Chikungunya Virus and NDP52: a deadly association?

Chikungunya virus (CHIKV) is the causative agent of an arthropod (mosquito) transmitted disease which is characterised by a high fever, rash, joint pain, and arthritis which was reported in 1952 in Tanzania but has spread since to Europe, the Americas, Asia, and Australia and currently epidemic in the Americas.

Confirmed cases of Chikungunya Virus infections in the Caribbean and continental
US as August 22nd 2014

Being a member of the Alphaviridae genus of the family Togaviridae related to Ross River virus, O'nyong'nyong virus, and Semliki Forest Virus (SFV), CHIKV has a positive strand ssRNA genome of 11.6 kb in size which encodes for both the structural and non-structural (nsP) proteins. In accordance with other prototype members of the Alphaviridae, the 5’ two thirds encodes for the four viral nsP (nsP 1-4) whereas the structural proteins are encoded within a subgenomic m 26S RNA, which in turn derives from a precursor 42S RNA.

Alphavirus genome, particle, and proteins

Both in vitro and in vivo, CHIKV can infect a wide variety of cells, including primary fibroblast cells, macrophages, astrocytes as well as hepatic cells. Similar to other alphaviruses, CHIKV infection has the capacity to induce caspase dependent apoptosis especially late infection. This process is preceded by autophagy (as discussed below) which might not only favour viral replication but also prevent apoptosis. Viral replication itself takes place in perinuclear replication centers (RCs) derived from endosomal and lysosomal membranes containing the three nsP in addition to the viral RNA dependent RNA Polymerase, akin to to the RTC induced by the Nidovirales, although viral RCs have also been observed close to the plasma membrane. Similar to the coronaviral N protein, the nsP2 of SFV also localises to the nucleolus where it associates with the ribosomal protein S6 (RpS6), thus might contribute to the shut off of host cell translation.

                          Induction of ER stress and apoptosis

Following the infection of glioblastoma cells with CHIKV, apoptosis as evidenced by DNA fragmentation, cleavage of PARP, nuclear condensation, loss of mitochondrial membrane potential, and activation of caspases can be observed at 48 h p.i. . Akin to cells infected with Japanese Encephalitis Virus (JEV), apoptosis is induced by the ER stress response, which in the case of SFV is characterised by the induction of IRE1 and ATF6 (but not PERK) pathways, involving the splicing of XBP1 as well as ATF6 mediated phosphorylation of eIF2α (subsequently increasing the expression of CHOP) as well up regulation of proteins inducting the antiviral response such as proteins of the RIG-I like receptor (RLR) pathway as well pro-inflammatory cytokines namely CXCL9, IL-6, TNF-α, and IL-1β within 24 h p.i. Interestingly, in contrast to Sindbis Virus (SINV), in CHIKV infected cells, the viral RdRP, nsP4, inhibits the phosphorylation of eIF2α following treatment with tunicamycin not only in mosquito (Aedes albopictus) C6/36 cells,  but also in HEK293T,  MRC-5 and BHK-21 cells,  similar to vaccinia virus K3L or Hepatitis C Virus NS5A. In the context of viral replication, the data support a model in which CHIKV nsP4 delays the activation of PERK mediated phosphorylation of eIF2α by at least 21 h p.i. compared to cells infected with SINV, although it has been not demonstrated that a recombinant SINV expressing CHIKV nsP4 has delayed pattern of eIF2α  phosphorylation similar to CHIKV .

CHIKV and the ER stress response: inhibition of PERK by nsP4 and
BiP by preE1/E2

In general the ER stress response is triggered however not by the accumulation of non-structural proteins at the ER, but by the envelope glycoproteins, namely the E1 and E2 proteins in a process that depends on a cellular BiP. In the case of SINV both the precursor of E2, PE2, and E1 are co-translationally inserted into the ER membrane prior to their transport to the cell surface via the Golgi where they are inserted into the plasma membrane by palmitoylated residues. The insertion into the ER membrane therefore does not induce the formation of the replication complex but is only transient in nature. Both proteins however might induce the ER stress pathways by two mechanisms, either depletion of lipid due to the formation of vesicles and/or via BiP. BiP is a molecular chaperone, which not only associates with unfolded proteins within the ER and facilitates correct folding but is also involved in transporting proteins across the ER membrane. In the case of SINV E2 and E1 proteins, BiP associates with both E2 and E1 within the ER and is implicated in their transport across the ER membrane. More importantly however (at least in terms of the UPR), in SINV infected cells, BiP also induces the ATF6 and IRE1 induced ER stress response, problem by releasing BiP from its interaction with ATF6, IRE1, and Caspase-4/-12.  As discussed in prior posts, the induction of both the ATF6 and IRE1 dependent ER stress response not only induces apoptosis, but also autophagy. Indeed cells infected with SFV, CHKV, or SINV exhibit the induction of the autophagy pathway prior to the induction of apoptosis and autophagy has been shown to be required for productive infection and CHIKV induced autophagy has been shown to delay caspase induced apoptosis.

                                       CHIKV and autophagy

In the case of CHIKV, autophagy not only has a cytoprotective function but also enhances viral replication and the switch from autophagy to viral assembly late in infection increases apoptosis induced by CHIKV.

In human and murine cells infected with CHIKV, the viral ubiqutinated capsid protein co-localises and co-immunoprecipates with p62/SQSTM1 mediated the UBA domain and subsequently is degraded via the formation of autophagosome and targeting to LAMP1 positive lysosomal structures; indeed, both the depletion of p62 and the expression of a p62/SQSTM1 ΔUBA mutant stabilise the capsid protein as well as treatment of infected with Bafilomycin A as well as increasing viral replication as measured by viral RNA and viral titers.

The viral capsid protein is degraded by p62/SQSTM1 and localised
to viral replication centers by NPD52

In cells infected with CHIKV or other members of the Alphaviridae, the nsPs associate with viral RNA to form the viral replication complexes (RC), which in turn are associated double membrane vesicles (DMV) -termed cytopathic vacuoles- located in the perinuclear region. The DMVs not only contain nsPs, viral RNA, and dsRNA intermediates, but also (in the case of SINV and SFV) but also markers of the endo-and lysosomal system such as TGN-46. As part of this complex, nsP2 in addition to the role in shutting off host cell translation and inducing apoptosis, also binds the viral RNA and forms autophagy like vesicles containing the viral RNA that are localised in the perinuclear region and positive for TGN-46. The latter structure is not only positive for nsP2, but also for the viral capsid protein and nsP3, thus representing the viral RC. The process of the localisation of nsP2-RNA complex is not only dependent on the nuclear localisation and the presence of the C-terminal domain, but also on a cellular protein, Nuclear Dot Protein (NDP52). NDP52 has been described as a receptor for xenophagy and extensive studied in cells infected with bacteria, in particular Listeria and Salmonella. In contrast to p62/SQSTM1, NDP52 lacks a UBA and therefore does not bind ubiqutinated proteins. In the case of CHIKV infected cells, NDP52 forms structures akin to but different from “classic” autophagosomes the viral capsid protein as well as nsP2, and dsRNA intermediates and LC3-C  -but not LC3-B- via binding to the non-canonical LIR of NDP52.

p62/SQSTM1 and NDP52

Binding to NDP52 therefore is being postulated to be required for viral assembly late in infection and contributes to the cytoxicity observed in cells in the late stages of viral infection. In the early stages of replication however, the viral proteins might preferentially degraded via selective, p62/SQSTM1 dependent, autophagy and thus allowing survival of the infected cells. Interestingly, the time at which this switch occurs might be different for CHIKV and SINV infected cells and thus might contribute to the pathology of the disease.

Targeting of viral nsP and structural proteins to TGN-46
positive structures may involve NDP52 and LC3-C 

Further to the role in targeting viral proteins to the RC, in the opinion of the author of these lines, NDP52 might be implicated in the clearance of damaged mitochondria by mitophagy at early timepoints p.i. . The induction of oxidative stress -characterised by increased levels in reactive oxygen species (ROS)- due to a decrease of antioxidant enzymes and an increase in the fold change of pro-inflammatory cytokines as a result of ER stress as well induction of mitochondrial damage leading to the release of Cytochrome C, not only induces apoptosis but also increases autophagy via inhibition of mTOR.

Switch between p62/SQSTM1 and NDP52 binding to structural proteins
may determine the localisation of these proteins and the induction of apoptosis as a
result of ER stress induced by the formation of vesicular structures

In summary, at early timepoints, the expression of the structural proteins of CHIKV, SINV, or SFV, induces ER  stress which in turn induce selective –p62/SQSTM1 dependent- autophagy, whereas at later timepoints the formation of replication centers in the perinuclear region is favoured by the localisation of viral proteins in a NDP52/LC3-C dependent pathway. Interestingly, microscopic studies using PALM, suggest that the capsid protein is located inside of double membrane structures, suggesting that the LC3-C/NDP52 coated vesicles fuse with the TGN-46 positive replication compartment.  

Apart from CHIKV, does NDP mediated localisation of viral proteins to their respective replication centers or complexes play a role during the replication of other viruses? The answer is…..we do not know. As always, the relevant experiments need to be done, but is it possible that both LC3-C and NDP52 are involved in localising components of the CoV replication centers to the ERGIC. In the case of MERS-CoV, this might explain why the virus is not cytotoxic in bats: similar to CHIKV, where the murine NDP52 does not bind viral proteins, bat derived bNDP52 (if it exists) might not bind MERS-CoV and thus target viral proteins for degradation in a p62/SQSTM1 dependent or independent manner. So if anyone in the US has a place for me to study this and other questions, I am up for it. Are you?

Further reading

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Abraham R, Mudaliar P, Padmanabhan A, & Sreekumar E (2013). Induction of cytopathogenicity in human glioblastoma cells by chikungunya virus. PloS one, 8 (9) PMID: 24086645 

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Judith D, Mostowy S, Bourai M, Gangneux N, Lelek M, Lucas-Hourani M, Cayet N, Jacob Y, Prévost MC, Pierre P, Tangy F, Zimmer C, Vidalain PO, Couderc T, & Lecuit M (2013). Species-specific impact of the autophagy machinery on Chikungunya virus infection. EMBO reports, 14 (6), 534-44 PMID: 23619093 

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Barry G, Fragkoudis R, Ferguson MC, Lulla A, Merits A, Kohl A, & Fazakerley JK (2010). Semliki forest virus-induced endoplasmic reticulum stress accelerates apoptotic death of mammalian cells. Journal of virology, 84 (14), 7369-77 PMID: 20427528