title: Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection.
abstract: BACKGROUND
  The genomes of plant viruses have limited coding capacity, and to complete their infectious cycles, viral factors must target, direct or indirectly, many host elements. However, the interaction networks between viruses and host factors are poorly understood. The genus Potyvirus is the largest group of plus-strand RNA viruses infecting plants. Potyviral nuclear inclusion a (NIa) plays many roles during infection. NIa is a polyprotein consisting of two domains, viral protein genome-linked (VPg) and protease (NIaPro), separated by an inefficiently utilized self-proteolytic site. To gain insights about the interaction between potyviral NIa and the host cell during infection, we constructed Tobacco etch virus (TEV, genus Potyvirus) infectious clones in which the VPg or the NIaPro domains of NIa were tagged with the affinity polypeptide Twin-Strep-tag and identified the host proteins targeted by the viral proteins by affinity purification followed by mass spectrometry analysis (AP-MS).
  
  
  RESULTS
  We identified 232 different Arabidopsis thaliana proteins forming part of complexes in which TEV NIa products were also involved. VPg and NIaPro specifically targeted 89 and 76 of these proteins, respectively, whereas 67 proteins were targeted by both domains and considered full-length NIa targets. Taking advantage of the currently known A. thaliana interactome, we constructed a protein interaction network between TEV NIa domains and 516 host proteins. The most connected elements specifically targeted by VPg were G-box regulating factor 6 and mitochondrial ATP synthase δ subunit; those specifically targeted by NIaPro were plasma membrane aquaporin PIP2;7 and actin 7, whereas those targeted by full-length NIa were heat shock protein 70-1 and photosystem protein LHCA3. Moreover, a contextualization in the global A. thaliana interactome showed that NIa targets are not more connected with other host proteins than expected by chance, but are in a position that allows them to connect with other host proteins in shorter paths. Further analysis of NIa-targeted host proteins revealed that they are mainly involved in response to stress, metabolism, photosynthesis, and localization. Many of these proteins are connected with the phytohormone ethylene.
  
  
  CONCLUSIONS
  Potyviral NIa targets many host elements during infection, establishing a network in which information is efficiently transmitted.
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. femargar@ibmcp.upv.es.
authors.forename: Fernando
authors.initials: F
authors.lastname: Martínez
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. guillermo.rodrigo@csic.es.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Rodrigo
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. vero88_@hotmail.com.
authors.forename: Verónica
authors.initials: V
authors.lastname: Aragonés
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. mvruiz@outlook.es.
authors.forename: Marta
authors.initials: M
authors.lastname: Ruiz
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. iris_lodewijk@hotmail.com.
authors.forename: Iris
authors.initials: I
authors.lastname: Lodewijk
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. uferna00@gmail.com.
authors.forename: Unai
authors.initials: U
authors.lastname: Fernández
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. sfelena@ibmcp.upv.es.|The Santa Fe Institute, Santa Fe, NM, USA. sfelena@ibmcp.upv.es.
authors.forename: Santiago F
authors.initials: SF
authors.lastname: Elena
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain. jadaros@ibmcp.upv.es.
authors.forename: José-Antonio
authors.initials: JA
authors.lastname: Daròs
mesh_terms: D054884:Host-Pathogen Interactions; D010935:Plant Diseases / Q000821:virology; D017800:Potyvirus / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D020543:Proteome; D040901:Proteomics / Q000379:methods; D014026:Nicotiana / Q000378:metabolism* / Q000821:virology*; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D020543:Proteome; D014764:Viral Proteins
references.citation: Science. 2011 Jul 29;333(6042):596-601
references.pmid: 21798943
references.citation: Mol Plant Microbe Interact. 2014 Nov;27(11):1199-210
references.pmid: 25099340
references.citation: Mol Cell Proteomics. 2014 Jan;13(1):184-203
references.pmid: 24169621
references.citation: Plant Cell. 2009 Aug;21(8):2485-502
references.pmid: 19700632
references.citation: Virology. 1995 Nov 10;213(2):517-25
references.pmid: 7491776
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references.pmid: 20435677
references.citation: Trends Plant Sci. 2006 Jan;11(1):40-5
references.pmid: 16343979
references.citation: Virology. 2008 Jul 20;377(1):216-25
references.pmid: 18501944
references.citation: Plant J. 2009 Nov;60(3):539-50
references.pmid: 19624472
references.citation: J Virol. 2011 Sep;85(17):9210-21
references.pmid: 21697470
references.citation: Science. 2011 Jul 29;333(6042):601-7
references.pmid: 21798944
references.citation: Nat Rev Genet. 2004 Feb;5(2):101-13
references.pmid: 14735121
references.citation: Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
references.pmid: 17593931
references.citation: J Gen Virol. 2008 Sep;89(Pt 9):2339-48
references.pmid: 18753244
references.citation: BMC Syst Biol. 2014;8:129
references.pmid: 25409737
references.citation: Nucleic Acids Res. 2015 Jan;43(Database issue):D470-8
references.pmid: 25428363
references.citation: Phytopathology. 2013 Aug;103(8):870-6
references.pmid: 23617337
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: J Virol. 1996 Oct;70(10):7039-48
references.pmid: 8794348
references.citation: J Biol Chem. 2004 Sep 10;279(37):38103-10
references.pmid: 15218030
references.citation: Plant Physiol. 2007 Dec;145(4):1211-9
references.pmid: 17932303
references.citation: New Phytol. 2014 Sep;203(4):1291-304
references.pmid: 24954157
references.citation: Nat Rev Mol Cell Biol. 2010 Aug;11(8):579-92
references.pmid: 20651708
references.citation: J Virol. 2000 Feb;74(4):1736-41
references.pmid: 10644344
references.citation: Mol Cell Proteomics. 2005 Sep;4(9):1265-72
references.pmid: 15958392
references.citation: Front Plant Sci. 2012 Dec 06;3:275
references.pmid: 23230447
references.citation: Protein Expr Purif. 2013 Nov;92(1):54-61
references.pmid: 24012791
references.citation: Plant Physiol. 2010 Jan;152(1):255-66
references.pmid: 19880609
references.citation: Virology. 2012 Dec 5;434(1):78-87
references.pmid: 23040510
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D975-82
references.pmid: 19015126
references.citation: Science. 2015 Feb 20;347(6224):1257601
references.pmid: 25700523
references.citation: J Virol. 2014 Sep;88(18):10725-37
references.pmid: 24991017
references.citation: Virus Res. 2010 May;149(2):234-40
references.pmid: 20152868
references.citation: Nature. 2012 Jul 26;487(7408):486-90
references.pmid: 22810585
references.citation: Plant Cell. 2010 Feb;22(2):523-35
references.pmid: 20154150
references.citation: Virology. 1997 Oct 27;237(2):327-36
references.pmid: 9356344
references.citation: Proteomics. 2012 May;12(10):1576-90
references.pmid: 22611051
references.citation: J Gen Virol. 2004 Apr;85(Pt 4):1055-63
references.pmid: 15039548
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Virology. 1995 Jun 20;210(1):194-201
references.pmid: 7793070
references.citation: J Virol. 2007 Oct;81(20):10905-13
references.pmid: 17670821
references.citation: Plant Cell. 1992 Jun;4(6):645-56
references.pmid: 1392589
references.citation: Plant Mol Biol. 2004 Mar;54(5):713-25
references.pmid: 15356390
references.citation: Science. 2002 Mar 8;295(5561):1852-8
references.pmid: 11884745
references.citation: J Virol. 1997 Nov;71(11):8624-31
references.pmid: 9343220
references.citation: PLoS Comput Biol. 2009 Apr;5(4):e1000350
references.pmid: 19503817
references.citation: Adv Virus Res. 2015;92:101-99
references.pmid: 25701887
references.citation: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14440-5
references.pmid: 8962070
references.citation: Nat Protoc. 2013 Aug;8(8):1551-66
references.pmid: 23868073
references.citation: PLoS One. 2008;3(6):e2397
references.pmid: 18545680
references.citation: Plant Physiol. 2012 Mar;158(3):1130-8
references.pmid: 22238422
references.citation: J Virol. 1999 Oct;73(10):8732-40
references.pmid: 10482627
references.citation: Annu Rev Cell Dev Biol. 2012;28:489-521
references.pmid: 22559264
references.citation: Virology. 1997 Jul 21;234(1):84-92
references.pmid: 9234949
references.citation: Mol Syst Biol. 2008;4:230
references.pmid: 18985028
references.citation: J Virol. 2004 Mar;78(5):2301-9
references.pmid: 14963126
references.citation: Plant J. 2008 Apr;54(1):56-68
references.pmid: 18182024
references.citation: Curr Biol. 2002 Jun 25;12(12):1046-51
references.pmid: 12123581
references.citation: Curr Opin Virol. 2012 Dec;2(6):719-24
references.pmid: 23017245
references.citation: J Virol. 1987 Aug;61(8):2540-8
references.pmid: 16789265
references.citation: PLoS One. 2011;6(7):e21800
references.pmid: 21789182
references.citation: Virology. 1996 Jun 15;220(2):535-8
references.pmid: 8661407
references.citation: J Gen Virol. 2014 Jul;95(Pt 7):1415-29
references.pmid: 24722679