Abstract
Viruses reshape the intracellular environment of their hosts, largely through protein-protein interactions, to co-opt processes necessary for viral infection and interference with antiviral defences. Due to genome size constraints and the concomitant limited coding capacity of viruses, viral proteins are generally multifunctional and have evolved to target diverse host proteins. Inference of the virus-host interaction network can be instrumental for understanding how viruses manipulate the host machinery and how re-wiring of specific pathways can contribute to disease. Here, we use affinity purification and mass spectrometry analysis (AP-MS) to define the global landscape of interactions between the geminivirus Tomato yellow leaf curl virus (TYLCV) and its host Nicotiana benthamiana. For this purpose, we expressed tagged versions of each of TYLCV-encoded proteins (C1/Rep, C2/TrAP, C3/REn, C4, V2, and CP) in planta in the presence of the virus. Using a quantitative scoring system, 728 high-confidence plant interactors were identified, and the interaction network of each viral protein was inferred; TYLCV-targeted proteins are more connected than average, and connect with other proteins through shorter paths, which would allow the virus to exert large effects with few interactions. Comparative analyses of divergence patterns between N. benthamiana and potato, a non-host Solanaceae, showed evolutionary constraints on TYLCV-targeted proteins. Our results provide a comprehensive overview of plant proteins targeted by TYLCV during the viral infection, which may contribute to uncovering the underlying molecular mechanisms of plant viral diseases and provide novel potential targets for anti-viral strategies and crop engineering. Interestingly, some of the TYLCV-interacting proteins appear to be convergently targeted by other pathogen effectors, which suggests a central role for these proteins in plant-pathogen interactions, and pinpoints them as potential targets to engineer broad-spectrum resistance to biotic stresses.
Highlights
Viruses reshape the intracellular environment during infection, both to co-opt processes necessary for the development of the viral infection and to interfere with antiviral defenses
Systems biology approaches have been applied to successfully uncover strategies used by the RNA viruses human immunodeficiency virus (HIV) and hepatitis C virus (HCV), and the DNA virus Kaposi’s sarcoma herpesvirus (KSHV), using affinity tag purification and mass spectrometry (AP-MS) [1,2,3,5]
Identification of Nicotiana benthamiana Proteins Associating with green fluorescent protein (GFP)-Tagged Tomato yellow leaf curl virus (TYLCV) Proteins
Summary
Viruses reshape the intracellular environment during infection, both to co-opt processes necessary for the development of the viral infection and to interfere with antiviral defenses. The number of interactions of a viral proteome is anticipated to be substantial, as indicated by recent high-throughput proteomics analyses of virus-host protein-protein interactions in mammalian cells [1,2,3,4,5,6] and in plants [7]. Systems-level analyses can identify pathways or proteins that are main targets of viruses [8,9], which would in turn make good targets for anti-viral strategies. Systems biology approaches have been applied to successfully uncover strategies used by the RNA viruses human immunodeficiency virus (HIV) and hepatitis C virus (HCV), and the DNA virus Kaposi’s sarcoma herpesvirus (KSHV), using affinity tag purification and mass spectrometry (AP-MS) [1,2,3,5]. AP-MS has been recently applied to define the interactome of the NIa protein from the potyvirus Tobacco etch virus [7]
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