Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry

Ohad Vonshak; Yiftach Divon; Stefanie Förste; David Garenne; Vincent Noireaux; Reinhard Lipowsky; Sophia Rudorf; Shirley S. Daube; Roy H. Bar-Ziv

doi:10.1038/s41565-020-0720-7

Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry

Ohad Vonshak, Yiftach Divon, Stefanie Förste, David Garenne, Vincent Noireaux, Reinhard Lipowsky, Sophia Rudorf, Shirley S. Daube, Roy H. Bar-Ziv

Physics and Astronomy (Twin Cities)

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Abstract

The assembly of protein machines in cells is precise, rapid, and coupled to protein synthesis with regulation in space and time. The assembly of natural and synthetic nanomachines could be similarly controlled by genetic programming outside the cell. Here, we present quasi-two-dimensional (2D) silicon compartments that enable programming of protein assembly lines by local synthesis from surface-immobilized DNA brushes. Using this platform, we studied the autonomous synthesis and assembly of a structural complex from a bacteriophage and a bacterial RNA-synthesizing machine. Local synthesis and surface capture of complexes provided high assembly yield and sensitive detection of spatially resolved assembly intermediates, with the 3D geometry of the compartment and the 2D pattern of brushes dictating the yield and mode of assembly steps. Localized synthesis of proteins in a single gene brush enhances their interactions, and displacement of their genes in separated brushes leads to step-by-step surface assembly. This methodology enables spatial regulation of protein synthesis, and deciphering, reconstruction and design of biological machine assembly lines.

Original language	English (US)
Pages (from-to)	783-791
Number of pages	9
Journal	Nature Nanotechnology
Volume	15
Issue number	9
DOIs	https://doi.org/10.1038/s41565-020-0720-7
State	Published - Sep 1 2020

Bibliographical note

Funding Information:
We acknowledge funding from the Israel Science Foundation (grant no. 1870/15), the United States–Israel Binational Science Foundation (grant no. 2014400), and the Minerva Foundation (grant no. 712274) for the work on the T4 wedges. We thank the Office of Naval Research (award no. N62909-18-1-2094) for funding the work on RNAP assembly. We thank M. Levy for discussions.

Publisher Copyright:
© 2020, The Author(s), under exclusive licence to Springer Nature Limited.

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Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

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abstract = "The assembly of protein machines in cells is precise, rapid, and coupled to protein synthesis with regulation in space and time. The assembly of natural and synthetic nanomachines could be similarly controlled by genetic programming outside the cell. Here, we present quasi-two-dimensional (2D) silicon compartments that enable programming of protein assembly lines by local synthesis from surface-immobilized DNA brushes. Using this platform, we studied the autonomous synthesis and assembly of a structural complex from a bacteriophage and a bacterial RNA-synthesizing machine. Local synthesis and surface capture of complexes provided high assembly yield and sensitive detection of spatially resolved assembly intermediates, with the 3D geometry of the compartment and the 2D pattern of brushes dictating the yield and mode of assembly steps. Localized synthesis of proteins in a single gene brush enhances their interactions, and displacement of their genes in separated brushes leads to step-by-step surface assembly. This methodology enables spatial regulation of protein synthesis, and deciphering, reconstruction and design of biological machine assembly lines.",

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Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry

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