Hepatitis C virus infection protein network

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  De Chassey, B ^a,b   Navratil, V ^b,c   Tafforeau, L ^a,b   Hiet, M S ^a,b,i   Aublin Gex, A ^a,b   Agaugue S ^a,b,j   Meiffren, G ^a,b   Pradezynski, F ^a,b   Faria, B F ^a,b   Chantier, T ^a,b   Le Breton, M ^a,b   Pellet, J ^a,b   Davoust, N ^a,b   Mangeot, P E ^a,b   Chaboud, A ^b,d   Penin, F ^b,d   Jacob, Y ^e   Vidalain, P O ^f   Vidal, M ^g   Andre P ^a,b,h   Rabourdin Combe, C ^a,b   Lotteau, V ^a,b,h   more..

^a INSERM   (France)

^b UNIVERSITÉ DE LYON   (France)

^c UMR 754   (France)

^d INSTITUT DE BIOLOGIE ET CHIMIE DES PROTÉINES   (France)

^e INSTITUT PASTEUR   (France)

^f CNRS   (France)

^g HARVARD MEDICAL SCHOOL   (United States)

^h CROIX ROUSSE HOSPITAL   (France)

ⁱ UNIVERSITY OF HEIDELBERG   (Germany)

^j SAINT LOUIS HOSPITAL   (France)

more..

Author keywords

Functional analysis; Hepatitis C; Interactome; Virus host cell

Indexed keywords

CELL PROTEIN; NONSTRUCTURAL PROTEIN 3; NONSTRUCTURAL PROTEIN 5A; STAT PROTEIN; TRANSFORMING GROWTH FACTOR BETA; VIRUS PROTEIN;

ARTICLE; FOCAL ADHESION; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; METABOLISM; PHYSIOLOGY; PROTEIN BINDING; TWO HYBRID SYSTEM;

HEPATITIS C VIRUS;

HEPACIVIRUS; HEPATITIS C; HUMANS; PROTEIN BINDING; TWO-HYBRID SYSTEM TECHNIQUES; VIRAL PROTEINS;

EID: 55549117151     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.66     Document Type: Article

References (66)

1. Albers M, Kranz H, Kober I, Kaiser C, Klink M, Suckow J, Kern R, Koegl M (2005) Automated yeast two-hybrid screening for nuclear receptor-interacting proteins. Mol Cell Proteomics 4: 205-213
2. Aoki-Kinoshita KF, Kanehisa M (2007) Gene annotation and pathway mapping in KEGG. Methods Mol Biol 396: 71-92
3. Appel N, Schaller T, Penin F, Bartenschlager R (2006) From structure to function: new insights into hepatitis C virus RNA replication. J Biol Chem 281: 9833-9836
4. Arbouzova NI, Bach EA, Zeidler MP (2006) Ken & barbie selectively regulates the expression of a subset of Jak/STAT pathway target genes. Curr Biol 16: 80-88
5. Bader GD, Betel D, Hogue CW (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250
6. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284
7. Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci USA 104: 7606-7611
8. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35: D572-D574
9. Combet C, Garnier N, Charavay C, Grando D, Crisan D, Lopez J, Dehne-Garcia A, Geourjon C, Bettler E, Hulo C, Le Mercier P, Bartenschlager R, Diepolder H, Moradpour D, Pawlotsky JM, Rice CM, Trepo C, Penin F, Deleage G (2007) euHCVdb: the European hepatitis C virus database. Nucleic Acids Res 35: D363-D366
10. D'Souza R, Sabin CA, Foster GR (2005) Insulin resistance plays a significant role in liver fibrosis in chronic hepatitis C and in the response to antiviral therapy. Am J Gastroenterol 100: 1509-1515
11. Dong B, Zhou Q, Zhao J, Zhou A, Harty RN, Bose S, Banerjee A, Slee R, Guenther J, Williams BR, Wiedmer T, Sims PJ, Silverman RH (2004) Phospholipid scramblase 1 potentiates the antiviral activity of interferon. J Virol 78: 8983-8993
12. Dyer MD, Murali TM, Sobral BW (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4: e32
13. Ekman D, Light S, Bjorklund AK, Elofsson A (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol 7: R45
14. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS et al (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293
15. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL (2007) The human disease network. Proc Natl Acad Sci USA 104: 8685-8690
16. Goh KI, Oh E, Jeong H, Kahng B, Kim D (2002) Classification of scale-free networks. Proc Natl Acad Sci USA 99: 12583-12588
17. Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2: e100
18. He CQ, Ding NZ, Fan W (2008) YY1 repressing peroxisome proliferator-activated receptor delta promoter. Mol Cell Biochem 308: 247-252
19. Hernandez P, Huerta-Cepas J, Montaner D, Al-Shahrour F, Valls J, Gomez L, Capella G, Dopazo J, Pujana MA (2007) Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics 8: 185
20. Huang H, Jedynak BM, Bader JS (2007) Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 3: e214
21. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42
22. Joy MP, Brock A, Ingber DE, Huang S (2005) High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005: 96-103
23. Kawaguchi T, Yoshida T, Harada M, Hisamoto T, Nagao Y, Ide T, Taniguchi E, Kumemura H, Hanada S, Maeyama M, Baba S, Koga H, Kumashiro R, Ueno T, Ogata H, Yoshimura A, Sata M (2004) Hepatitis C virus down-regulates insulin receptor substrates 1 and 2 through up-regulation of suppressor of cytokine signaling 3. Am J Pathol 165: 1499-1508
24. Kedersha NL, Rome LH (1986) Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA. J Cell Biol 103: 699-709
25. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B (2007) IntAct - open source resource for molecular interaction data. Nucleic Acids Res 35: D561-D565
26. Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MD, Landro JA, Chambers SP, Markland W, Lepre CA, O'Malley ET, Harbeson SL, Rice CM, Murcko MA, Caron PR, Thomson JA (1996) Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87: 343-355
27. Kurisaki K, Kurisaki A, Valcourt U, Terentiev AA, Pardali K, Ten Dijke P, Heldin CH, Ericsson J, Moustakas A (2003) Nuclear factor YY1 inhibits transforming growth factor beta- and bone morphogenetic protein-induced cell differentiation. Mol Cell Biol 23: 4494-4510
28. Lee CH, Chawla A, Urbiztondo N, Liao D, Boisvert WA, Evans RM, Curtiss LK (2003) Transcriptional repression of atherogenic inflammation: modulation by PPARdelta. Science 302: 453-457
29. Lehmann MJ, Sherer NM, Marks CB, Pypaert M, Mothes W (2005) Actin- and myosin-driven movement of viruses along filopodia precedes their entry into cells. J Cell Biol 170: 317-325
30. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543
31. Lim J, Hao T, Shaw C, Patel AJ, Szabo G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabasi AL, Vidal M, Zoghbi HY (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801-814
32. Lohmann V, Korner F, Koch J, Herian U, Theilmann L, Bartenschlager R (1999) Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285: 110-113
33. Lonardo A, Adinolfi LE, Loria P, Carulli N, Ruggiero G, Day CP (2004) Steatosis and hepatitis C virus: mechanisms and significance for hepatic and extrahepatic disease. Gastroenterology 126: 586-597
34. Lozach PY, Lortat-Jacob H, de Lacroix de Lavalette A, Staropoli I, Foung S, Amara A, Houles C, Fieschi F, Schwartz O, Virelizier JL, Arenzana-Seisdedos F, Altmeyer R (2003) DC-SIGN and L-SIGN are high affinity binding receptors for hepatitis C virus glycoprotein E2. J Biol Chem 278: 20358-20366
35. Lu Z, Cohen KB, Hunter L (2007) GeneRIF quality assurance as summary revision. Pac Symp Biocomput 269-280
36. Mai RT, Yeh TS, Kao CF, Sun SK, Huang HH, Wu Lee YH (2006) Hepatitis C virus core protein recruits nucleolar phosphoprotein B23 and coactivator p300 to relieve the repression effect of transcriptional factor YY1 on B23 gene expression. Oncogene 25: 448-462
37. Miao H, Burnett E, Kinch M, Simon E, Wang B (2000) Activation of EphA2 kinase suppresses integrin function and causes focal-adhesion-kinase dephosphorylation. Nat Cell Biol 2: 62-69
38. Moradpour D, Penin F, Rice CM (2007) Replication of hepatitis C virus. Nat Rev Microbiol 5: 453-463
39. Negro F (2006) Insulin resistance and HCV: will new knowledge modify clinical management? J Hepatol 45: 514-519
40. Pazienza V, Clement S, Pugnale P, Conzelman S, Foti M, Mangia A, Negro F (2007) The hepatitis C virus core protein of genotypes 3a and 1b downregulates insulin receptor substrate 1 through genotype-specific mechanisms. Hepatology 45: 1164-1171
41. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32: D497-D501
42. Poynard T, McHutchison J, Manns M, Trepo C, Lindsay K, Goodman Z, Ling MH, Albrecht J (2002) Impact of pegylated interferon alfa-2b and ribavirin on liver fibrosis in patients with chronic hepatitis C. Gastroenterology 122: 1303-1313
43. Ramirez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M (2007) Computational analysis of human protein interaction networks. Proteomics 7: 2541-2552
44. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A (2008) Text processing through Web services: calling whatizit. Bioinformatics 24: 296-298
45. Romero-Gomez M (2006) Insulin resistance and hepatitis C. World J Gastroenterol 12: 7075-7080
46. Romero-Gomez M, Del Mar Viloria M, Andrade RJ, Salmeron J, Diago M, Fernandez-Rodriguez CM, Corpas R, Cruz M, Grande L, Vazquez L, Munoz-De-Rueda P, Lopez-Serrano P, Gila A, Gutierrez ML, Perez C, Ruiz-Extremera A, Suarez E, Castillo J (2005) Insulin resistance impairs sustained response rate to peginterferon plus ribavirin in chronic hepatitis C patients. Gastroenterology 128: 636-641
47. Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C (2004) Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 14: 2128-2135
48. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178
49. Sahu SK, Gummadi SN, Manoj N, Aradhyam GK (2007) Phospholipid scramblases: an overview. Arch Biochem Biophys 462: 103-114
50. Schuppan D, Krebs A, Bauer M, Hahn EG (2003) Hepatitis C and liver fibrosis. Cell Death Differ 10(Suppl 1): S59-S67
51. Shintani Y, Fujie H, Miyoshi H, Tsutsumi T, Tsukamoto K, Kimura S, Moriya K, Koike K (2004) Hepatitis C virus infection and diabetes: direct involvement of the virus in the development of insulin resistance. Gastroenterology 126: 840-848
52. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539
53. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968
54. Strader DB, Wright T, Thomas DL, Seeff LB (2004) Diagnosis, management, and treatment of hepatitis C. Hepatology 39: 1147-1171
55. Tan SL, Ganji G, Paeper B, Proll S, Katze MG (2007) Systems biology and the host response to viral infection. Nat Biotechnol 25: 1383-1389
56. Taremi SS, Beyer B, Maher M, Yao N, Prosise W, Weber PC, Malcolm BA (1998) Construction, expression, and characterization of a novel fully activated recombinant single-chain hepatitis C virus protease. Protein Sci 7: 2143-2149
57. Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239-242
58. Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8: R39
59. Vidalain PO, Boxem M, Ge H, Li S, Vidal M (2004) Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32: 363-370
60. Wachi S, Yoneda K, Wu R (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 21: 4205-4208
61. Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, van den Heuvel S, Vidal M (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328: 575-592
62. Walhout AJ, Vidal M (2001) High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24: 297-306
63. Wang D, Long J, Dai F, Liang M, Feng XH, Lin X (2008) BCL6 represses Smad signaling in transforming growth factor-beta resistance. Cancer Res 68: 783-789
64. Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20: 2138-2139
65. Wiedmer T, Zhao J, Li L, Zhou Q, Hevener A, Olefsky JM, Curtiss LK, Sims PJ (2004) Adiposity, dyslipidemia, and insulin resistance in mice with targeted deletion of phospholipid scramblase 3 (PLSCR3). Proc Natl Acad Sci USA 101: 13296-13301
66. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305