Abstract
Protein aggregation is determined by 5–15 amino acids peptides of the target protein sequence, so-called aggregation-prone regions (APRs) that specifically self-associate to form β-structured inclusions. The presence of APRs in a target protein can be predicted by a dedicated algorithm, such as TANGO. Synthetic aggregation-prone proteins are designed by expressing specific APRs fused to a fluorescent carrier for stability and visualization. Previously, the stable expression of these proteins in Zea mays (maize) has been demonstrated to induce aggregation of target proteins with specific localization, such as the starch-degrading enzyme α-glucan water dikinase, giving rise to plants displaying knockdown phenotypes. Here, we describe how to design synthetic aggregation-prone proteins to harness the sequence specificity of APRs to generate aggregation-associated phenotypes in a targeted manner and in different subcellular compartments. This method points toward the application of induced targeted aggregation as a useful tool to knock down protein functions in maize and to generate crops with improved traits.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Betti C, Vanhoutte I, Coutuer S, De Rycke R, Mishev K, Vuylsteke M, Aesaert S, Rombaut D, Gallardo R, De Smet F, Xu J, Van Lijsebettens M, Van Breusegem F, Inzé D, Rousseau F, Schymkowitz J, Russinova E (2016) Sequence-Specific protein aggregation generates defined protein knockdowns in plants. Plant Physiol 171(2):773–787
Tyedmers J, Mogk A, Bukau B (2010) Cellular strategies for controlling protein aggregation. Nat Rev Mol Cell Biol 11:777–788
Rousseau F, Serrano L, Schymkowitz JWH (2006) How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol 355:1037 1047
Goldschmidt L, Teng PK, Riek R, Eisenberg D (2010) Identifying the amylome, proteins capable of forming amyloid like fibrils. Proc Natl Acad Sci U S A 107:3487 3492
Mitraki A (2010) Protein aggregation: from inclusion bodies to amyloid and biomaterials. Adv Protein Chem Struct Biol 79:89–125
Ganesan A, Debulpaep M, Wilkinson H, Van Durme J, De Baets G, Jonckheere W, Ramakers M, Ivarsson Y, Zimmermann P, Van Eldere J, Schymkowitz J, Rousseau F (2014) Selectivity of aggregation-determining interactions. J Mol Biol 427:236–247
Fernandez Escamilla A-M, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22:1302 1306
De Baets G, Van Durme J, Rousseau F, Schymkowitz J (2014) A genome-wide sequence-structure analysis suggests aggregation gatekeepers constitute an evolutionary constrained functional class. J Mol Biol 426:2405–2412
Hallauer AR, Lamkey KR, White PR (1997) Registration of five inbred lines of maize: B102, B103, B104, B105, and B106. Crop Sci 37:1405–1406
Coussens G, Aesaert S, Verelst W, Demeulenaere M, De Buck S, Njuguna E, Inzé D, Van Lijsebettens M (2012) Brachypodium distachyon promoters as efficient building blocks for transgenic research in maize. J Exp Bot 63:4263–4273
Voinnet O, Lederer C, Baulcombe DC (2000) A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell 103:157–167
Karimi M, Bleys A, Vanderhaeghen R, Hilson P (2007) Building blocks for plant gene assembly. Plant Physiol 145:1183–1191
Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21:3718–3731
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Acknowledgments
This work was supported by grants from the Agency for Innovation by Science and Technology (“Strategisch Basisonderzoek” project no. 60839), Ghent University (“Industrieel Onderzoeksfonds” F2011/IOF-Advanced121 and F2014/IOF-StarTT261 and Multidisciplinary Research Partnership “Biotechnology for a Sustainable Economy” no. 01MRB510W), the Interuniversity Attraction Poles Program (IUAP VII/29), initiated by the Belgian State, Science Policy Office, University of Leuven, and the European Research Council under the European Union’s Horizon 2020 Framework Programme (ERC Grant agreement 647458). We thank Martine De Cock for proofreading the chapter.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Betti, C., Schymkowitz, J., Rousseau, F., Russinova, E. (2018). Selective Knockdowns in Maize by Sequence-Specific Protein Aggregation. In: Lagrimini, L. (eds) Maize. Methods in Molecular Biology, vol 1676. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7315-6_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7315-6_6
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7314-9
Online ISBN: 978-1-4939-7315-6
eBook Packages: Springer Protocols