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Demonstration of de novo chemotaxis in E. coli using a real-time, quantitative, and digital-like approach

Tzila Davidov, Naor Granik, Sharbel Zahran, Inbal Adir, Ofek Elul, Tal Fried, Asif Gil, Bar Mayo, Shilo Ohayon, Shiran Sarig, Nofar Shasha, Shirane Tsedef, Shani Weiner, Michal Brunwasser-Meirom, Alexandra Ereskovsky, Noa Katz, Beate Kaufmann, Yuri Haimov, Heidi Leonard, Ester Segal, View ORCID ProfileRoee Amit
doi: https://doi.org/10.1101/114207
Tzila Davidov
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Naor Granik
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
3Department of Electrical Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Sharbel Zahran
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Inbal Adir
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
4Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Ofek Elul
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Tal Fried
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
5Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Asif Gil
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Bar Mayo
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Shilo Ohayon
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Shiran Sarig
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Nofar Shasha
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
5Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Shirane Tsedef
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Shani Weiner
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Michal Brunwasser-Meirom
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Alexandra Ereskovsky
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Noa Katz
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Beate Kaufmann
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Yuri Haimov
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Heidi Leonard
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Ester Segal
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
7The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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Roee Amit
1iGEM-Technion 2016, Technion-Israel Institute of Technology, Haifa, Israel 3200000
2Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel 3200000
7The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel 3200000
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  • ORCID record for Roee Amit
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Abstract

Chemotaxis is the movement of an organism in response to an external chemical stimulus. This system enables bacteria to sense their immediate environment and adapt to changes in its chemical composition. Bacterial chemotaxis is mediated by chemoreceptors, membrane proteins that bind an effector and transduce the signal to the downstream proteins. From a synthetic biology perspective, the natural chemotactic repertoire is of little use since bacterial chemoreceptors have evolved to sense specific ligands that either benefit or harm the cell. Here we demonstrate that using a combined computational design approach together with a quantitative, real-time, and digital detection approach, we can rapidly design, manufacture, and characterize a synthetic chemoreceptor in E. coli for histamine (a ligand for which there are no known chemoreceptors). First, we employed a computational protocol that uses the Rosetta bioinformatics software together with high threshold filters to design mutational variants to the native Tar ligand binding domain that target histamine. Second, we tested different ligand-chemoreceptors pairs with a novel chemotaxis assay, based on optical reflectance interferometry of porous silicon (PSi) optical transducers, enabling label-free quantification of chemotaxis by monitoring real-time changes in the optical readout (expressed as the effective optical thickness, EOT). We found that different ligands can be characterized by an individual set of fingerprints in our assay. Namely, a binary, digital-like response in EOT change (i.e. positive or negative) that differentiates between attractants and repellants, the amplitude of change of EOT response, and the rate by which steady state in EOT change is reached. Using this assay, we were able to positively identify and characterize a single mutational chemoreceptor variant for histamine that mediated chemotaxis comparably to the natural Tar-aspartate system. Our results demonstrate the possibility of not only expanding the natural chemotaxis repertoire, but also provide a new quantitative assay by which to characterize the efficacy of the chemotactic response.

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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 4.0 International license.
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Posted March 06, 2017.
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Demonstration of de novo chemotaxis in E. coli using a real-time, quantitative, and digital-like approach
Tzila Davidov, Naor Granik, Sharbel Zahran, Inbal Adir, Ofek Elul, Tal Fried, Asif Gil, Bar Mayo, Shilo Ohayon, Shiran Sarig, Nofar Shasha, Shirane Tsedef, Shani Weiner, Michal Brunwasser-Meirom, Alexandra Ereskovsky, Noa Katz, Beate Kaufmann, Yuri Haimov, Heidi Leonard, Ester Segal, Roee Amit
bioRxiv 114207; doi: https://doi.org/10.1101/114207
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Demonstration of de novo chemotaxis in E. coli using a real-time, quantitative, and digital-like approach
Tzila Davidov, Naor Granik, Sharbel Zahran, Inbal Adir, Ofek Elul, Tal Fried, Asif Gil, Bar Mayo, Shilo Ohayon, Shiran Sarig, Nofar Shasha, Shirane Tsedef, Shani Weiner, Michal Brunwasser-Meirom, Alexandra Ereskovsky, Noa Katz, Beate Kaufmann, Yuri Haimov, Heidi Leonard, Ester Segal, Roee Amit
bioRxiv 114207; doi: https://doi.org/10.1101/114207

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