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CRISPRi-based circuits for genetic computation in plants

Muhammad Adil Khan, Gabrielle Herring, View ORCID ProfileMarina Oliva, Elliott Fourie, Jia Yuan Zhu, Benjamin Johnston, Jahnvi Pflüger, View ORCID ProfileTessa Swain, View ORCID ProfileChristian Pflüger, View ORCID ProfileJames Lloyd, View ORCID ProfileDavid Secco, View ORCID ProfileIan Small, View ORCID ProfileBrendan Kidd, View ORCID ProfileRyan Lister
doi: https://doi.org/10.1101/2022.07.01.498372
Muhammad Adil Khan
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Gabrielle Herring
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Marina Oliva
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Elliott Fourie
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Jia Yuan Zhu
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Benjamin Johnston
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Jahnvi Pflüger
2Harry Perkins Institute of Medical Research, The University of Western Australia, WA, Australia
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Tessa Swain
2Harry Perkins Institute of Medical Research, The University of Western Australia, WA, Australia
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  • ORCID record for Tessa Swain
Christian Pflüger
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
2Harry Perkins Institute of Medical Research, The University of Western Australia, WA, Australia
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James Lloyd
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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David Secco
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Ian Small
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
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Brendan Kidd
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
3CSIRO Synthetic Biology Future Science Platform, QLD, Australia
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  • For correspondence: brendan.kidd@uwa.edu.au ryan.lister@uwa.edu.au
Ryan Lister
1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, WA, Australia
2Harry Perkins Institute of Medical Research, The University of Western Australia, WA, Australia
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  • For correspondence: brendan.kidd@uwa.edu.au ryan.lister@uwa.edu.au
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Abstract

Synthetic gene circuits can enable new cellular behaviours by integrating multiple input signals into customisable genetic programs. However, gene circuit development in plants has been limited by a lack of orthogonal and modular parts required for their construction. Here, we present a tool-kit of reversible CRISPRi-based gene circuits for use in plants. First, we created a range of engineered repressible promoters of different strengths and used them as integrators for the construction of NOT and NOR gates in Arabidopsis cells. Next, we determined the optimal processing system to express sgRNAs from RNA Pol II promoters to introduce NOR gate programmability and interface it with host regulatory sequences. Finally, we connected multiple NOR gates together in layered arrangements to create OR, NIMPLY, and AND logic functions. Our CRISPRi circuits are orthogonal, compact, reversible, programmable, and modular, providing a new platform for sophisticated and deliberate spatio-temporal control of gene expression in plants.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://zenodo.org/record/6783186#.Yr2ucHZByUl

  • http://dx.doi.org/10.17504/protocols.io.yxmvmn1d6g3p/v1

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 01, 2022.
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CRISPRi-based circuits for genetic computation in plants
Muhammad Adil Khan, Gabrielle Herring, Marina Oliva, Elliott Fourie, Jia Yuan Zhu, Benjamin Johnston, Jahnvi Pflüger, Tessa Swain, Christian Pflüger, James Lloyd, David Secco, Ian Small, Brendan Kidd, Ryan Lister
bioRxiv 2022.07.01.498372; doi: https://doi.org/10.1101/2022.07.01.498372
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CRISPRi-based circuits for genetic computation in plants
Muhammad Adil Khan, Gabrielle Herring, Marina Oliva, Elliott Fourie, Jia Yuan Zhu, Benjamin Johnston, Jahnvi Pflüger, Tessa Swain, Christian Pflüger, James Lloyd, David Secco, Ian Small, Brendan Kidd, Ryan Lister
bioRxiv 2022.07.01.498372; doi: https://doi.org/10.1101/2022.07.01.498372

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