@article {Orlov728907, author = {Igor Orlov and Caroline Hemmer and L{\'e}a Ackerer and Bernard Lorber and Ahmed Ghannam and Vianney Poignavent and Kamal Hleibieh and Claude Sauter and Corinne Schmitt-Keichinger and Lor{\`e}ne Belval and Jean-Michel Hily and Aur{\'e}lie Marmonier and V{\'e}ronique Komar and Sophie Gersch and Pascale Schellenberger and Patrick Bron and Emmanuelle Vigne and Serge Muyldermans and Olivier Lemaire and G{\'e}rard Demangeat and Christophe Ritzenthaler and Bruno P. Klaholz}, title = {Structural basis of nanobody-recognition of grapevine fanleaf virus and of virus resistance loss}, elocation-id = {728907}, year = {2019}, doi = {10.1101/728907}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Grapevine fanleaf virus (GFLV) is a picorna-like plant virus transmitted by nematodes that affects vineyards worldwide. Nanobody (Nb)-mediated resistance against GFLV has been created recently and shown to be highly effective in plants including grapevine, but the underlying mechanism is unknown. Here we present the high-resolution cryo-EM structure of the GFLV-Nb23 complex which provides the basis for the molecular recognition by the nanobody. The structure reveals a composite binding site bridging over 3 domains of the capsid protein (CP) monomer. The structure provides a precise mapping of the Nb23 epitope on the GFLV capsid in which the antigen loop is accommodated through an induced fit mechanism. Moreover, we uncover and characterize several resistance-breaking GFLV isolates with amino acids mapping within this epitope, including C-terminal extensions of the CP, which would sterically interfere with Nb binding. Escape variants with such extended CP fail to be transmitted by nematodes linking Nb-mediated resistance to vector transmission. Together, these data provide insights into the molecular mechanism of Nb23-mediated recognition of GFLV and of virus resistance loss.Significance Grapevine fanleaf virus (GFLV) is a picorna-like plant virus that severely impacts vineyards worldwide. While Nanobodies (Nb) confer resistance to GFLV in plants the underlying molecular mechanism of action is unknown. Here we present the high-resolution cryo-EM structure of the GFLV-Nb complex. It uncovers the conformational epitope on the capsid surface which is a composite binding site into which the antigen loop is accommodated through an induced fit mechanism. Furthermore, we describe several resistance-breaking isolates of GFLV with reduced Nb binding capacity. Those that carry a C-terminal extension also fail to be transmitted by nematodes. Together, these data provide structure-function insights into the Nb-GFLV recognition and the molecular mechanism leading to loss of resistance.}, URL = {https://www.biorxiv.org/content/early/2019/08/08/728907}, eprint = {https://www.biorxiv.org/content/early/2019/08/08/728907.full.pdf}, journal = {bioRxiv} }