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Selective knockdowns in maize by sequence-specific protein aggregation

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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.
Keywords
APR, Protein interference, Protein knockdown technology, Sequence-specific aggregation, β-sheet inclusions

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Chicago
Betti, Camilla, Joost Schymkowitz, Frederic Rousseau, and Eugenia Russinova. 2018. “Selective Knockdowns in Maize by Sequence-specific Protein Aggregation.” In Maize : Methods and Protocols, ed. L Mark Lagrimini, 1676:109–127. New York, NY, USA: Springer Humana Press.
APA
Betti, C., Schymkowitz, J., Rousseau, F., & Russinova, E. (2018). Selective knockdowns in maize by sequence-specific protein aggregation. In L. M. Lagrimini (Ed.), Maize : methods and protocols (Vol. 1676, pp. 109–127). New York, NY, USA: Springer Humana Press.
Vancouver
1.
Betti C, Schymkowitz J, Rousseau F, Russinova E. Selective knockdowns in maize by sequence-specific protein aggregation. In: Lagrimini LM, editor. Maize : methods and protocols. New York, NY, USA: Springer Humana Press; 2018. p. 109–27.
MLA
Betti, Camilla, Joost Schymkowitz, Frederic Rousseau, et al. “Selective Knockdowns in Maize by Sequence-specific Protein Aggregation.” Maize : Methods and Protocols. Ed. L Mark Lagrimini. Vol. 1676. New York, NY, USA: Springer Humana Press, 2018. 109–127. Print.
@incollection{8561882,
  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 \ensuremath{\beta}-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 \ensuremath{\alpha}-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.},
  author       = {Betti, Camilla and Schymkowitz, Joost and Rousseau, Frederic and Russinova, Eugenia},
  booktitle    = {Maize : methods and protocols},
  editor       = {Lagrimini, L Mark},
  isbn         = {9781493973149},
  issn         = {1064-3745},
  keyword      = {APR,Protein interference,Protein knockdown technology,Sequence-specific aggregation,\ensuremath{\beta}-sheet inclusions},
  language     = {eng},
  pages        = {109--127},
  publisher    = {Springer Humana Press},
  series       = {Methods in Molecular Biology},
  title        = {Selective knockdowns in maize by sequence-specific protein aggregation},
  url          = {http://dx.doi.org/10.1007/978-1-4939-7315-6\_6},
  volume       = {1676},
  year         = {2018},
}

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