title: Sequence-Specific Protein Aggregation Generates Defined Protein Knockdowns in Plants.
abstract: Protein aggregation is determined by short (5-15 amino acids) aggregation-prone regions (APRs) of the polypeptide sequence that self-associate in a specific manner to form β-structured inclusions. Here, we demonstrate that the sequence specificity of APRs can be exploited to selectively knock down proteins with different localization and function in plants. Synthetic aggregation-prone peptides derived from the APRs of either the negative regulators of the brassinosteroid (BR) signaling, the glycogen synthase kinase 3/Arabidopsis SHAGGY-like kinases (GSK3/ASKs), or the starch-degrading enzyme α-glucan water dikinase were designed. Stable expression of the APRs in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) induced aggregation of the target proteins, giving rise to plants displaying constitutive BR responses and increased starch content, respectively. Overall, we show that the sequence specificity of APRs can be harnessed to generate aggregation-associated phenotypes in a targeted manner in different subcellular compartments. This study points toward the potential application of induced targeted aggregation as a useful tool to knock down protein functions in plants and, especially, to generate beneficial traits in crops.
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Camilla
authors.identifier: 0000-0003-3522-6440
authors.initials: C
authors.lastname: Betti
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Isabelle
authors.identifier: 0000-0003-2878-134X
authors.initials: I
authors.lastname: Vanhoutte
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Silvie
authors.identifier: 0000-0002-7539-1005
authors.initials: S
authors.lastname: Coutuer
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Riet
authors.identifier: 0000-0001-8270-7015
authors.initials: R
authors.lastname: De Rycke
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Kiril
authors.identifier: 0000-0001-5849-8786
authors.initials: K
authors.lastname: Mishev
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Stijn
authors.initials: S
authors.lastname: Aesaert
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Debbie
authors.initials: D
authors.lastname: Rombaut
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Rodrigo
authors.identifier: 0000-0003-1584-3564
authors.initials: R
authors.lastname: Gallardo
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Frederik
authors.initials: F
authors.lastname: De Smet
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Mieke
authors.initials: M
authors.lastname: Van Lijsebettens
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Frank
authors.identifier: 0000-0002-3147-0860
authors.initials: F
authors.lastname: Van Breusegem
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.).
authors.forename: Dirk
authors.identifier: 0000-0002-3217-8407
authors.initials: D
authors.lastname: Inzé
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.) frederic.rousseau@switch.vib-kuleuven.be joost.schymkowitz@switch.vib-kuleuven.be eugenia.russinova@psb.vib-ugent.be.
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.) frederic.rousseau@switch.vib-kuleuven.be joost.schymkowitz@switch.vib-kuleuven.be eugenia.russinova@psb.vib-ugent.be.
authors.forename: Joost
authors.identifier: 0000-0003-2020-0168
authors.initials: J
authors.lastname: Schymkowitz
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium (C.B., I.V., S.C., R.D.R., K.M., S.A., D.R., M.V.L., F.V.B., D.I., E.R.);Switch Laboratory, VIB, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S.);Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium (R.G., F.D.S., J.X., F.R., J.S); andGnomixx, 9000 Gent, Belgium (M.V.) frederic.rousseau@switch.vib-kuleuven.be joost.schymkowitz@switch.vib-kuleuven.be eugenia.russinova@psb.vib-ugent.be.
authors.forename: Eugenia
authors.identifier: 0000-0002-0569-1977
authors.initials: E
authors.lastname: Russinova
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D060406:Brassinosteroids / Q000378:metabolism; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D055785:Gene Knockdown Techniques; D038362:Glycogen Synthase Kinase 3 / Q000235:genetics / Q000378:metabolism; D049452:Green Fluorescent Proteins; D010641:Phenotype; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D030821:Plants, Genetically Modified; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D016415:Sequence Alignment; D015398:Signal Transduction; D003313:Zea mays / Q000166:cytology / Q000235:genetics* / Q000378:metabolism
chemical_list: D060406:Brassinosteroids; D010940:Plant Proteins; D049452:Green Fluorescent Proteins; D038362:Glycogen Synthase Kinase 3