Biosensors Characterization: Formal methods from the Perspective of Proteome Fractions DOI Creative Commons
Nicolás A. Vaccari, Dahlin Zevallos-Aliaga, Tom H. Peeters

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 1, 2023

Abstract Many studies characterize transcription factors and other regulatory elements to control the expression of heterologous genes in recombinant systems. However, most lack a formal approach analyse parameters context-specific variations these components. This study addresses this gap by establishing convenient methods for characterising circuits. We model bacterial cell as collection small number proteome fractions. Then, we derive fraction over time obtain general theorem describing its change function fraction, which represents specific portion total biosynthesis flux cell. Formal deduction reveals that when reaches maximum, it becomes equivalent fraction. equation enables reliable measurement through direct protein quantification. In addition, experimental data demonstrate linear correlation between production rate growth significant period. suggests constant within window. The fractions estimated from slopes intervals those obtained maximum amount points can both be independently fitted Hill function. case an IPTG biosensor, five cellular contexts, determined method slope produced similar dose-response parameters. Additionally, analysing two more biosensors, mercury cumate detection, effectively applied various systems, generating

Язык: Английский

Coupling of aptamers with reduced graphene oxide for detection of herpes simplex virus 2 protein marker DOI

Olga Antipova,

Mariya Iv. Trukhanova, Marianna V. Kharlamova

и другие.

Fullerenes Nanotubes and Carbon Nanostructures, Год журнала: 2025, Номер unknown, С. 1 - 12

Опубликована: Апрель 3, 2025

Язык: Английский

Процитировано

1

Biosensors Characterisation: Formal methods from the Perspective of Proteome Fractions DOI Creative Commons
Nicolás A. Vaccari, Dahlin Zevallos-Aliaga, Tom H. Peeters

и другие.

Synthetic Biology, Год журнала: 2025, Номер 10(1)

Опубликована: Янв. 1, 2025

Abstract Many studies characterize transcription factors and other regulatory elements to control gene expression in recombinant systems. However, most lack a formal approach analyse the inherent context-specific variations of these components. This study addresses this gap by establishing framework from which convenient methods are inferred circuits. We modelled bacterial cell as collection proteome fractions. Deriving time-dependent fraction, we obtained general theorem that describes its change function specific portion total biosynthesis flux cell. Formal deduction reveals when fraction reaches maximum, it becomes equivalent fraction. equation enables reliable measurement through direct protein quantification. In addition, experimental data demonstrate linear correlation between production rate growth over significant time period. suggests constant within window. For an Isopropyl β- d-1-thiogalactopyranoside (IPTG) biosensor, five cellular contexts, fractions determined maximum method slope produced strikingly similar dose–response parameters independently fit Hill function. Furthermore, analysing two more biosensors, for mercury cumate detection, can be applied effectively various Therefore, concepts presented here provide obtaining parameters, clearly defining interval their validity offering interpreting typical biosensor outputs terms physiology. Graphical Nutrients, transformed action Nutrient Fixators (purple arrow), used at ρ Protein biosynthesis. The is multiplied fR, fC, fH, fQ obtain (black arrows) each ΦR, ΦC, ΦH, ΦQ, respectively. graph Growth versus Proteome Fraction Production Rate, (green lines) observed, equal condition.

Язык: Английский

Процитировано

0

Harnessing Synthetic Biology for Sustainable Industrial Innovation: Advances, Challenges, and Future Direction DOI
Emmanuel Chimeh Ezeako, Barine Innocent Nwiloh,

Malachy Chigozie Odo

и другие.

Biochemical Engineering Journal, Год журнала: 2025, Номер unknown, С. 109777 - 109777

Опубликована: Май 1, 2025

Язык: Английский

Процитировано

0

A generalizable approach for programming protease-responsive conformationally inhibited artificial transcriptional factors DOI Creative Commons
Yinxia Liu, Lingyun Zhao,

James E. Long

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Май 17, 2025

Synthetic genetic circuits that harness programmable protein modules and artificial transcription factors (ATF) to devise event-triggerable cascaded pathways represent an essential class of tools for studying cell biology. Fine-tuning the general structural functionality ATFs is important constructing orthogonal composable transcriptional regulators. Here, we report design a protease-responsive conformationally inhibited system (PRCIS). By intramolecularly linking free DNA-binding domains ATF confined dimerized regions, binding inactivated. The function DNA reinstated upon proteolytic cleavage linkages, activating downstream gene expressions. versatility PRCIS demonstrated through its adaptability various proteases, showcasing high activation ratios specificity. Furthermore, development PRCIS-based triple-orthogonal dual-orthogonal chemical-inducible platforms Boolean logic operations are elaborated in this paper, providing generalizable synthetic

Язык: Английский

Процитировано

0

Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast DOI Creative Commons

Patarasuda Chaisupa,

Md Mahbubur Rahman,

Sherry B. Hildreth

и другие.

ACS Synthetic Biology, Год журнала: 2024, Номер 13(9), С. 2804 - 2819

Опубликована: Авг. 28, 2024

Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, animals. Many microbes synthesize perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), prevalent natural auxin, which influences their ability colonize Understanding biosynthesis in fungi may allow us better control interkingdom relationships microbiomes from agricultural soils human gut. Despite this importance, a biological tool for measuring with high spatial temporal resolution has not been engineered fungi. In study, we present suite genetically encoded, ratiometric, protein-based biosensors designed model yeast

Язык: Английский

Процитировано

1

Biosensor‐Guided Engineering of a Baeyer‐Villiger Monooxygenase for Aliphatic Ester Production DOI Creative Commons
Thaleia Sakoleva,

Florian Vesenmaier,

Lena R Koch

и другие.

ChemBioChem, Год журнала: 2024, Номер 26(1)

Опубликована: Сен. 25, 2024

Abstract Esters are valuable aroma compounds and can be produced enzymatically by Baeyer‐Villiger monooxygenases (BVMOs) from (aliphatic) ketone precursors. However, a genetically encoded biosensor system for the assessment of BVMO activity detection reaction products is missing. In this work, we assembled synthetic enzyme cascade – featuring an esterase, alcohol dehydrogenase, LuxAB in heterologous host Escherichia coli . Target esters BVMO, subsequently cleaved, corresponding oxidized through artificial pathway. Ultimately, aldehyde detected vivo LuxAB, luciferase Photorhabdus luminescens that emits bioluminescence upon oxidation aldehydes to carboxylates. This greatly accelerated screening selection active variants focused library, omitting commonly used low‐throughput chromatographic analysis. Engineered enzymes accepted linear aliphatic ketones such as 2‐undecanone 2‐dodecanone exhibited improved ester formation.

Язык: Английский

Процитировано

1

Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors DOI
Brecht De Paepe, Marjan De Mey

ACS Synthetic Biology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 22, 2024

Since the description of

Язык: Английский

Процитировано

1

Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells DOI
Yuting Wu, Wentao Kong,

Jacqueline Van Stappen

и другие.

Journal of the American Chemical Society, Год журнала: 2024, Номер unknown

Опубликована: Дек. 31, 2024

Genetically encoded fluorescent protein and fluorogenic RNA sensors are indispensable tools for imaging biomolecules in cells. To expand the toolboxes improve generalizability stability of this type sensor, we report herein a genetically DNA aptamer (GEFDA) sensor by linking dimethylindole red with an ATP aptamer. The design enhances fluorescence 4-fold at 650 nm presence ATP. Additionally, upon dimerization, it improves signal-to-noise ratio 2-3 folds. We further integrated into plasmid to create GEFDA sensing live bacterial mammalian This work expanded employing aptamers, which offer enhanced over proteins RNAs, providing novel tool real-time monitoring even broader range small molecular metabolites biological systems.

Язык: Английский

Процитировано

0

Genetically encoded biosensors for the circular plastics bioeconomy DOI Creative Commons
Micaela Chacón, Neil Dixon

Metabolic Engineering Communications, Год журнала: 2024, Номер 19, С. e00255 - e00255

Опубликована: Ноя. 28, 2024

Язык: Английский

Процитировано

0

Biosensors Characterization: Formal methods from the Perspective of Proteome Fractions DOI Creative Commons
Nicolás A. Vaccari, Dahlin Zevallos-Aliaga, Tom H. Peeters

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 1, 2023

Abstract Many studies characterize transcription factors and other regulatory elements to control the expression of heterologous genes in recombinant systems. However, most lack a formal approach analyse parameters context-specific variations these components. This study addresses this gap by establishing convenient methods for characterising circuits. We model bacterial cell as collection small number proteome fractions. Then, we derive fraction over time obtain general theorem describing its change function fraction, which represents specific portion total biosynthesis flux cell. Formal deduction reveals that when reaches maximum, it becomes equivalent fraction. equation enables reliable measurement through direct protein quantification. In addition, experimental data demonstrate linear correlation between production rate growth significant period. suggests constant within window. The fractions estimated from slopes intervals those obtained maximum amount points can both be independently fitted Hill function. case an IPTG biosensor, five cellular contexts, determined method slope produced similar dose-response parameters. Additionally, analysing two more biosensors, mercury cumate detection, effectively applied various systems, generating

Язык: Английский

Процитировано

0