Genome-wide analysis of host factors in nodavirus RNA replication

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Hao, Linhui ^a   Lindenbach, Brett ^a,d   Wang, Xiaofeng ^a,e   Dye, Billy ^a,f   Kushner, David ^a,g   He, Qiuling ^b,h   Newton, Michael ^b,c   Ahlquist, Paul ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b University of Wisconsin Madison   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^d YALE UNIVERSITY   (United States)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^f Motlow State Community College   (United States)

^g DICKINSON COLLEGE   (United States)

^h NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENOMIC RNA; HOST FACTOR; SINGLE STRANDED DNA; VIRUS RNA;

ARTICLE; CELL NUCLEUS; CYTOPLASM; DELETION MUTANT; DNA MODIFICATION; GENE DELETION; GENE EXPRESSION; GENETIC ASSOCIATION; HIGH THROUGHPUT SCREENING; MITOCHONDRION; NODAVIRUS; NONHUMAN; NORTHERN BLOTTING; PROTEIN PROCESSING; REPORTER GENE; RNA PROCESSING; VIRUS REPLICATION; VIRUS STRAIN; WILD TYPE; GENETICS; HIGH THROUGHPUT SEQUENCING; PHYSIOLOGY; PROCEDURES; RNA VIRUS;

GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RNA VIRUSES; RNA, VIRAL; VIRUS REPLICATION;

EID: 84899670175     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095799     Document Type: Article

References (48)

1. Hao L, He Q, Wang Z, Craven M, Newton MA, et al. (2013) Limited agreement of independent rnai screens for virus-required host genes owes more to false-negative than false-positive factors. PLoS Comput Biol 9: e1003235.
2. Cherry S, Perrimon N (2004) Entry is a rate-limiting step for viral infection in a Drosophila melanogaster model of pathogenesis. Nat Immunol 5: 81-87. (Pubitemid 38081472)
3. Stertz S, Shaw ML (2011) Uncovering the global host cell requirements for influenza virus replication via RNAi screening. Microbes Infect 13: 516-525.
4. Price BD, Roeder M, Ahlquist P (2000) DNA-Directed expression of functional flock house virus RNA1 derivatives in Saccharomyces cerevisiae, heterologous gene expression, and selective effects on subgenomic mRNA synthesis. J Virol 74: 11724-11733. (Pubitemid 32222322)
5. Dye BT, Miller DJ, Ahlquist P (2005) In vivo self-interaction of nodavirus RNA replicase protein a revealed by fluorescence resonance energy transfer. J Virol 79: 8909-8919. (Pubitemid 40934802)
6. Ball LA (1995) Requirements for the self-directed replication of flock house virus RNA 1. J Virol 69: 2722.
7. Dasgupta R, Cheng LL, Bartholomay LC, Christensen BM (2003) Flock house virus replicates and expresses green fluorescent protein in mosquitoes. J Gen Virol 84: 1789-1797. (Pubitemid 36805914)
8. Schwartz M, Chen J, Janda M, Sullivan M, den Boon J, et al. (2002) A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids. Mol Cell 9: 505-514. (Pubitemid 34273782)
9. Lu R, Maduro M, Li F, Li HW, Broitman-Maduro G, et al. (2005) Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Nature 436: 1040-1043. (Pubitemid 41191689)
10. Kopek BG, Perkins G, Miller DJ, Ellisman MH, Ahlquist P (2007) Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle. PLoS Biol 5: e220.
11. Kushner DB, Lindenbach BD, Grdzelishvili VZ, Noueiry AO, Paul SM, et al. (2003) Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proc Natl Acad Sci U S A 100: 15764-15769. (Pubitemid 38021064)
12. Panavas T, Serviene E, Brasher J, Nagy PD (2005) Yeast genome-wide screen reveals dissimilar sets of host genes affecting replication of RNA viruses. Proc Natl Acad Sci U S A 102: 7326-7331. (Pubitemid 40696378)
13. Lindenbach BD, Sgro JY, Ahlquist P (2002) Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication. J Virol 76: 3905-3919. (Pubitemid 34250555)
14. Van Wynsberghe PM, Chen HR, Ahlquist P (2007) Nodavirus RNA replication protein a induces membrane association of genomic RNA. J Virol 81: 4633-4644. (Pubitemid 46668661)
15. Huang S, Qu Y (2006) The loss in power when the test of differential expression is performed under a wrong scale. J Comput Biol 13: 786-797. (Pubitemid 43801005)
16. Sanford W (1985) Applied linear regression. John Wiley & Sons.
17. Cherry S, Doukas T, Armknecht S, Whelan S, Wang H, et al. (2005) Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev 19: 445-452. (Pubitemid 40256276)
18. Miller DJ, Schwartz MD, Ahlquist P (2001) Flock house virus RNA replicates on outer mitochondrial membranes in Drosophila cells. J Virol 75: 11664-11676. (Pubitemid 33063258)
19. Rutter J, Probst BL, McKnight SL (2002) Coordinate regulation of sugar flux and translation by PAS kinase. Cell 111: 17-28.
20. Burchett SA, Scott A, Errede B, Dohlman HG (2001) Identification of novel pheromone-response regulators through systematic overexpression of 120 protein kinases in yeast. J Biol Chem 276: 26472-26478.
21. Mulugu S, Bai W, Fridy PC, Bastidas RJ, Otto JC, et al. (2007) A conserved family of enzymes that phosphorylate inositol hexakisphosphate. Science 316: 106-109. (Pubitemid 46559528)
22. George R, Beddoe T, Landl K, Lithgow T (1998) The yeast nascent polypeptide-associated complex initiates protein targeting to mitochondria in vivo. Proc Natl Acad Sci U S A 95: 2296-2301. (Pubitemid 28145935)
23. Costanzo M, Nishikawa JL, Tang X, Millman JS, Schub O, et al. (2004) CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell 117: 899-913. (Pubitemid 38798856)
24. Wickner RB (1996) Double-stranded RNA viruses of Saccharomyces cerevisiae. Microbiol Rev 60: 250-265.
25. Saha D, Banerjee S, Bashir S, Vijayraghavan U (2012) Context dependent splicing functions of Bud31/Ycr063w define its role in budding and cell cycle progression. Biochem Biophys Res Commun 424: 579-585.
26. Bonetti D, Anbalagan S, Lucchini G, Clerici M, Longhese MP (2013) Tbf1 and Vid22 promote resection and non-homologous end joining of DNA double-strand break ends. EMBO J 32: 275-289.
27. Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, et al. (2009) Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol 7: e1000213.
28. Sanyal K, Ghosh SK, Sinha P (1998) The MCM16 gene of the yeast Saccharomyces cerevisiae is required for chromosome segregation. Mol Gen Genet 260: 242-250. (Pubitemid 28548324)
29. Gimenez-Barcons M, Alves-Rodrigues I, Jungfleisch J, Van Wynsberghe PM, Ahlquist P, et al. (2013) The cellular decapping activators LSm1, Pat1, and Dhh1 control the ratio of subgenomic to genomic Flock House virus RNAs. J Virol 87: 6192-6200.
30. Noueiry AO, Diez J, Falk SP, Chen J, Ahlquist P (2003) Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation. Mol Cell Biol 23: 4094-4106. (Pubitemid 36666415)
31. McCartney AW, Greenwood JS, Fabian MR, White KA, Mullen RT (2005) Localization of the tomato bushy stunt virus replication protein p33 reveals a peroxisome-to-endoplasmic reticulum sorting pathway. Plant Cell 17: 3513-3531.
32. White KA, Nagy PD (2004) Advances in the molecular biology of tombusviruses: gene expression, genome replication, and recombination. Prog Nucleic Acid Res Mol Biol 78: 187-226. (Pubitemid 39752480)
33. Ahlquist P (2006) Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nat Rev Microbiol 4: 371-382.
34. Johnson KL, Ball LA (1997) Replication of flock house virus RNAs from primary transcripts made in cells by RNA polymerase II. J Virol 71: 3323-3327. (Pubitemid 27121576)
35. Selling BH, Allison RF, Kaesberg P (1990) Genomic RNA of an insect virus directs synthesis of infectious virions in plants. Proc Natl Acad Sci U S A 87: 434-438.
36. Dasgupta R, Garcia BH 2nd, Goodman RM (2001) Systemic spread of an RNA insect virus in plants expressing plant viral movement protein genes. Proc Natl Acad Sci U S A 98: 4910-4915. (Pubitemid 32397056)
37. Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, et al. (2008) Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135: 49-60.
38. Takeuchi H, Matano T (2008) Host factors involved in resistance to retroviral infection. Microbiol Immunol 52: 318-325.
39. Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, et al. (2008) RNA interference screen for human genes associated with West Nile virus infection. Nature 455: 242-245.
40. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: 921-926. (Pubitemid 351263756)
41. Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, et al. (2009) A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 5: 298-307.
42. Hao L, Sakurai A, Watanabe T, Sorensen E, Nidom CA, et al. (2008) Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454: 890-893.
43. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, et al. (2009) Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5: e1000437.
44. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P (1992) Multifunctional yeast high-copy-number shuttle vectors. Gene 110: 119-122.
45. Dye BT, Hao L, Ahlquist P (2005) High-throughput isolation of Saccharomyces cerevisiae RNA. Biotechniques 38: 868, 870.
46. Gancarz BL, Hao L, He Q, Newton MA, Ahlquist P (2011) Systematic identification of novel, essential host genes affecting bromovirus RNA replication. PLoS One 6: e23988.
47. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445. (Pubitemid 37033947)
48. Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62: 2674-2679.