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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Integrating bioelectronics with cell-based synthetic biology

Nature Reviews Bioengineering, Год журнала: 2025, Номер unknown

Опубликована: Янв. 7, 2025

Язык: Английский

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Machine learning for synthetic gene circuit engineering

Current Opinion in Biotechnology, Год журнала: 2025, Номер 92, С. 103263 - 103263

Опубликована: Янв. 27, 2025

Язык: Английский

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DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes

Molecular Cell, Год журнала: 2023, Номер 83(10), С. 1573 - 1587.e8

Опубликована: Май 1, 2023

DNA supercoiling has emerged as a major contributor to gene regulation in bacteria, but how impacts transcription dynamics eukaryotes is unclear. Here, using single-molecule dual-color nascent imaging budding yeast, we show that transcriptional bursting of divergent and tandem GAL genes coupled. Temporal coupling neighboring requires rapid release supercoils by topoisomerases. When accumulate, one inhibits at its adjacent genes. Transcription inhibition the results from destabilized binding factor Gal4. Moreover, wild-type yeast minimizes supercoiling-mediated maintaining sufficient levels Overall, discover fundamental differences control between bacteria ensures proper expression

Язык: Английский

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Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression

Molecular Microbiology, Год журнала: 2024, Номер 122(1), С. 81 - 112

Опубликована: Июнь 7, 2024

Abstract DNA in bacterial chromosomes is organized into higher‐order structures by DNA‐binding proteins called nucleoid‐associated (NAPs) or chromatin (BCPs). BCPs often bind to near loci transcribed RNA polymerase (RNAP) and can either increase decrease gene expression. To understand the mechanisms which alter transcription, one must consider both steric effects topological forces that arise when deviates from its fully relaxed double‐helical structure. Transcribing RNAP creates negative (−) supercoils upstream positive (+) downstream whenever are unable rotate freely. This supercoiling generates resist forward translocation of through unless constrained relieved topoisomerases. also may enhance stress overall inhibit aid transcription. Here, we review current understanding how RNAP, BCPs, topology interplay control

Язык: Английский

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High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

Опубликована: Фев. 18, 2025

Torsional stress in chromatin plays a fundamental role cellular functions, influencing key processes such as transcription, replication, and organization. Transcription other may generate be regulated by torsional stress. In the genome, interplay of these creates complicated patterns both positive (+) negative (-) torsion. However, challenge generating an accurate torsion map is determining zero-torsion baseline signal, which conflated with accessibility. Here, we introduce high-resolution method based on intercalator trimethylpsoralen (TMP) to address this challenge. We describe establish while preserving state genome S. cerevisiae . This approach enables mapping accessibility cell. Our analysis shows transcription-generated domains consistent twin-supercoiled-domain model transcription suggests for recruiting topoisomerases regulating 3D architecture via cohesin. Significantly, reveal that insulator sequence-specific factors decouple between divergent promoters, whereas spreads promoters lacking factors, suggesting serves regulatory mechanism regions. Although insulators are known gene expression, our finding provides physical explanation how decoupling occur. new potential path forward using TMP measure without confounding contribution chromatin.

Язык: Английский

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Transcriptional and post-transcriptional controls for tuning gene expression in plants

Current Opinion in Plant Biology, Год журнала: 2022, Номер 71, С. 102315 - 102315

Опубликована: Ноя. 30, 2022

Язык: Английский

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Resource-aware construct design in mammalian cells

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июнь 16, 2023

Abstract Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report quantification resource load imposed by different mammalian components and identify construct designs with increased performance reduced footprint. We use these to generate improved synthetic circuits optimise co-expression transfected cassettes, shedding light on how this useful for bioproduction biotherapeutic applications. This work provides scientific community a framework consider demand when designing constructs achieve robust optimised gene expression.

Язык: Английский

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DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Окт. 30, 2023

DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects dynamic equilibrium opposite activities topoisomerases, which are required relax mechanical stresses that inevitably produced during replication gene transcription. Supercoiling affects all scales spatio-temporal organization bacterial DNA, from base pair large scale conformation. Highlighted in vitro vivo 1960s 1970s, respectively, first physical models were proposed concomitantly order predict deformation properties double helix. About fifteen years later, polymer physics demonstrated on larger plectonemic nature tree-like supercoiled DNA. Since then, works have tried establish a better understanding multiple structuring physiological thermodynamic far equilibrium. The purpose this essay address upcoming challenges by thoroughly exploring relevance, predictive capacity, limitations current models, with specific focus structural beyond We discuss more particularly problem conformations, interplay between transcription replication, its role nucleoid formation and, finally, scaling up models. Our primary objective foster increased collaboration physicists biologists. To achieve this, we reduced respective jargon minimum provide some explanatory background material for two communities.

Язык: Английский

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Single-molecule visualization of twin-supercoiled domains generated during transcription

Nucleic Acids Research, Год журнала: 2023, Номер unknown

Опубликована: Дек. 12, 2023

Abstract Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation genetic processes all domains life. It has become common knowledge that, during transcription, DNA-dependent RNA polymerase (RNAP) induces positive ahead it (downstream) negative supercoils its wake (upstream), as rotation RNAP around axis upon tracking helical groove gets constrained due to drag on transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with vitro real-time visualization at single-molecule scale. Upon binding promoter site supercoiled molecule, merges into one large pinned plectoneme residing apex. Transcription by real time demonstrates that up- downstream are generated simultaneously equal portions, agreement model. Experiments carried out presence RNases A H, revealed an additional viscous transcript not necessary for induce supercoils. The latter results contrast current consensus simulations origin twin-supercoiled domains, pointing mechanistic cause underlying supercoil generation transcription.

Язык: Английский

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