruits multiple ubiquitin E3 ligases to activate antiviral signaling cascades
eLife
Phosphorylation of RIG-I by casein kinase II inhibits its antiviral response
J Virol
The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
Nat Immunol
Recognition of viral nucleic acids in innate immunity
Rev Med Virol
TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity
Nature
Interferon-inducible antiviral effectors
Nat Rev Immunol
Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5’-diphosphates
Nature
Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I
Nat Struc Mol Biol
Structural basis of RNA recognition and activation by innate immune receptor RIG-I
Nature
The RIG-I ATPase domain structure reveals insights into ATP-dependent antiviral signalling
EMBO Rep
Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA
Cell
Regulation of innate antiviral defenses through a shared repressor domain in RIG-I and LGP2
Proc Natl Acad Sci
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