Light-driven synchronization of optogenetic clocks DOI Open Access
Maria Cristina Cannarsa, Filippo Liguori, Nicola Pellicciotta

и другие.

Опубликована: Авг. 29, 2024

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these that drives population complete desynchronization. Here we introduce optorepressilator, an optically controllable clock combines repressilator, three-node synthetic network E. coli , with optogenetic module enabling reset, delay, or advance its phase using optical inputs. We demonstrate optorepressilators be synchronized by transient green light exposure entrained oscillate indefinitely train short pulses, through mechanism reminiscent natural circadian clocks. Furthermore, investigate system’s response detuned external stimuli observing multiple regimes global synchronization. Integrating experiments and mathematical modeling, show entrainment is robust understood quantitatively from single cell level.

Язык: Английский

Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback DOI Creative Commons
Joaquı́n Gutiérrez, Sant Kumar, Mustafa Khammash

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Авг. 16, 2022

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies synthetic biology bioproduction. However, the difficulty controlling composition microbial consortia over time hinders their optimal use many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements computer-controlled optogenetic modulation bacterial growth to implement precise robust compositional control two-strain E. coli community. In addition, develop general framework dynamic modeling genetic circuits physiological context host-aware model determine parameters our closed-loop system. Our succeeds stabilizing strain ratio multiple parallel co-cultures at arbitrary levels changing these targets time, opening door implementation programs communities.

Язык: Английский

Процитировано

59
Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production DOI Creative Commons
Moritz Benisch, Dirk Benzinger, Sant Kumar

и другие.

Metabolic Engineering, Год журнала: 2023, Номер 77, С. 32 - 40

Опубликована: Март 11, 2023

In biotechnological protein production processes, the onset of unfolding at high gene expression levels leads to diminishing yields and reduced efficiency. Here we show that in silico closed-loop optogenetic feedback control unfolded response (UPR) S. cerevisiae clamps rates intermediate near-optimal values, leading significantly improved product titers. Specifically, a fully-automated custom-built 1L-photobioreactor, used cybergenetic system steer level UPR yeast desired set-point by optogenetically modulating α-amylase, hard-to-fold protein, based on real-time measurements UPR, resulting 60% higher This proof-of-concept study paves way for advanced optimal biotechnology strategies diverge from complement current employing constitutive overexpression or genetically hardwired circuits.

Язык: Английский

Процитировано

22
Rapid Optogenetic Clustering in the Cytoplasm with BcLOVclust DOI Creative Commons
Zikang Huang, William Benman, Liang Dong

и другие.

Journal of Molecular Biology, Год журнала: 2024, Номер 436(3), С. 168452 - 168452

Опубликована: Янв. 21, 2024

Язык: Английский

Процитировано

9
Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations DOI Creative Commons
Kieran Sweeney, Megan N. McClean

Cell Reports, Год журнала: 2023, Номер 42(5), С. 112426 - 112426

Опубликована: Апрель 22, 2023

Environmental information may be encoded in the temporal dynamics of transcription factor (TF) activation and subsequently decoded by gene promoters to enact stimulus-specific expression programs. Previous studies this behavior focused on encoding decoding TF nuclear localization dynamics, yet cells control activity TFs myriad ways, including regulating their ability bind DNA. Here, we use light-controlled mutants yeast Msn2 as a model system investigate how promoter is affected changes We find that directly decode effects changing affinity are highly dependent, illustrating could regulate DNA binding concert for improved expression.

Язык: Английский

Процитировано

14
Unlocking the potential of optogenetics in microbial applications DOI Creative Commons
Moritz Benisch,

Stephanie K. Aoki,

Mustafa Khammash

и другие.

Current Opinion in Microbiology, Год журнала: 2023, Номер 77, С. 102404 - 102404

Опубликована: Ноя. 30, 2023

Optogenetics is a powerful approach that enables researchers to use light dynamically manipulate cellular behavior. Since the first published of optogenetics in synthetic biology, field has expanded rapidly, yielding vast array tools and applications. Despite its immense potential for achieving high spatiotemporal precision, predominantly been employed as substitute conventional chemical inducers. In this short review, we discuss key features microbial highlight applications understanding cocultures, bioproduction, biomaterials, therapeutics, which more fully utilized realize goals not previously possible by other methods.

Язык: Английский

Процитировано

14
Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits DOI Creative Commons
Diego Alba Burbano, Ryan Cardiff, Benjamin I. Tickman

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(30)

Опубликована: Июль 18, 2023

Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found naturally occurring biological systems. We develop an approach creating high-performing activatable promoters that can be assembled into deep, wide, and CRISPR-activation -interference (CRISPRa/i) GRNs. By integrating sequence-based design vivo screening, we engineer achieve up 1,000-fold dynamic range

Язык: Английский

Процитировано

11
Light-inducible protein degradation in E. coli with the LOVdeg tag DOI Creative Commons
Nathan Tague,

Cristian Coriano-Ortiz,

Michael B. Sheets

и другие.

eLife, Год журнала: 2024, Номер 12

Опубликована: Янв. 25, 2024

Molecular tools for optogenetic control allow spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism because it can be highly modular, used in tandem with other mechanisms, maintain functionality throughout growth phases. Here, we engineered LOVdeg, tag that appended to interest inducible Escherichia coli using blue light. We demonstrate the modularity LOVdeg by range proteins, including LacI repressor, CRISPRa activator, AcrB efflux pump. Additionally, utility pairing existing enhance performance developing combined EL222 system. Finally, use metabolic engineering application post-translational metabolism. Together, our results highlight system introduce powerful new tool bacterial optogenetics.

Язык: Английский

Процитировано

4
Toward Multiplexed Optogenetic Circuits DOI Creative Commons

Ari Dwijayanti,

Congqiang Zhang, Chueh Loo Poh

и другие.

Frontiers in Bioengineering and Biotechnology, Год журнала: 2022, Номер 9

Опубликована: Янв. 5, 2022

Owing to its ubiquity and easy availability in nature, light has been widely employed control complex cellular behaviors. Light-sensitive proteins are the foundation such diverse multilevel adaptive regulations a large range of organisms. Due their remarkable properties potential applications engineered systems, exploration engineering natural light-sensitive have significantly contributed expand optogenetic toolboxes with tailor-made performances synthetic genetic circuits. Progressively, more systems designed which multiple photoreceptors, each sensing dedicated wavelength, combined simultaneously coordinate responses single cell. In this review, we highlight recent works challenges on multiplexed circuits for dynamic regulation breakthrough biotechnological applications.

Язык: Английский

Процитировано

15
Redox active plant phenolic, acetosyringone, for electrogenetic signaling DOI Creative Commons
Fauziah Rahma Zakaria, Chen‐Yu Chen, Jinyang Li

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 26, 2024

Abstract Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H 2 O ) as an inducer gene expression. Here we report redox-active phenolic plant signaling molecule acetosyringone (AS) also induce expression from regulon. AS must oxidized, however, reduced state present under normal conditions cannot Thus, serves “pro-signaling molecule” activated by its oxidation—in our case application oxidizing potential electrode. We show not induced if imposed electrode in mid-physiological range. Electronically sliding applied either oxidative or reductive extremes induces this but through different mechanisms: reduction form H oxidation AS. Fundamentally, work reinforces emerging concept redox depends more on molecular activities than structure. From applications perspective, creation electronically programmed “pro-signal” dramatically expands toolbox for electronic control biological responses microbes, including complex environments, cell-based materials, biomanufacturing.

Язык: Английский

Процитировано

3
Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro DOI Creative Commons
Zachary P. Harmer, Jaron Thompson,

David Cole

и другие.

ACS Synthetic Biology, Год журнала: 2024, Номер 13(5), С. 1424 - 1433

Опубликована: Апрель 29, 2024

The ability to control cellular processes using optogenetics is inducer-limited, with most optogenetic systems responding blue light. To address this limitation, we leverage an integrated framework combining Lustro, a powerful high-throughput platform, and machine learning tools enable multiplexed over light-sensitive systems. Specifically, identify light induction conditions for sequential activation as well preferential switching between pairs of split transcription factors in the budding yeast, Saccharomyces cerevisiae. We use data generated from Lustro build Bayesian optimization that incorporates data-driven learning, uncertainty quantification, experimental design prediction system behavior identification optimal control. This work lays foundation designing more advanced synthetic biological circuits incorporating optogenetics, where multiple circuit components can be controlled designer programs, broad implications biotechnology bioengineering.

Язык: Английский

Процитировано

3