Context-dependent redesign of robust synthetic gene circuits

Trends in biotechnology, Год журнала: 2024, Номер 42(7), С. 895 - 909

Опубликована: Фев. 5, 2024

Cells provide dynamic platforms for executing exogenous genetic programs in synthetic biology, resulting highly context-dependent circuit performance. Recent years have seen an increasing interest understanding the intricacies of circuit–host relationships, their influence on bioengineering workflow, and devising strategies to alleviate undesired effects. We overview how emerging interactions, such as growth feedback resource competition, impact both deterministic stochastic behaviors. also emphasize control mitigating these unwanted This review summarizes latest advances current state host-aware resource-aware design gene circuits.

Язык: Английский

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A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Март 4, 2024

Abstract Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive binding kinetics can guide the design of strategies countering these However, in bacteria availability cell growth rate are interlinked, which complicates resource-aware biocircuit design. Capturing this interdependence requires coarse-grained bacterial models balance accurate representation metabolic regulation against simplicity interpretability. We propose E. coli model combines ease simplified coupling analysis with appreciation mechanisms processes relevant Reliably capturing known phenomena, it provides unifying explanation to disparate empirical relations between gene expression. Considering biomolecular controller makes cell-wide ribosome robust perturbations, we showcase our model’s usefulness numerically prototyping biocircuits deriving analytical guidance.

Язык: Английский

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Model-guided gene circuit design for engineering genetically stable cell populations in diverse applications

Journal of The Royal Society Interface, Год журнала: 2025, Номер 22(223)

Опубликована: Фев. 1, 2025

Maintaining engineered cell populations’ genetic stability is a key challenge in synthetic biology. Synthetic constructs compete with host cell’s native genes for expression resources, burdening the and impairing its growth. This creates selective pressure favouring mutations which alleviate this growth defect by removing gene expression. Non-functional mutants thus spread populations, eventually making them lose functions. Past work has attempted to limit mutation coupling survival. However, these approaches are highly context-dependent must be tailor-made each particular circuit retained. By contrast, we develop analyse biomolecular controller depresses mutant independently of mutated gene’s identity. Modelling shows how our design can deployed alongside various circuits without any re-engineering components, outperforming extant gene-specific mitigation strategies. Our controller’s performance evaluated using novel simulation approach leverages resource-aware modelling directly link circuit’s parameters population-level behaviour. design’s adaptability promises mitigate an expanded range applications, while analyses provide blueprint models design.

Язык: Английский

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Multi-Layer Autocatalytic Feedback Enables Integral Control Amidst Resource Competition and Across Scales

ACS Synthetic Biology, Год журнала: 2025, Номер unknown

Опубликована: Март 21, 2025

Integral feedback control strategies have proven effective in regulating protein expression unpredictable cellular environments. These strategies, grounded model-based designs and theory, advanced synthetic biology applications. Autocatalytic integral controllers, utilizing positive autoregulation for action, are one class of simplest architectures to design integrators. This controllers offers unique features, such as robustness against dilution effects growth, well the potential realizations across different biological scales, owing their similarity self-regenerative behaviors widely observed nature. Despite this, has not yet been fully exploited. One key reason, we discuss, is that effectiveness often hindered by resource competition context-dependent couplings. study addresses these challenges using a multilayer strategy. Our enabled population-level multicellular integrators, where function emerges property coordinated interactions distributed cell populations coexisting consortium. We provide generalized mathematical framework modeling complex genetic networks, supporting intracellular circuits. The use our proposed autocatalytic examined two typical tasks pose significant relevance applications: concentration regulation ratiometric control. define task solve it variant controller. controller motifs demonstrated through range application examples, from precise gene ratios embedded population growth coculture composition within engineered microbial ecosystems. findings offer versatile approach achieving robust adaptation homeostasis subcellular scales.

Язык: Английский

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Harnessing and Mimicking Bacterial Features to Combat Cancer: From Living Entities to Artificial Mimicking Systems

Advanced Materials, Год журнала: 2024, Номер 36(35)

Опубликована: Авг. 1, 2024

Bacterial-derived micro-/nanomedicine has garnered considerable attention in anticancer therapy, owing to the unique natural features of bacteria, including specific targeting ability, immunogenic benefits, physicochemical modifiability, and biotechnological editability. Besides, bacterial components have also been explored as promising drug delivery vehicles. Harnessing these features, cutting-edge biotechnologies applied attenuated tumor-targeting bacteria with properties or functions for potent effective cancer treatment, strategies gene-editing genetic circuits. Further, advent bacteria-inspired micro-/nanorobots mimicking artificial systems furnished fresh perspectives formulating developing highly efficient systems. Focusing on advantages this review delves into advances bacteria-derived treatment recent years, which experienced a process from living entities Meanwhile, summary relative clinical trials is provided primary challenges impeding their application are discussed. Furthermore, future directions suggested combat cancer.

Язык: Английский

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Computational Synthetic Biology Enabled through JAX: A Showcase

ACS Synthetic Biology, Год журнала: 2024, Номер 13(9), С. 3046 - 3050

Опубликована: Сен. 4, 2024

Mathematical modeling is indispensable in synthetic biology but remains underutilized. Tackling problems, from optimizing gene networks to simulating intracellular dynamics, can be facilitated by the ever-growing body of approaches, they mechanistic, stochastic, data-driven, or AI-enabled. Thanks progress AI community, robust frameworks have emerged enable researchers access complex computational hardware and compilation. Previously, these focused solely on deep learning, been developed point where running different forms computation relatively simple, as made possible, notably, JAX library. Running simulations at scale GPUs speeds up research, which compounds larger-scale experiments greater usability code. As underexplored biology, we demonstrate its utility three example projects ranging directed evolution, each with an accompanying demonstrative Jupyter notebook. We hope that tutorials serve democratize flexible scaling, faster run-times, easy GPU portability, mathematical enhancements (such automatic differentiation) brings, all only minor restructuring

Язык: Английский

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Resource allocation in biochemically structured metabolic networks

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 27, 2024

Abstract Microbes tune their metabolism to environmental challenges by changing protein expression levels, metabolite concentrations, and reaction rates simultaneously. Here, we establish an analytical model for microbial resource allocation that integrates enzyme biochemistry the global architecture of metabolic networks. We describe production biomass from external nutrients in pathways Michaelis-Menten enzymes compute maximizes growth under constraints mass conservation dilution cell growth. This predicts generic patterns growth-dependent proteome metabolome. In a nutrient-rich medium, optimal depends primarily on individual synthesis steps, while concentrations fluxes decrease along successive reactions pathway. Under nutrient limitation, levels change linearly with rate, direction depending again enzyme’s biochemistry. Metabolite show stronger, nonlinear decline rate. identify simple, metabolite-based regulatory logic which cells can be tuned near-optimal Finally, our evolutionary stable states networks, including local biochemical parameters fraction, empirical data.

Язык: Английский

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Noise Reduction in Resource-Coupled Multi-Module Gene Circuits through Antithetic Feedback Control

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 24, 2024

Gene circuits within the same host cell often experience coupling, stemming from competition for limited resources during transcriptional and translational processes. This resource introduces an additional layer of noise to gene expression. Here we present three multi-module antithetic control strategies: negatively competitive regulation (NCR) controller, alongside local global controllers, aimed at reducing expression context competition. Through stochastic simulations fluctuation-dissipation theorem (FDT) analysis, our findings highlight superior performance NCR controller in levels. Our research provides effective strategy attenuating resource-driven offers insight into development robust circuits.

Язык: Английский

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Model-guided gene circuit design for engineering genetically stable cell populations in diverse applications

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Abstract Maintaining engineered cell populations’ genetic stability is a key challenge in synthetic biology. Synthetic constructs compete with host cell’s native genes for expression resources, burdening the and impairing its growth. This creates selective pressure favouring mutations which alleviate this growth defect by removing gene expression. Non-functional mutants thus spread populations, eventually making them lose functions. Past work has attempted to limit mutation coupling survival. However, these approaches are highly context-dependent must be tailor-made each particular circuit retained. In contrast, we develop analyse biomolecular controller depresses mutant independently of mutated gene’s identity. Modelling shows how our design can deployed alongside various circuits without any re-engineering components, outperforming extant gene-specific mitigation strategies. Our controller’s performance evaluated using novel simulation approach leverages resource-aware modelling directly link circuit’s parameters population-level behaviour. design’s adaptability promises mitigate an expanded range applications, whilst analyses provide blueprint models design.

Язык: Английский

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Energy Aware Technology Mapping of Genetic Logic Circuits

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 27, 2024

Abstract Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers -as caused by the additional burden artificial genetic circuits-shifts a cell’s priority survival, also impairing functionality circuit. Moreover, recent works have shown importance expenditure in information transmission. Despite organisms being non-equilibrium models capable accounting for response curves not yet employed design automation (GDA) software. To this end, we introduce Aware Technology Mapping, automated logic circuits with respect efficiency functionality. The basis is an aware steady state (NESS) model gene expression, capturing characteristics like -which link entropy production rate- transcriptional bursting, relevant eukaryotes as well prokaryotes. Our evaluation shows that circuit’s functional performance disjoint optimization goals. For our benchmark, improves 37.2% on average when comparing functionally optimized variants. We discover linear increase overall protein expression circuit size, where Mapping allows designing one two gates smaller. Structural variants improve further, while results show Pareto dominance among structures single Boolean function. By incorporating demand into design, enables design. This extends current GDA tools complements approaches coping vivo . TOC Graphic

Язык: Английский

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