1
|
Gaurav N, Kumar S, Raghavendhar S, Tripathi PK, Gupta S, Arya R, Patel AK. Transcriptome analysis of Huh7 cells upon Chikungunya virus infection and capsid transfection reveals regulation of distinct cellular and metabolic pathways. Virology 2024; 589:109953. [PMID: 38043141 DOI: 10.1016/j.virol.2023.109953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Chikungunya virus (CHIKV) causes persistent arthritis and neurological problems imposing a huge burden globally. The present study aims to understand the interaction mechanism of Chikungunya virus and CHIKV-capsid in Huh7 cells. The RNA-sequencing and qRT-PCR method was used for the transcript and gene profiles of CHIKV virus and CHIKV capsid alone. Transcriptional analysis showed capsid induced 1114 and 956 differentially expressed genes (DEGs) to be upregulated and downregulated respectively, while in virus, 933 genes were upregulated and 956 were downregulated. Total 202 DEGs were common in both capsid and virus; and nine were validated using qRT-PCR. Identified DEGs were found to be associated with metabolic pathways such as Diabetes, cardiac disease, and visual impairment. Further, knock-down study on one of the DEGs (MafA) responsible for insulin regulation showed low viral proteins expression suggesting a reduction in virus-infection. Thus, the study provides insight into the interplay of the virus-host factors assisting virus replication.
Collapse
Affiliation(s)
- Nitika Gaurav
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; University of Colorado, Anschutz Medical Campus, Colorado, USA
| | - Shivani Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Siva Raghavendhar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; Division of Infectious Diseases, University of Utah, Salt Lake City, UT, 84132, USA
| | - Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India; Indian Council of Medical Research, National Institute of Malaria Research, Ranchi, Jharkhand, 834010, India
| | - Shipra Gupta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ravi Arya
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| |
Collapse
|
2
|
Gaurav N, Tripathi PK, Kumar V, Chugh A, Sundd M, Patel AK. Role of nuclear localization signals in the DNA delivery function of Chikungunya virus capsid protein. Arch Biochem Biophys 2021; 702:108822. [PMID: 33722536 DOI: 10.1016/j.abb.2021.108822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Capsids of several RNA viruses are reported to have unconventional roles attributed to their subcellular trafficking property. The capsid of CHIKV is also found to localize in the nucleus, but the rationale is not yet clear. To understand the role of the nuclear-localized capsid, we examined the nucleic acid binding and cargo delivery activity of the CHIKV capsid. We used bacterially purified capsid protein to probe the binding affinity with CHIKV genome-specific and non-specific nucleic acids. We found that the capsid was able to bind non-specifically to different forms of nucleic acids. The successful transfection of GFP-tagged plasmid DNA by CHIKV capsid protein shows the DNA delivery ability of the protein. Further, we selected and investigated the DNA binding and cargo delivery activity of commercially synthesized Nuclear Localization Signal sequences (NLS 1 and NLS2) of capsid protein. Both peptides showed comparable DNA binding affinity, however, only the NLS1 peptide was capable of delivering plasmid DNA inside the cell. Furthermore, the cellular uptake study using the FITC-labelled NLS1 peptide was performed to highlight the membrane penetrating ability. Structural analysis was performed using circular dichroism and NMR spectroscopy to elucidate the transfection ability of the NLS1 peptides. Our findings suggest that the capsid of CHIKV might influence cellular trafficking in the infected cell via non-specific interactions. Our study also indicates the significance of NLS sequences in the multifunctionality of CHIKV capsid protein.
Collapse
Affiliation(s)
- Nitika Gaurav
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vivek Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| |
Collapse
|
3
|
NF-κB Activation Promotes Alphavirus Replication in Mature Neurons. J Virol 2019; 93:JVI.01071-19. [PMID: 31554691 DOI: 10.1128/jvi.01071-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022] Open
Abstract
Alphaviruses are enveloped, positive-sense RNA viruses that are important causes of viral encephalomyelitis. Sindbis virus (SINV) infects the neurons of rodents and is a model for studying factors that regulate infection of neuronal cells. The outcome of alphavirus infection of the central nervous system is dependent on neuronal maturation status. Differentiated mature neurons survive and control viral replication better than undifferentiated immature neurons. The cellular factors involved in age-dependent susceptibility include higher levels of antiapoptotic and innate immune factors in mature neurons. Because NF-κB pathway activation is required for the initiation of both apoptosis and the host antiviral response, we analyzed the role of NF-κB during SINV infection of differentiated and undifferentiated rat neuronal cells. SINV infection induced canonical NF-κB activation, as evidenced by the degradation of IκBα and the phosphorylation and nuclear translocation of p65. Inhibition or deletion of the upstream IκB kinase substantially reduced SINV replication in differentiated but not in undifferentiated neuronal cells or mouse embryo fibroblasts. NF-κB inhibition did not affect the establishment of infection, replication complex formation, the synthesis of nonstructural proteins, or viral RNA synthesis in differentiated neurons. However, the translation of structural proteins was impaired, phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α) was decreased, and host protein synthesis was maintained, suggesting that NF-κB activation was involved in the regulation of translation during infection of mature neurons. Inhibition or deletion of double-stranded RNA-activated protein kinase (PKR) also decreased eIF2α phosphorylation, the translation of viral structural proteins, and virus production. Therefore, canonical NF-κB activation synergizes with PKR to promote SINV replication in differentiated neurons by facilitating viral structural protein translation.IMPORTANCE Mosquito-borne alphaviruses are a significant and growing cause of viral encephalomyelitis worldwide. The outcome of alphaviral neuronal infections is host age dependent and greatly affected by neuronal maturation status, with differentiated, mature neurons being more resistant to infection than undifferentiated, immature neurons. The biological factors that change during neuronal maturation and that influence the outcome of viral infection are currently only partially defined. These studies investigated the role of NF-κB in determining the outcome of alphaviral infection in mature and immature neurons. Inhibition of canonical NF-κB activation decreased alphavirus replication in mature neurons by regulating protein synthesis and limiting the production of the viral structural proteins but had little effect on viral replication in immature neurons or fibroblasts. Therefore, NF-κB is a signaling pathway that influences the maturation-dependent outcome of alphaviral infection in neurons and that highlights the importance of cellular context in determining the effects of signal pathway activation.
Collapse
|
4
|
Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses. Virology 2013; 446:123-32. [PMID: 24074574 PMCID: PMC3818703 DOI: 10.1016/j.virol.2013.07.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/11/2013] [Accepted: 07/20/2013] [Indexed: 02/08/2023]
Abstract
Viral capsid proteins (CPs) are characterized by their role in forming protective shells around viral genomes. However, CPs have additional and important roles in the virus infection cycles and in the cellular responses to infection. These activities involve CP binding to RNAs in both sequence-specific and nonspecific manners as well as association with other proteins. This review focuses on CPs of both plant and animal-infecting viruses with positive-strand RNA genomes. We summarize the structural features of CPs and describe their modulatory roles in viral translation, RNA-dependent RNA synthesis, and host defense responses. We review regulatory activities of the capsid proteins of (+)-strand RNA viruses. Activities of capsid proteins due to RNA binding and protein binding. Effects of capsid proteins on viral processes. Effects of capsid proteins on cellular processes. Regulatory activities of the capsid proteins are affected by capsid concentrations.
Collapse
|
5
|
Abstract
Capsid proteins are obligatory components of infectious virions. Their primary structural function is to protect viral genomes during entry and exit from host cells. Evidence suggests that these proteins can also modulate the activity and specificity of viral replication complexes. More recently, it has become apparent that they play critical roles at the virus–host interface. Here, we discuss how capsid proteins of RNA viruses interact with key host cell proteins and pathways to modulate cell physiology in order to benefit virus replication. Capsid–host cell interactions may also have implications for viral disease. Understanding how capsids regulate virus–host interactions may lead to the development of novel antiviral therapies based on targeting the activities of cellular proteins.
Collapse
Affiliation(s)
- Steven Willows
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Shangmei Hou
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Tom C Hobman
- Department of Li Ka Shing Institute of Virology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| |
Collapse
|
6
|
Ilkow CS, Willows SD, Hobman TC. Rubella virus capsid protein: a small protein with big functions. Future Microbiol 2010; 5:571-84. [PMID: 20353299 DOI: 10.2217/fmb.10.27] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Virus replication occurs in the midst of a life or death struggle between the virus and the infected host cell. To limit virus replication, host cells can activate a number of antiviral pathways, the most drastic of which is programmed cell death. Whereas large DNA viruses have the luxury of encoding accessory proteins whose main function is to interfere with host cell defences, the genomes of RNA viruses are not large enough to encode proteins of this type. Recent studies have revealed that proteins encoded by RNA viruses often play multiple roles in the battles between viruses and host cells. In this article, we discuss the many functions of the rubella virus capsid protein. This protein has well-defined roles in virus assembly, but recent research suggests that it also functions to modulate virus replication and block host cell defences.
Collapse
Affiliation(s)
- Carolina S Ilkow
- Department of Cell Biology, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
| | | | | |
Collapse
|
7
|
Rubella virus capsid protein interacts with poly(a)-binding protein and inhibits translation. J Virol 2008; 82:4284-94. [PMID: 18305028 DOI: 10.1128/jvi.02732-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During virus assembly, the capsid proteins of RNA viruses bind to genomic RNA to form nucleocapsids. However, it is now evident that capsid proteins have additional functions that are unrelated to nucleocapsid formation. Specifically, their interactions with cellular proteins may influence signaling pathways or other events that affect virus replication. Here we report that the rubella virus (RV) capsid protein binds to poly(A)-binding protein (PABP), a host cell protein that enhances translational efficiency by circularizing mRNAs. Infection of cells with RV resulted in marked increases in the levels of PABP, much of which colocalized with capsid in the cytoplasm. Mapping studies revealed that capsid binds to the C-terminal half of PABP, which interestingly is the region that interacts with other translation regulators, including PABP-interacting protein 1 (Paip1) and Paip2. The addition of capsid to in vitro translation reaction mixtures inhibited protein synthesis in a dose-dependent manner; however, the capsid block was alleviated by excess PABP, indicating that inhibition of translation occurs through a stoichiometric mechanism. To our knowledge, this is the first report of a viral protein that inhibits protein translation by sequestration of PABP. We hypothesize that capsid-dependent inhibition of translation may facilitate the switch from viral translation to packaging RNA into nucleocapsids.
Collapse
|
8
|
Urbanowski MD, Ilkow CS, Hobman TC. Modulation of signaling pathways by RNA virus capsid proteins. Cell Signal 2008; 20:1227-36. [PMID: 18258415 PMCID: PMC7127581 DOI: 10.1016/j.cellsig.2007.12.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 12/18/2007] [Indexed: 01/16/2023]
Abstract
Capsid proteins are structural components of virus particles. They are nucleic acid-binding proteins whose main recognized function is to package viral genomes into protective structures called nucleocapsids. Research over the last 10 years indicates that in addition to their role as genome guardians, viral capsid proteins modulate host cell signaling networks. Disruption or alteration of intracellular signaling pathways by viral capsids may benefit replication of the virus by affecting innate immunity and in some cases, may underlie disease progression. In this review, we describe how the capsid proteins from medically relevant RNA viruses interact with host cell signaling pathways.
Collapse
Affiliation(s)
| | - Carolina S. Ilkow
- Department of Cell Biology, University of Alberta, Edmonton, Canada T6G 2H7
| | - Tom C. Hobman
- Department of Cell Biology, University of Alberta, Edmonton, Canada T6G 2H7
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada T6G 2H7
- Corresponding author. Department of Cell Biology, University of Alberta, Edmonton, Canada T6G 2H7. Tel.: +1 780 492 6485; fax: +1 780 492 0450.
| |
Collapse
|
9
|
Aguilar PV, Weaver SC, Basler CF. Capsid protein of eastern equine encephalitis virus inhibits host cell gene expression. J Virol 2007; 81:3866-76. [PMID: 17267491 PMCID: PMC1866141 DOI: 10.1128/jvi.02075-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV) causes sporadic but often severe cases of human and equine neurological disease in North America. To determine how EEEV may evade innate immune responses, we screened individual EEEV proteins for the ability to rescue the growth of a Newcastle disease virus expressing green fluorescent protein (NDV-GFP) from the antiviral effects of interferon (IFN). Only expression of the EEEV capsid facilitated NDV-GFP replication. Inhibition of the antiviral effects of IFN by the capsid appears to occur through a general inhibition of cellular gene expression. For example, the capsid inhibited the expression of several reporter genes under the control of RNA polymerase II promoters. In contrast, capsid did not inhibit expression from a T7 RNA polymerase promoter construct, suggesting that the inhibition of gene expression is specific and is not a simple manifestation of toxicity. The inhibition correlated both with capsid-induced phosphorylation of eukaryotic initiation factor 2 alpha and with capsid-mediated inhibition of cellular mRNA accumulation. Mapping analysis identified the N terminus as the region important for the inhibition of host gene expression, suggesting that this inhibition is independent of capsid protease activity. Finally, when cell lines containing EEEV replicons encoding capsid were selected, replicons consistently acquired mutations that deleted all or part of the capsid, for example, amino acids 18 to 135. Given that the amino terminus of the capsid is required to inhibit host cell gene expression, these data suggest that capsid expression from the replicons is ultimately toxic to host cells, presumably because of its ability to inhibit gene expression.
Collapse
Affiliation(s)
- Patricia V Aguilar
- Department of Microbiology, Box 1124, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | | | | |
Collapse
|
10
|
Grandgirard D, Studer E, Monney L, Belser T, Fellay I, Borner C, Michel MR. Alphaviruses induce apoptosis in Bcl-2-overexpressing cells: evidence for a caspase-mediated, proteolytic inactivation of Bcl-2. EMBO J 1998; 17:1268-78. [PMID: 9482724 PMCID: PMC1170475 DOI: 10.1093/emboj/17.5.1268] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bcl-2 oncogene expression plays a role in the establishment of persistent viral infection by blocking virus-induced apoptosis. This might be achieved by preventing virus-induced activation of caspase-3, an IL-1beta-converting enzyme (ICE)-like cysteine protease that has been implicated in the death effector phase of apoptosis. Contrary to this model, we show that three cell types highly overexpressing functional Bcl-2 displayed caspase-3 activation and underwent apoptosis in response to infection with alphaviruses Semliki Forest and Sindbis as efficiently as vector control counterparts. In all three cell types, overexpressed 26 kDa Bcl-2 was cleaved into a 23 kDa protein. Antibody epitope mapping revealed that cleavage occurred at one or two target sites for caspases within the amino acid region YEWD31 (downward arrow) AGD34 (downward arrow) A, removing the N-terminal BH4 region known to be essential for the death-protective activity of Bcl-2. Preincubation of cells with the caspase inhibitor Z-VAD prevented Bcl-2 cleavage and partially restored the protective activity of Bcl-2 against virus-induced apoptosis. Moreover, a murine Bcl-2 mutant having Asp31, Asp34 and Asp36 substituted by Glu was resistant to proteolytic cleavage and abrogated apoptosis following virus infection. These findings indicate that alphaviruses can trigger a caspase-mediated inactivation of Bcl-2 in order to evade the death protection imposed by this survival factor.
Collapse
Affiliation(s)
- D Grandgirard
- Institute of Medical Microbiology, University of Berne, Friedbuehlstrasse 51, CH-3010 Berne, Switzerland
| | | | | | | | | | | | | |
Collapse
|