Discovery of host-viral protein complexes during infection

Methods in Molecular Biology

Volumn 1064, Issue , 2013, Pages 43-70

  Rowles, Daniell L ^a   Terhune, Scott S ^b   Cristea, Ileana M ^a  

^a PRINCETON UNIVERSITY   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

Cryogenic cell lysis; Epitope tag; Immunoaffinity purification; Infection; Mass spectrometry; Protein complex; Protein protein interactions; Proteomics; Virus host interactions

Indexed keywords

VIRUS PROTEIN;

ANTIBODY AFFINITY; ARTICLE; CONTROLLED STUDY; CYTOLYSIS; HERPES SIMPLEX VIRUS 1; HUMAN CYTOMEGALOVIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PURIFICATION; PSEUDORABIES HERPETOVIRUS; SINDBIS VIRUS; VIRUS INFECTION; WEST NILE FLAVIVIRUS;

ANIMALS; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNOCHROMATOGRAPHY; INFECTION; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; PROTEOMICS; VIRAL PROTEINS; VIRUSES;

EID: 84884176527     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-601-6_4     Document Type: Article

References (25)

1. Cristea IM, Williams R, Chait BT, Rout MP (2005) Fluorescent proteins as proteomic probes. Mol Cell Proteomics 4:1933-1941
2. Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR (2006) Tracking and elucidating alphavirus-host protein interactions. J Biol Chem 281: 30269-30278
3. Cristea IM, Chait BT (2011) Affinity purification of protein complexes, Cold Spring Harbor Protocols 2011, pdb prot5611.
4. Cristea IM, Chait BT (2011) Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harbor Protocols 2011, pdb prot5610.
5. Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM (2010) A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics 9:851-860
6. Cristea IM, Moorman NJ, Terhune SS, Cuevas CD, O'Keefe ES, Rout MP, Chait BT, Shenk T (2010) Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein. J Virol 84:7803-7814
7. Fehr AR, Gualberto NC, Savaryn JP, Terhune SS, Yu D (2012) Proteasome-dependent disruption of the E3 ubiquitin ligase anaphasepromoting complex by HCMV protein pUL21a. PLoS Pathog 8:e1002789
8. Cristea IM, Rozjabek H, Molloy KR, Karki S, White LL, Rice CM, Rout MP, Chait BT, MacDonald MR (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
9. Reitsma JM, Savaryn JP, Faust K, Sato H, Halligan BD, Terhune SS (2011) Antiviral inhibition targeting the HCMV kinase pUL97 requires pUL27-dependent degradation of Tip60 acetyltransferase and cell-cycle arrest. Cell Host Microbe 9:103-114
10. Youn S, Li T, McCune BT, Edeling MA, Fremont DH, Cristea IM, Diamond MS (2012) Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of west nile virus. J Virol 86:7360-7371
11. Moorman NJ, Cristea IM, Terhune SS, Rout MP, Chait BT, Shenk T (2008) Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. Cell Host Microbe 3:253-262
12. Terhune SS, Moorman NJ, Cristea IM, Savaryn JP, Cuevas-Bennett C, Rout MP, Chait BT, Shenk T (2010) Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA. PLoS Pathog 6:e1000965
13. Greco TM, Yu F, Guise AJ, Cristea IM (2011) Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics 10(M110):004317
14. Tsai YC, Greco TM, Boonmee A, Miteva Y, Cristea IM (2012) Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics 11(M111):015156
15. Blanco MA, Aleckovic M, Hua Y, Li T, Wei Y, Xu Z, Cristea IM, Kang Y (2011) Identification of staphylococcal nuclease domain-containing 1 (SND1) as a Metadherin-interacting protein with metastasis-promoting functions. J Biol Chem 286:19982-19992
16. Li T, Diner BA, Chen J, and Cristea IM (2012) Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc Natl Acad Sci USA 109: 10558-10563.
17. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030-1032
18. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green fluorescent protein as a marker for gene expression. Science 263:802-805
19. Hopp TP, Prickett KS, Price VL, Libby RT, March CJ, Cerretti DR, Urdal DL, Conlon RJ (1988) A short polypeptide marker sequence useful for recombinant protein identification and purification. Nat Biotechnol 6:1204-1210
20. Greco TM, Miteva Y, Conlon FL, Cristea IM (2012) Complementary proteomic analysis of protein complexes. Methods Mol Biol 917:391-407
21. Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359-362
22. Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI (2011) SAINT: probabilistic scoring of affinity purificationmass spectrometry data. Nat Methods 8: 70-73
23. Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, Chait BT (2005) I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res 4:1752-1756
24. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, Boydston EA, Holmes MC, Gregory PD, Greally JM, Rafii S, Yang C, Scambler PJ, Garrick D, Gibbons RJ, Higgs DR, Cristea IM, Urnov FD, Zheng D, Allis CD (2010) Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140: 678-691
25. Selimi F, Cristea IM, Heller E, Chait BT, Heintz N (2009) Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol 7:e83