Topology analysis and visualization of Potyvirus protein-protein interaction network

Background: One of the central interests of Virology is the identification of host factors that contribute to virus infection. Despite tremendous efforts, the list of factors identified remains limited. With omics techniques, the focus has changed from identifying and thoroughly characterizing individual host factors to the simultaneous analysis of thousands of interactions, framing them on the context of protein-protein interaction networks and of transcriptional regulatory networks. This new perspective is allowing the identification of direct and indirect viral targets. Such information is available for several members of the Potyviridae family, one of the largest and more important families of plant viruses. Results: After collecting information on virus protein-protein interactions from different potyviruses, we have processed it and used it for inferring a protein-protein interaction network. All proteins are connected into a single network component. Some proteins show a high degree and are highly connected while others are much less connected, with the network showing a significant degree of dissortativeness. We have attempted to integrate this virus protein-protein interaction network into the largest protein-protein interaction network of Arabidopsis thaliana, a susceptible laboratory host. To make the interpretation of data and results easier, we have developed a new approach for visualizing and analyzing the dynamic spread on the host network of the local perturbations induced by viral proteins. We found that local perturbations can reach the entire host protein-protein interaction network, although the efficiency of this spread depends on the particular viral proteins. By comparing the spread dynamics among viral proteins, we found that some proteins spread their effects fast and efficiently by attacking hubs in the host network while other proteins exert more local effects. Conclusions: Our findings confirm that potyvirus protein-protein interaction networks are highly connected, with some proteins playing the role of hubs. Several topological parameters depend linearly on the protein degree. Some viral proteins focus their effect in only host hubs while others diversify its effect among several proteins at the first step. Future new data will help to refine our model and to improve our predictions.This work was supported by the Spanish Ministerio de Economia y Competitividad grants BFU2012-30805 (to SFE), DPI2011-28112-C04-02 (to AF) and DPI2011-28112-C04-01 (to JP). The first two authors are recipients of fellowships from the Spanish Ministerio de Economia y Competitividad: BES-2012-053772 (to GB) and BES-2012-057812 (to AF-F).Bosque, G.; Folch Fortuny, A.; Picó Marco, JA.; Ferrer, A.; Elena Fito, SF. (2014). Topology analysis and visualization of Potyvirus protein-protein interaction network. BMC Systems Biology. 129(8):1-15. doi:10.1186/s12918-014-0129-8S1151298Gibbs A, Ohshima K: Potyviruses and the digital revolution. Annu Rev Phytopathol. 2010, 48: 205-223. 10.1146/annurev-phyto-073009-114404.Spence NJ, Phiri NA, Hughes SL, Mwaniki A, Simons S, Oduor G, Chacha D, Kuria A, Ndirangu S, Kibata GN, Marris GC: Economic impact of turnip mosaic virus, cauliflower mosaic virus and beet mosaic virus in three Kenyan vegetables. Plant Pathol. 2007, 56: 317-323. 10.1111/j.1365-3059.2006.01498.x.Ward CW, Shukla DD: Taxonomy of potyviruses: current problems and some solutions. Intervirology. 1991, 32: 269-296.Riechmann JL, Laín S, García JA: Highlights and prospects of potyvirus molecular biology. J Gen Virol. 1992, 73 (Pt 1): 1-16. 10.1099/0022-1317-73-1-1.Elena SF, Rodrigo G: Towards an integrated molecular model of plant-virus interactions. Curr Opin Virol. 2012, 2: 719-724. 10.1016/j.coviro.2012.09.004.Wei T, Zhang C, Hong J, Xiong R, Kasschau KD, Zhou X, Carrington JC, Wang A: Formation of complexes at plasmodesmata for potyvirus intercellular movement is mediated by the viral protein P3N-PIPO. PLoS Pathog. 2010, 6: e1000962-10.1371/journal.ppat.1000962.Chung BY-W, Miller WA, Atkins JF, Firth AE: An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci. 2008, 105: 5897-5902. 10.1073/pnas.0800468105.Allison R, Johnston RE, Dougherty WG: The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein. Virology. 1986, 154: 9-20. 10.1016/0042-6822(86)90425-3.Domier LL, Franklin KM, Shahabuddin M, Hellmann GM, Overmeyer JH, Hiremath ST, Siaw MF, Lomonossoff GP, Shaw JG, Rhoads RE: The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Res. 1986, 14: 5417-5430. 10.1093/nar/14.13.5417.Revers F, Le Gall O, Candresse T, Maule AJ: New advances in understanding the molecular biology of plant/potyvirus interactions. Mol Plant Microbe Interact. 1999, 12: 367-376. 10.1094/MPMI.1999.12.5.367.Urcuqui-Inchima S, Haenni AL, Bernardi F: Potyvirus proteins: a wealth of functions. Virus Res. 2001, 74: 157-175. 10.1016/S0168-1702(01)00220-9.Merits A, Rajamäki M-L, Lindholm P, Runeberg-Roos P, Kekarainen T, Puustinen P, Mäkeläinen K, Valkonen JPT, Saarma M: Proteolytic processing of potyviral proteins and polyprotein processing intermediates in insect and plant cells. J Gen Virol. 2002, 83: 1211-1221.Adams MJ, Antoniw JF, Beaudoin F: Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol. 2005, 6: 471-487. 10.1111/j.1364-3703.2005.00296.x.Zheng H, Yan F, Lu Y, Sun L, Lin L, Cai L, Hou M, Chen J: Mapping the self-interacting domains of TuMV HC-Pro and the subcellular localization of the protein. Virus Genes. 2011, 42: 110-116. 10.1007/s11262-010-0538-8.Culver JN, Padmanabhan MS: Virus-induced disease: altering host physiology one interaction at a time. Annu Rev Phytopathol. 2007, 45: 221-243. 10.1146/annurev.phyto.45.062806.094422.De Las Rivas J, Fontanillo C: Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol. 2010, 6: e1000807-10.1371/journal.pcbi.1000807.Bornke F: Protein Interaction Networks. Anal Biol Netw. Edited by: Junker BH, Schreiber F. 2008, John Wiley & Sons, Inc, Hoboken, NJ, USA, 207-232. 10.1002/9780470253489.ch9.Phizicky EM, Fields S: Protein-protein interactions: methods for detection and analysis. Microbiol Rev. 1995, 59: 94-123.Brückner A, Polge C, Lentze N, Auerbach D, Schlattner U: Yeast two-hybrid, a powerful tool for systems biology. Int J Mol Sci. 2009, 10: 2763-2788. 10.3390/ijms10062763.Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature. 1989, 340: 245-246. 10.1038/340245a0.Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams S-L, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415: 180-183. 10.1038/415180a.Hu C-D, Chinenov Y, Kerppola TK: Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell. 2002, 9: 789-798. 10.1016/S1097-2765(02)00496-3.Kodama Y, Hu C-D: An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratio. Biotechniques. 2010, 49: 793-805. 10.2144/000113519.Rual J-F, 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, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, et al: Towards a proteome-scale map of the human protein-protein interaction network. Nature. 2005, 437: 1173-1178. 10.1038/nature04209.Venkatesan K, Rual J-F, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh K-I, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet A-S, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, et al: An empirical framework for binary interactome mapping. Nat Methods. 2008, 6: 83-90. 10.1038/nmeth.1280.Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000, 403: 623-627. 10.1038/35001009.Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci. 2001, 98: 4569-4574. 10.1073/pnas.061034498.Uetz P, Dong Y-A, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J: Herpesviral protein networks and their interaction with the human proteome. Science. 2006, 311: 239-242. 10.1126/science.1116804.Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong Y-A, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J: Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 2009, 5: e1000570-10.1371/journal.ppat.1000570.Rodrigo G, Carrera J, Ruiz-Ferrer V, del Toro FJ, Llave C, Voinnet O, Elena SF: A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One. 2012, 7: e40526-10.1371/journal.pone.0040526.Newman MEJ: The structure and function of complex networks. SIAM Rev. 2003, 45: 167-256. 10.1137/S003614450342480.Watts DJ, Strogatz SH: Collective dynamics of "small-world" networks. Nature. 1998, 393: 440-442. 10.1038/30918.Albert R, Barabási A-L: Statistical mechanics of complex networks. Rev Mod Phys. 2002, 74: 47-97. 10.1103/RevModPhys.74.47.Boccaletti S, Latora V, Moreno Y, Chávez M, Hwang D: Complex networks: structure and dynamics. Phys Rep. 2006, 424: 175-308. 10.1016/j.physrep.2005.10.009.Barabási A-L, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004, 5: 101-113. 10.1038/nrg1272.Albert R, DasGupta B, Hegde R, Sivanathan GS, Gitter A, Gürsoy G, Paul P, Sontag E: Computationally efficient measure of topological redundancy of biological and social networks. Phys Rev E. 2011, 84: 036117-10.1103/PhysRevE.84.036117.Cho D-Y, Kim Y-A, Przytycka TM: Chapter 5: network biology approach to complex diseases. PLoS Comput Biol. 2012, 8: e1002820-10.1371/journal.pcbi.1002820.Russell RB, Aloy P: Targeting and tinkering with interaction networks. Nat Chem Biol. 2008, 4: 666-673. 10.1038/nchembio.119.Winterbach W, Mieghem PV, Reinders M, Wang H, de Ridder D: Topology of molecular interaction networks. BMC Syst Biol. 2013, 7: 90-10.1186/1752-0509-7-90.Pržulj N: Protein-protein interactions: making sense of networks via graph-theoretic modeling. Bioessays. 2011, 33: 115-123. 10.1002/bies.201000044.Yook S-H, Oltvai ZN, Barabási A-L: Functional and topological characterization of protein interaction networks. Proteomics. 2004, 4: 928-942. 10.1002/pmic.200300636.Pržulj N, Wigle DA, Jurisica I: Functional topology in a network of protein interactions. Bioinformatics. 2004, 20: 340-348. 10.1093/bioinformatics/btg415.Elena SF, Carrera J, Rodrigo G: A systems biology approach to the evolution of plant-virus interactions. Curr Opin Plant Biol. 2011, 14: 372-377. 10.1016/j.pbi.2011.03.013.Zilian E, Maiss E: Detection of plum pox potyviral protein-protein interactions in planta using an optimized mRFP-based bimolecular fluorescence complementation system. J Gen Virol. 2011, 92: 2711-2723. 10.1099/vir.0.033811-0.Lin L, Shi Y, Luo Z, Lu Y, Zheng H, Yan F, Chen J, Chen J, Adams MJ, Wu Y: Protein-protein interactions in two potyviruses using the yeast two-hybrid system. Virus Res. 2009, 142: 36-40. 10.1016/j.virusres.2009.01.006.Guo D, Rajamäki M-L, Saarma M, Valkonen JPT: Towards a protein interaction map of potyviruses: protein interaction matrixes of two potyviruses based on the yeast two-hybrid system. J Gen Virol. 2001, 82: 935-939.Shen WT, Wang MQ, Yan P, Gao L, Zhou P: Protein interaction matrix of papaya ringspot virus type P based on a yeast two-hybrid system. Acta Virol. 2010, 54: 49-54. 10.4149/av_2010_01_49.Kang S, Ws L, Kh K: A protein interaction map of soybean mosaic virus strain G7H based on the yeast two-hybrid system. Mol Cells. 2004, 18: 122-126.Yambao MLM, Masuta C, Nakahara K, Uyeda I: The central and C-terminal domains of VPg of Clover yellow vein virus are important for VPg-HCPro and VPg-VPg interactions. J Gen Virol. 2003, 84: 2861-2869. 10.1099/vir.0.19312-0.Evidence for network evolution in an Arabidopsis interactome map. Science. 2011, 333: 601-607. 10.1126/science.1203877.Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13: 2498-2504. 10.1101/gr.1239303.Fouss F, Francoisse K, Yen L, Pirotte A, Saerens M: An experimental investigation of kernels on graphs for collaborative recommendation and semisupervised classification. Neural Netw Off J Int Neural Netw Soc. 2012, 31: 53-72. 10.1016/j.neunet.2012.03.001.Bass JIF, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJM: Using networks to measure similarity between genes: association index selection. Nat Methods. 2013, 10: 1169-1176. 10.1038/nmeth.2728.Newman MEJ: Assortative mixing in networks. Phys Rev Lett. 2002, 89: 208701-10.1103/PhysRevLett.89.208701

Simultaneous Mutations in Multi-Viral Proteins Are Required for Soybean mosaic virus to Gain Virulence on Soybean Genotypes Carrying Different R Genes

BACKGROUND: Genetic resistance is the most effective and sustainable approach to the control of plant pathogens that are a major constraint to agriculture worldwide. In soybean, three dominant R genes, i.e., Rsv1, Rsv3 and Rsv4, have been identified and deployed against Soybean mosaic virus (SMV) with strain-specificities. Molecular identification of virulent determinants of SMV on these resistance genes will provide essential information for the proper utilization of these resistance genes to protect soybean against SMV, and advance knowledge of virus-host interactions in general. METHODOLOGY/PRINCIPAL FINDINGS: To study the gain and loss of SMV virulence on all the three resistance loci, SMV strains G7 and two G2 isolates L and LRB were used as parental viruses. SMV chimeras and mutants were created by partial genome swapping and point mutagenesis and then assessed for virulence on soybean cultivars PI96983 (Rsv1), L-29 (Rsv3), V94-5152 (Rsv4) and Williams 82 (rsv). It was found that P3 played an essential role in virulence determination on all three resistance loci and CI was required for virulence on Rsv1- and Rsv3-genotype soybeans. In addition, essential mutations in HC-Pro were also required for the gain of virulence on Rsv1-genotype soybean. To our best knowledge, this is the first report that CI and P3 are involved in virulence on Rsv1- and Rsv3-mediated resistance, respectively. CONCLUSIONS/SIGNIFICANCE: Multiple viral proteins, i.e., HC-Pro, P3 and CI, are involved in virulence on the three resistance loci and simultaneous mutations at essential positions of different viral proteins are required for an avirulent SMV strain to gain virulence on all three resistance loci. The likelihood of such mutations occurring naturally and concurrently on multiple viral proteins is low. Thus, incorporation of all three resistance genes in a soybean cultivar through gene pyramiding may provide durable resistance to SMV

Evolution and Origin of PVY

International audienceThe mechanisms by which Potato virus Y variants are generated and selected are still unclear. Spontaneous mutations generated by uncorrected replication error and recombination events between viral isolates during co-infection of plant cells are the main likely source of genetic diversity. This high level of diversity generation is essential for virus evolution and survival in different environments. Different PVY strain groups have appeared over time: firstly, non-recombinant PVYC, PVYO and PVYN strains and, more recently, recombinant PVYN-Wi and PVYNTN strains with novel biological characteristics and the ability to cause potato tuber necrotic ringspot disease (PTNRD). Increased fitness of the recombinant strains appears to have enabled them to replace the non-recombinant variants in most potato growing areas of the world. Partial sequencing of PVY genome (P1, HC-Pro, CP, recombinant junctions) and whole genome sequencing has shown that non-recombinant and recombinant variants are present in potatoes and other plant hosts. Phylogenetic analyses have been applied to document changes in viral isolates and to establish the relationships between different viral isolates. Traditional phylogenetic analysis was, however, developed for bifurcating phylogenies and not for analysing recombination, as a result of which this presents challenges to these analyses which will be outlined in this chapter. The ongoing worldwide studies on PVY characterisation suggest that new variants with distinct biological properties are likely to be uncovered in the future. Emerging technologies such as next generation sequencing will provide valuable insights into PVY population dynamics and evolution in future