Deciphering the host-pathogen protein interface in chikungunya virus-mediated sickness

Archives of Virology

Volumn 158, Issue 6, 2013, Pages 1159-1172

  Rana, Jyoti ^a   Sreejith, R ^a   Gulati, Sahil ^a   Bharti, Isha ^a   Jain, Surangna ^a   Gupta, Sanjay ^a  

^a JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

AEDES; ALPHAVIRUS INFECTION; ANIMAL; APOPTOSIS; ARTICLE; AUTOPHAGY; CHIKUNGUNYA ALPHAVIRUS; DROSOPHILA MELANOGASTER; GENETIC TRANSCRIPTION; HOST PATHOGEN INTERACTION; HUMAN; INFLAMMATION; PATHOPHYSIOLOGY; PHYSIOLOGY; PROTEIN SYNTHESIS; VIROLOGY;

AEDES; ALPHAVIRUS INFECTIONS; ANIMALS; APOPTOSIS; AUTOPHAGY; CHIKUNGUNYA VIRUS; DROSOPHILA MELANOGASTER; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLAMMATION; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC; VIRAL PROTEINS; VIRAL STRUCTURAL PROTEINS;

CHIKUNGUNYA VIRUS; DENGUE VIRUS; DENGUE VIRUS GROUP; HUMAN IMMUNODEFICIENCY VIRUS;

EID: 84878574165     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-013-1602-1     Document Type: Article

References (114)

1. Higgs S (2006) The 2005-2006 chikungunya epidemic in the Indian Ocean. Vector Borne Zoonotic Dis 6: 115-116.
2. Rezza G, Nicoletti L, Angelini R et al (2007) Infection with chikungunya virus in Italy: an outbreak in a temperate region. Lancet 370(9602): 1840-1846.
3. Wang E, Volkova E, Adams AP et al (2008) Chimeric alphavirus vaccine candidates for chikungunya. Vaccine 26: 5030-5039.
4. Tsetsarkin K, Higgs S, McGee C et al (2006) Infectious clones of chikungunya virus (La Reunion isolate) for vector competence studies. Vector Borne Zoonotic Dis 6: 325-337.
5. Arpino C, Curatolo P, Rezza G (2009) Chikungunya and the nervous system: what we do and do not know. Rev Med Virol 19: 121-129.
6. Chandak R, Kashyap S, Kabra D, Karandikar P, Saha SS, Morey SH, Purohit J, Girdhar I, Taori M, Daginawala HF (2009) Neurological complications of chikungunya virus infection. Neurol India 57(2): 177-180.
7. Hardy JL, Houk EJ, Kramer LD, Reeves WC (1983) Intrinsic factors affecting vector competence of mosquitoes for arboviruses. Annu Rev Entomol 28: 229-262.
8. Aloy P, Russell RB (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19: 161.
9. Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364.
10. Davis FP, Braberg H, Shen MY et al (2006) Protein complex compositions predicted by structural similarity. Nucleic Acids Res 34: 2943-2952.
11. Dyer MD, Murali TM, Sobral BW (2007) Computational prediction of hostpathogen protein protein interactions. Bioinformatics 23: I159-I166.
12. Lee SA, Chan C, Tsai CH et al (2008) Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics 9: S11.
13. Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J (2009) Prediction of interactions between HIV-1 and human proteins by information integration. Pac Symp Biocomput 14: 516-527.
14. Evans P, Dampier W, Ungar L, Tozeren A (2009) Prediction of HIV-1 virus host protein interactions using virus and host sequence motifs. BMC Med Genomics 2: 27.
15. Doolittle JM, Gomez SM (2010) Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 7: 82.
16. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A (2007) Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16: 2585.
17. Franzosa EA, Xia Y (2011) Structural principles within the human-virus protein-protein interaction network. PNAS 108(26): 10538-10543.
18. Zhang QC, Petrey D, Deng L et al (2012) Structure based prediction of protein-protein interactions on a genome wide scale. Nature 490: 556-561.
19. Davey NE, Trave G, Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36(3): 159-169.
20. Doolittle JM, Gomez SM (2011) Mapping protein interactions between dengue virus and its human and insect hosts. PLoS Neg Trop Dis 5(2): e954.
21. Sreejith R, Rana J, Dudha N, Kumar K, Gabrani R, Sharma SK, Gupta A, Vrati S, Chaudhary VK, Gupta S (2012) Mapping of interactions among chikungunya virus nonstructural proteins. Virus Res 169(1): 231-236.
22. Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28: 235-242.
23. Yang Z (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9.
24. Dudha N, Appaiahgari MB, Bharati K, Gupta D, Gupta Y, Kumar K, Gabrani R, Sharma SK, Gupta A, Chaudhary VK, Vrati S, Gupta S (2012) Molecular cloning and characterization of chikungunya virus genes from Indian isolate of 2006 outbreak. J Pharm Res 5(7): 3860-3863.
25. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138.
26. Holm L, Kaariainen S, Rosenstrom P, Schenkel A (2008) Searching protein structure databases with DaliLite v. 3. Bioinformatics 24: 2780.
27. Mishra GR, Suresh M, Kumaran K et al (2006) Human protein reference database-2006 update. Nucleic Acids Res 34: D411-D414.
28. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 1(34): 535-539.
29. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A et al (2009) The IntAct molecular interaction database in 2010. Nucleic Acids Res 38: D525-D531.
30. Berglund AC, Sjolund E, Ostlund G, Sonnhammer ELL (2007) InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res 33: D76-D480.
31. Crosby MA, Goodman JL, Strelets VB et al (2006) FlyBase: genomes by the dozen. Nucleic Acids Res 00: D1-D6.
32. Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
33. Yu J, Pacifico S, Liu G, Finley R (2008) DroID: the Drosophila interactions database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9: 461.
34. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29.
35. Dennis G, Sherman B, Hosack D et al (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4: R60.
36. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
37. McCarthy F, Wang N, Magee GB et al (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7: 229.
38. Atasheva S, Gorchakov R, English R, Frolov I, Frolova E (2007) Development of Sindbis viruses encoding nsP2/GFP chimeric proteins and their application for studying nsP2 functioning. J Virol 81: 5046-5057.
39. Burnham AJ, Gong L, Hardy RW (2007) Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA. Virology 367: 212-221.
40. Cristea IM, Rozjabek H, Molloy KR et al (2010) Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication. J Virol 84: 6720-6732.
41. Frolova E, Gorchakov R, Garmashova N, Atasheva S, Vergara LA, Frolov I (2006) Formation of nsP3-specific protein complexes during Sindbis virus replication. J Virol 80: 4122-4134.
42. Gorchakov R, Garmashova N, Frolova E, Frolov I (2008) Different types of nsP3-containing protein complexes in Sindbis virus-infected cells. J Virol 82: 10088-10101.
43. Montgomery SA, Berglund P, Beard CW, Johnston RE (2006) Ribosomal protein S6 associates with alphavirus nonstructural protein 2 and mediates expression from alphavirus messages. J Virol 80: 7729-7739.
44. Tchankouo-Nguetcheu S, Khun H, Pincet L, Roux P, Bahut M, Huerre M, Guette C, Choume V (2010) Differential protein modulation in midguts of Aedes aegypti infected with chikungunya and dengue 2 viruses. PLoS One 5(10): e13149.
45. Zhang X, Fugere M, Day R, Kielian M (2003) Furin processing and proteolytic activation of Semliki forest virus. J Virol 77: 2981-2989.
46. Krejbich-Trotot P, Denizotm M, Hourau JJ et al (2011) Chikungunya virus mobilizes the apoptotic machinery to invade host cell defenses. FASEB J 25(1): 314-325.
47. Dhanwani R, Khan M, Alam SI, Rao PVL, Parida M (2011) Differential proteome analysis of chikungunya virus infected new-born mice tissues reveal implication of stress, inflammatory and apoptotic pathways in disease pathogenesis. Proteomics 11: 1936-1951.
48. Bouraï M, Lucas-Hourani M, Gad HH et al (2012) Mapping of chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component. J Virol 86(6): 3121-3133.
49. Foss JJ, Domeradzka NE, Baggen J, Geertsema C, Flipse J, Vlak JM, Pijlman GP (2012) Chikungunya virus nsP3 blocks stress granule assembly by recruitment of G3BP into cytoplasmic foci. J Virol 86(19): 10873-10879.
50. Salvador B, Zhou Y, Michault A, Muench MO, Simmons G (2009) Characterization of chikungunya pseudotyped viruses: identification of refractory cell lines and demonstration of cellular tropism differences mediated by mutations in E1 glycoprotein. Virology 393: 33-41.
51. Leung JYS, Ng MML, Chu JJH (2011) Replication of alphaviruses: a review on the entry process of alphaviruses into cells. Adv Virol 24: 9640.
52. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG (1993) hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62: 289-321.
53. Shaw ML, Stone KL, Colangelo CM, Gulcicek EE, Palese P (2008) Cellular proteins in influenza virus particles. PLoS Path 4: e1000085.
54. Thangamani S, Higgs S, Ziegler S, Vanlandingham D, Tesh R, Wikel S (2010) Host immune response to mosquito-transmitted chikungunya virus differs from that elicited by needle inoculated virus. PLoS One 5(8): e12137.
55. Schmid D, Munz C (2007) Innate and adaptive immunity through autophagy. Immunity 27(1): 11-21.
56. Joubert PE, Werneke SW, de la Calle C et al (2012) Chikungunya virus-induced autophagy delays caspase dependent cell death. J Exp Med 209: 1029-1047.
57. Dengjel J, Schoor O, Fischer R et al (2005) Autophagy promotes MHC class II presentation of peptides from intracellular source proteins. Proc Natl Acad Sci USA 102: 7922-7927.
58. English L, Chemali M, Duron J, Rondeau C, Laplante A, Gingras D, Alexander D, Leib D, Norbury C, Lippé R, Desjardins M (2009) Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection. Nat Immunol 10: 480-487.
59. Uhl M, Kepp O, Jusforgues-Saklani H, Vicencio JM, Kroemer G, Albert ML (2009) Autophagy within the antigen donor cell facilitates efficient antigen cross-priming of virus-specific CD8+ T cells. Cell Death Differ 16: 991-1005.
60. Crotzer VL, Blum JS (2010) Autophagy and adaptive immunity. Immunology 131: 9-17.
61. Jackson WT, Giddings TH, Taylor MP et al (2005) Subversion of cellular autophagosomal machinery by RNA viruses. PLoS Biol 3(5): e156.
62. Prentice E, Jerome WG, Yoshimori T et al (2004) Coronavirus replication complex formation utilizes components of cellular autophagy. J Biol Chem 279(11): 10136-10141.
63. Lee YR, Lei HY, Liu MT et al (2008) Autophagic machinery activated by dengue virus enhances virus replication. Virology 374(2): 240-248.
64. Wong J, Zhang J, Si X et al (2008) Autophagosome supports coxsackie virus B3 replication in host cells. J Virol 82(18): 9143-9153.
65. Krejbich-Trotot P, Gay B, Li-Pat-Yuen G et al (2011) Chikungunya triggers an autophagic process which promotes viral replication. Virol J 8: 432.
66. Thorburn A (2008) Apoptosis and autophagy: regulatory connections between two supposedly different processes. Apoptosis 13: 1-9.
67. Djavaheri-Mergny M, Maiuri MC, Kroemer G (2010) Cross talk between apoptosis and autophagy by caspase-mediated cleavage of Beclin 1. Oncogene 29: 1717-1719.
68. Kang R, Zeh HJ, Lotze MT, Tang D (2011) The Beclin 1 network regulates autophagy and apoptosis. Cell Death Differ 18: 571-580.
69. Lee AH, Iwakoshi NN, Glimcher LH (2003) XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response. Mol Cell Biol 23: 7448-7459.
70. McGuckin MA, Eri RD, Das I, Lourie R, Florin TH (2010) ER stress and the unfolded protein response in intestinal inflammation. Am J Physiol Gastrointest Liver Physiol 298: G820-G832.
71. Urano F, Wang X, Bertolotti A, Zhang Y, Chung P, Harding HP, Ron D (2000) Coupling of stress in the ER to activation of JNK protein kinases by transmembrane protein kinase IRE1. Science 287: 664-666.
72. Cataldi A (2010) Cell responses to oxidative stressors. Curr Pharm Des 16: 1387-1395.
73. Djavaheri-Mergny M, Amelotti M, Mathieu J, Besançon F, Bauvy C, Codogno P (2007) Regulation of autophagy by NFkappaB transcription factor and reactives oxygen species. Autophagy 3: 390-392.
74. Filomeni G, Desideri E, Cardaci S, Rotilio G, Ciriolo MR (2010) Under the ROS thiol network is the principal suspect for autophagy commitment. Autophagy 6: 999-1005.
75. Guo WJ, Ye SS, Cao N, Huang J, Gao J, Chen QY (2010) ROS mediated autophagy was involved in cancer cell death induced by novel copper(II) complex. Exp Toxicol Pathol 62: 577-582.
76. Alexander A, Cai SL, Kim J et al (2010) ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS. Proc Natl Acad Sci USA 107: 4153-4158.
77. Alexander A, Kim J, Walker CL (2010) ATM engages the TSC2/ mTORC1 signaling node to regulate autophagy. Autophagy 6: 672-673.
78. Zoncu R, Efeyan A, Sabatini DM (2011) mTOR: from growth signal integration to cancer, diabetes and ageing. Nat Rev Mol Cell Biol 12: 21-35.
79. Thomson AW, Turnquist HR, Raimondi G (2009) Immunoregulatory functions of mTOR inhibition. Nat Rev Immunol 9: 324-337.
80. Danial NN, Korsmeyer SJ (2004) Cell death: critical control points. Cell 116: 205-219.
81. Kurokawa M, Kornbluth S (2009) Caspases and kinases in a death grip. Cell 138: 838-854.
82. Wilson NS, Dixit V, Ashkenazi A (2009) Death receptor signal transducers: nodes of coordination in immune signaling networks. Nat Immunol 10: 348-355.
83. Kurokawa M, Kornbluth S (2010) Stalling in mitosis and releasing the apoptotic brake. EMBO J 29: 2255-2257.
84. Kroemer G, Galluzzi L, Brenner C (2007) Mitochondrial membrane permeabilization in cell death. Physiol Rev 87: 99-163.
85. Dhanwani R, Khan M, Bhaskar ASB et al (2012) Characterization of chikungunya virus infection in human neuroblastoma SH-SY5Y cells: role of apoptosis in neuronal cell death. Virus Res 163: 563-572.
86. Gorchakov R, Frolova E, Frolo I (2005) Inhibition of transcription and translation in Sindbis virus infected cells. J Virol 79: 9397-9409.
87. Tamm K, Merits A, Sarand I (2008) Mutations in nuclear localization signal of nsP2 influence RNA synthesis, protein expression and cytotoxicity of Semliki forest virus. J Gen Virol 89: 676-686.
88. Garmashova N, Gorchakov R, Frolova E, Frolov I (2006) Sindbis virus nonstructural protein nsP2 is cytotoxic and inhibits cellular transcription. J Virol 80: 5686-5696.
89. Fazakerley JK, Boyd A, Mikkola ML, Karriainen L (2002) A single amino acid change in the nuclear localization sequence of the nsP2 protein affects the neurovirulance of Semliki forest virus. J Virol 76: 392-396.
90. Inglis SC (1982) Inhibition of host protein synthesis and degradation of cellular mRNAs during infection by influenza and herpes simplex virus. Mol Cell Biol 2(12): 1644-1648.
91. Beloso A, Martinez C, Valcarcel J, Santaren JF, Ortin J (1992) Degradation of cellular mRNA during influenza virus infection: its possible role in protein synthesis shutoff. J Gen Virol 73: 575-581.
92. Lindquist ME, Mainou BA, Dermody TS, Crowe JE Jr (2011) Activation of protein kinase R is required for induction of stress granule by respiratory syncytial virus but dispensable for viral replication. Virology 413: 103-110.
93. McInerney GM, Kedersha NL, Kaufman RJ, Anderson P, Liljestrom P (2005) Importance of eIF2α phosphorylation and stress granule assembly in alphavirus translation regulation. Mol Biol Cell 16: 3753-3763.
94. Ventoso I, Sanz MA, Molina S, Berlanga JJ, Carrasco L, Esteban M (2006) Translational resistance of late alphavirus mRNA to eIF2α phosphorylation: a strategy to overcome the antiviral effect of protein kinase PKR. Genes Dev 20: 87-100.
95. Stetson DB, Medzhitov R (2006) Type I interferons in host defense. Immunity 25: 373-381.
96. Sourisseau M, Schilte C, Casartelli N, Trouillet C, Guivel-Benhassine F, Rudnicka D et al (2007) Characterization of reemerging chikungunya virus. PLoS Path 3: e89.
97. Her Z, Malleret B, Chan M et al (2010) Active infection of human blood monocytes by chikungunya virus triggers an innate immune response. J Immunol 184: 5903-5913.
98. Schilte C, Couderc T, Chretien F et al (2010) Type I IFN controls chikungunya virus via its action on nonhematopoietic cells. J Exp Med 207: 429-442.
99. Werneke SW, Schilte C, Rohatgi A et al (2011) ISG15 is critical in the control of chikungunya virus infection independent of UbE1L mediated conjugation. PLoS Pathog 7: e1002322.
100. Ng LFP, Chow A, Sun YJ et al (2009) IL-1beta, IL-6, and RANTES as biomarkers of chikungunya severity. PLoS ONE 4: e4261.
101. Broz P, Monack DM (2011) Molecular mechanisms of inflammasome activation during microbial infections. Immunol Rev 243: 174-190.
102. Thompson MR, Kaminski JJ, Kurt-Jones EA, Fitzgerald KA (2011) Pattern recognition receptors and the innate immune response to viral infection. Viruses 3: 920-940.
103. Kumar H, Kawai T, Akira S (2011) Pathogen recognition by the innate immune system. Int Rev Immunol 30: 16-34.
104. Bowie AG, Unterholzner L (2008) Viral evasion and subversion of pattern-recognition receptor signalling. Nat Rev Immunol 8: 911-922.
105. Carty M, Bowie AG (2010) Recent insights into the role of toll-like receptors in viral infection. Clin Exp Immunol 161: 397-406.
106. Hiscott J, Lin R, Nakhaei P, Paz S (2006) Master-CARD: a priceless link to innate immunity. Trends Mol Med 12: 53-56.
107. Loo YM, Gale M (2011) Immune signaling by RIG-Ilike receptors. Immunity 34: 680-692.
108. White LK, Sali T, Alvarado D et al (2011) Chikungunya virus induces IPS-1-dependent innate immune activation and protein kinase R-independent translational shutoff. J Virol 85: 606-620.
109. Takaoka A, Yanai H (2006) Interferon signaling network in innate defense. Cell Microbiol 8(6): 907-922.
110. Fros JJ, Liu WJ, Prow NA et al (2010) Chikungunya virus nonstructural protein 2 inhibits type I/II interferon stimulated JAK-STAT signaling. J Virol 84: 10877-10887.
111. Couderc T, Chrétien F, Schilte C et al (2008) A mouse model for chikungunya: young age and inefficient type-I interferon signaling are risk factors for severe disease. PLoS Path 4: e29.
112. Akahata W, Yang ZY, Andersen H et al (2010) A VLP vaccine for epidemic chikungunya virus protects nonhuman primates against infection. Nat Med 16(3): 334-338.
113. AbuBakar S, Sam IC, Wong PF, MatRahim N, Hooi PS, Roslan N (2007) Reemergence of endemic chikungunya, Malaysia. Emer Infect Dis 13(1): 147-149.
114. Antar AA, Konopka JL, Campbell JA et al (2009) Junctional adhesion molecule-A is required for hematogenous dissemination of reovirus. Cell Host Microbe 5(1): 59-71.