A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice

Ferdinand Greiss; Nicolas Lardon; Leonie Schütz; Yoav Barak; Shirley S. Daube; Elmar Weinhold; Vincent Noireaux; Roy Bar-Ziv

doi:10.1038/s41467-024-45186-2

A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice

Ferdinand Greiss^*, Nicolas Lardon, Leonie Schütz, Yoav Barak, Shirley S. Daube, Elmar Weinhold, Vincent Noireaux, Roy Bar-Ziv^*

^*Corresponding author for this work

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

Abstract

Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.

Original language	English
Article number	883
Number of pages	12
Journal	Nature Communications
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-45186-2
Publication status	Published - 29 Jan 2024

Bibliographical note

We thank the Nanofabrication unit at the Weizmann Institute for support in the manufacturing process, the Forchheimer plasmid collection for the bacterial strain and plasmids, O. Vonshak and Y. Divon for providing the gp genes, D. Garenne for helping prepare the cell lysate, and H. Hofmann and A. Dupin for critically reading the manuscript. We thank J. Kumar for many fruitful discussions and finally, we thank J. Götz for her encouragement in this study. F.G. would like to thank EMBO (ALTF 598-2017) and Feinberg Graduate School for financial support with a long-term postdoctoral fellowship. We acknowledge funding from the Israel Science Foundation (R.B.Z. and S.S.D., grant no. 2723/19), the United States—Israel Binational Science Foundation (R.B.Z. and V.N. grant no. 2018208), the Isak Ferdinand and Dwosia Artmann Research Fund for Biological Physics, the Human Frontier Science Program (V.N., grant no. RGP0037/2015), and the Minerva Foundation (R.B.Z. and S.S.D., grant no. 712274). N.L. acknowledges the funding of the Max Planck Society. The research of N.L. was conducted within the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society. Y.B. is the incumbent of the Beatrice Barton Research Fellowship. E.W. acknowledges financial support from the German-Israeli Foundation for Scientific Research and Development (I−1196−195.9/2012).

Publisher Copyright:
© 2024, The Author(s).

All Science Journal Classification (ASJC) codes

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

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Cite this

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title = "A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice",

abstract = "Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.",

author = "Ferdinand Greiss and Nicolas Lardon and Leonie Sch{\"u}tz and Yoav Barak and Daube, {Shirley S.} and Elmar Weinhold and Vincent Noireaux and Roy Bar-Ziv",

note = "We thank the Nanofabrication unit at the Weizmann Institute for support in the manufacturing process, the Forchheimer plasmid collection for the bacterial strain and plasmids, O. Vonshak and Y. Divon for providing the gp genes, D. Garenne for helping prepare the cell lysate, and H. Hofmann and A. Dupin for critically reading the manuscript. We thank J. Kumar for many fruitful discussions and finally, we thank J. G{\"o}tz for her encouragement in this study. F.G. would like to thank EMBO (ALTF 598-2017) and Feinberg Graduate School for financial support with a long-term postdoctoral fellowship. We acknowledge funding from the Israel Science Foundation (R.B.Z. and S.S.D., grant no. 2723/19), the United States—Israel Binational Science Foundation (R.B.Z. and V.N. grant no. 2018208), the Isak Ferdinand and Dwosia Artmann Research Fund for Biological Physics, the Human Frontier Science Program (V.N., grant no. RGP0037/2015), and the Minerva Foundation (R.B.Z. and S.S.D., grant no. 712274). N.L. acknowledges the funding of the Max Planck Society. The research of N.L. was conducted within the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society. Y.B. is the incumbent of the Beatrice Barton Research Fellowship. E.W. acknowledges financial support from the German-Israeli Foundation for Scientific Research and Development (I−1196−195.9/2012). Publisher Copyright: {\textcopyright} 2024, The Author(s).",

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N2 - Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.

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A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice

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