Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of Nicotiana benthamiana by affinity purification and tandem mass spectrometry

References

1. Andret-Link P, Laporte C, Valat L, Ritzenthaler C, Demangeat G et al. Grapevine fanleaf virus: Still a major threat to the grapevine industry. J Plant Pathol 2004; 86:183–195
   [Google Scholar]
2. Karasev AV, Dasgupta I, Fuchs M, Iwanami T. Secoviridae 2019
   [Google Scholar]
3. Schmitt-Keichinger C, Hemmer C, Berthold F, Ritzenthaler C. Molecular, Cellular, and Structural Biology of Grapevine fanleaf virus. Grapevine VirusesMolecular, cellular, and structural biology of grapevine fanleaf virus. Grapevine Viruses Springer: Molecular Biology, Diagnostics and Management; 2017 pp 83–107
   [Google Scholar]
4. Thompson JR, Dasgupta I, Fuchs M, Iwanami T, Karasev AV et al. ICTV virus taxonomy profile: Secoviridae. J Gen Virol 2017; 98:529–531 [View Article]
   [Google Scholar]
5. Ritzenthaler C, Viry M, Pinck M, Margis R, Fuchs M et al. Complete nucleotide sequence and genetic organization of grapevine Fanleaf nepovirus rna1. J Gen Virol 1991; 72:2357–2365 [View Article]
   [Google Scholar]
6. Margis R, Viry M, Pinck M, Pinck L. Cloning and in vitro characterization of the grapevine fanleaf virus proteinase cistron. Virology 1991; 185:779–787 [View Article][PubMed]
   [Google Scholar]
7. Vigne E, Gottula J, Schmitt-Keichinger C, Komar V, Ackerer L et al. A strain-specific segment of the RNA-dependent RNA polymerase of grapevine fanleaf virus determines symptoms in Nicotiana species. J Gen Virol 2013; 94:2803–2813 [View Article]
   [Google Scholar]
8. Viry M, Serghini MA, Hans F, Ritzenthaler C, Pinck M et al. Biologically active transcripts from cloned cDNA of genomic grapevine fanleaf nepovirus RNAs. J Gen Virol 1993; 74:169–174 [View Article]
   [Google Scholar]
9. Martin IR, Vigne E, Berthold F, Komar V, Lemaire O et al. The 50 distal amino acids of the 2AHP homing protein of Graprevine fanleaf virus elicit a hypersensitive reaction on Nicotiana occidentalis. Mol Plant Pathol 2018; 19:731–743 [View Article][PubMed]
   [Google Scholar]
10. Osterbaan LJ, Choi J, Kenney J, Flasco M, Vigne E et al. The identity of a single residue of the RNA-dependent RNA polymerase of grapevine fanleaf virus modulates vein clearing in Nicotiana benthamiana . Mol Plant Microbe Interact 2019; 32:790–801 [View Article][PubMed]
    [Google Scholar]
11. Fuchs M, Schmitt-Keichinger C, Sanfaçon H. A renaissance in nepovirus research provides new insights into their molecular interface with hosts and vectors. Adv Virus Res 2017; 97:61–105 [View Article]
    [Google Scholar]
12. Southern JA, Young DF, Heaney F, Baumgartner WK, Randall RE. Identification of an epitope on the P and V proteins of simian virus 5 that distinguishes between two isolates with different biological characteristics. Journal of General Virology 1991; 72:1551–1557 [View Article]
    [Google Scholar]
13. Hopp TP, Prickett KS, Price VL, Libby RT, March CJ et al. A short polypeptide marker sequence useful for recombinant protein identification and purification. Nat Biotechnol 1988; 6:1204–1210 [View Article]
    [Google Scholar]
14. Hopp TP, Gallis B, Prickett KS. Metal-binding properties of a calcium-dependent monoclonal antibody. Mol Immunol 1996; 33:601–688 [View Article][PubMed]
    [Google Scholar]
15. Schembri L, Dalibart R, Tomasello F, Legembre P, Ichas F et al. The HA tag is cleaved and loses immunoreactivity during apoptosis. Nat Methods 2007; 4:107–108 [View Article][PubMed]
    [Google Scholar]
16. Zeng Q, Si X, Horstmann H, Xu Y, Hong W et al. prenylation-dependent association of protein-tyrosine phosphatases PRL-1, -2, and -3 with the plasma membrane and the early endosome. J Biol Chem 2000; 275:21444–21452 [View Article]
    [Google Scholar]
17. Osterbaan LJ, Schmitt-Keichinger C, Vigne E, Fuchs M. Optimal systemic grapevine fanleaf virus infection in Nicotiana benthamiana following agroinoculation. J Virol Methods 2018; 257:16–21 [View Article][PubMed]
    [Google Scholar]
18. DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM et al. Insights into the polerovirus–plant interactome revealed by coimmunoprecipitation and mass spectrometry. Mol Plant Microbe Interact 2015; 28:467–481 [View Article][PubMed]
    [Google Scholar]
19. Nölke G, Cobanov P, Uhde-Holzem K, Reustle G, Fischer R et al. Grapevine fanleaf virus (GFLV)-specific antibodies confer GFLV and Arabis mosaic virus (ArMV) resistance in Nicotiana benthamiana . Mol Plant Pathol 2009; 10:41–49 [View Article][PubMed]
    [Google Scholar]
20. Jovel J, Walker M, Sanfaçon H. Recovery of Nicotiana benthamiana plants from a necrotic response induced by a nepovirus is associated with RNA silencing but not with reduced virus titer. J Virol 2007; 81:12285–12297 [View Article][PubMed]
    [Google Scholar]
21. Dufresne PJ, Thivierge K, Cotton S, Beauchemin C, Ide C et al. Heat shock 70 protein interaction with Turnip mosaic virus RNA-dependent RNA polymerase within virus-induced membrane vesicles. Virology 2008; 374:217–227 [View Article][PubMed]
    [Google Scholar]
22. Ritzenthaler C, Laporte C, Gaire F, Dunoyer P, Schmitt C et al. Grapevine fanleaf virus replication occurs on endoplasmic reticulum-derived membranes. J Virol 2002; 76:8808–8819 [View Article][PubMed]
    [Google Scholar]
23. Chisholm J, Zhang G, Wang A, Sanfaçon H. Peripheral association of a polyprotein precursor form of the RNA-dependent RNA polymerase of Tomato ringspot virus with the membrane-bound viral replication complex. Virology 2007; 368:133–144 [View Article][PubMed]
    [Google Scholar]
24. Clark M, Lister R, Bar-Joseph M. ELISA techniques. Weisbach A, Weisbach H. eds In Methods for Plant Molecular Biology Cambridge, MA, USA: New York: Academic Press; 1988 pp 742–766
    [Google Scholar]
25. Kessner D, Chambers M, Burke R, Agus D, Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008; 24:2534–2536 [View Article][PubMed]
    [Google Scholar]
26. Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA et al. A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 2012; 25:1523–1530 [View Article][PubMed]
    [Google Scholar]
27. Ma K, Vitek O, Nesvizhskii AI. A statistical model-building perspective to identification of MS/MS spectra with Peptideprophet. BMC Bioinformatics 2012; 13:
    [Google Scholar]
28. Gao ZP, Q-B Y, Zhao TT, Ma Q, Chen GX et al. A functional component of the transcriptionally active chromosome complex, Arabidopsis pTAC14, interacts with pTAC12/HEMERA and regulates plastid gene expression. Plant Physiology 2011; 157:1733–1745
    [Google Scholar]
29. Medina-Puche L, Tan H, Dogra V, Wu M, Rosas-Diaz T et al. A novel pathway linking plasma membrane and chloroplasts is co-opted by pathogens to suppress salicylic acid-dependent defences. Cell 2020; 182:1109–1124 [View Article][PubMed]
    [Google Scholar]
30. Chen X, Hao L, Pan J, Zheng X, Jiang G et al. Spl5, a cell death and defense-related gene, encodes a putative splicing factor 3b subunit 3 (sf3b3) in rice. Mol Breeding 2011; 30:939–949 [View Article]
    [Google Scholar]
31. Kyei GB, Meng S, Ramani R, Niu A, Lagisetti C et al. Splicing factor 3B subunit 1 interacts with HIV Tat and plays a role in viral transcription and reactivation from latency. mBio 2018; 9: [View Article][PubMed]
    [Google Scholar]
32. Wu G, Cui X, Chen H, Renaud JB, Yu K et al. Dynamin-like proteins of endocytosis in plants are coopted by potyviruses to enhance virus infection. Journal of Virology 2018; 92:23
    [Google Scholar]
33. Choi D, Lee HY, Seo YE, Lee JH, Lee SE et al. Plant NLR targets P-type ATPase for executing plasma membrane depolarization leading to calcium influx and cell death. bioRxiv 2020 [View Article]
    [Google Scholar]