Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants DOI Creative Commons
Sávio Siqueira Ferreira, Mauricio S. Antunes

New Phytologist, Journal Year: 2024, Volume and Issue: 243(2), P. 674 - 687

Published: May 16, 2024

Synthetic biology has the potential to revolutionize biotechnology, public health, and agriculture. Recent studies have shown enormous of plants as chassis for synthetic applications. However, tools precisely manipulate metabolic pathways bioproduction in are still needed. We used bacterial allosteric transcription factors (aTFs) that control gene expression a ligand-specific manner tested their ability repress semi-synthetic promoters plants. also modulation repression activity response specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we designed genetic circuits capable computing Boolean logic operations. Three CouR, FapR, TtgR, achieved c. 95% respective target promoters. For sixfold de-repression could be triggered by inducing its ligand accumulation, showing use biosensor. Moreover, AND, NAND, IMPLY, NIMPLY operations integrate metabolite levels input circuit. showed biosensors can implemented detect metabolites activate circuit follows predefined logic, demonstrating exerting over facilitating natural products.

Language: Английский

DNA synthesis technologies to close the gene writing gap DOI Open Access

Alex Hoose,

Richard Vellacott,

Marko Storch

et al.

Nature Reviews Chemistry, Journal Year: 2023, Volume and Issue: 7(3), P. 144 - 161

Published: Jan. 23, 2023

Language: Английский

Citations

141
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology DOI Creative Commons
Buddhini Ranawaka, Jiyuan An, Michał T. Lorenc

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(9), P. 1558 - 1571

Published: Aug. 10, 2023

Abstract Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness versatility, we have produced high-quality chromosome-level genome assemblies, coupled transcriptome, epigenome, microRNA transposable element datasets, for the ubiquitously used LAB strain related wild accession, QLD. In addition, single nucleotide polymorphism maps been two laboratory strains four accessions. Despite loss of five chromosomes from ancestral tetraploid, expansion intergenic regions, widespread segmental allopolyploidy, advanced diploidization evidence recent bursts Copia pseudovirus (Copia) mobility not seen in other genomes, subgenomes N. show large regions synteny across Solanaceae. QLD many genetic, metabolic phenotypic differences, including disparate RNA interference responses, but are highly interfertile amenable to editing both transient stable transformation. The LAB/QLD combination has potential be as useful Columbia-0/Landsberg errecta partnership, utilized early pioneering days Arabidopsis genomics today.

Language: Английский

Citations

52
A century of studying plant secondary metabolism—From “what?” to “where, how, and why?” DOI Creative Commons
Richard A. Dixon, Alexandra J. Dickinson

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 48 - 66

Published: Jan. 2, 2024

Abstract Over the past century, early advances in understanding identity of chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why synthesized first place. Many small specific kingdom been termed secondary metabolites, despite fact can play primary essential roles structure, development, response environment. The 100 yr witnessed elucidation function, localization, biosynthesis selected metabolites. Nevertheless, many mysteries remain about vast diversity produced by plants their biology. From work characterizing unpurified extracts, modern integration ‘omics technology discover genes metabolite perception, research (bio)chemistry has knowledge with substantial benefits for society, including human medicine agricultural biotechnology. Here, we review history this offer suggestions future areas exploration. We also highlight some recently developed technologies leading ongoing advances.

Language: Английский

Citations

37
Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit DOI Creative Commons
Vayu Maini Rekdal, Casper R. B. van der Luijt, Yan Chen

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 14, 2024

Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing nutritional value, sensory appeal, and scalability fungal foods, tools demonstrated use cases bioengineered production by edible strains lacking. Here, we develop modular synthetic biology toolkit Aspergillus oryzae, an fungus used fermented protein production, meat alternatives. Our includes CRISPR-Cas9 method gene integration, neutral loci, tunable promoters. We elevate intracellular levels nutraceutical ergothioneine flavor-and color molecule heme biomass. The strain overproducing is red readily formulated into imitation patties with minimal processing. These findings highlight enhance foods provide useful applications beyond.

Language: Английский

Citations

20
Choreographing root architecture and rhizosphere interactions through synthetic biology DOI Creative Commons
Carin J. Ragland, Kevin Shih, José R. Dinneny

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 14, 2024

Abstract Climate change is driving extreme changes to the environment, posing substantial threats global food security and bioenergy. Given direct role of plant roots in mediating plant-environment interactions, engineering form function root systems their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control gene expression microbial for years a surge advances has heralded extension this approach multicellular species. Targeting tools affect structure, exudation, microbe activity on surfaces provide multiple strategies advancement climate-ready crops.

Language: Английский

Citations

18
Predictive genetic circuit design for phenotype reprogramming in plants DOI Creative Commons
Ci Kong, Yin Yang, Tiancong Qi

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 16, 2025

Plants, with intricate molecular networks for environmental adaptation, offer groundbreaking potential reprogramming predictive genetic circuits. However, realizing this goal is challenging due to the long cultivation cycle of plants, as well lack reproducible, quantitative methods and well-characterized parts. Here, we establish a rapid (~10 days), quantitative, framework in plants. A group orthogonal sensors, modular synthetic promoters, NOT gates are constructed quantitatively characterized. model developed predict designed circuits' behavior accurately. Our versatile robust framework, validated by constructing 21 two-input circuits high prediction accuracy (R2 = 0.81), enables multi-state phenotype control both Arabidopsis thaliana Nicotiana benthamiana response chemical inducers. study achieves predictable design application offering valuable tools engineering plant traits biotechnology agriculture. The gene plants has been lagging behind other organisms. authors report designing reprograming expression hypersensitive response.

Language: Английский

Citations

2
The complexities of proanthocyanidin biosynthesis and its regulation in plants DOI Creative Commons
Keji Yu,

Yushuang Song,

Jinxing Lin

et al.

Plant Communications, Journal Year: 2022, Volume and Issue: 4(2), P. 100498 - 100498

Published: Nov. 26, 2022

Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits human health, bitterness astringency food products. They also potential targets for carbon sequestration climate mitigation. In recent years, from model species commercial crops, research has moved closer elucidating the flux control channeling, subunit biosynthesis polymerization, transport mechanisms, regulatory networks involved in plant PA metabolism. This review extends conventional understanding with findings provide new insights address lingering questions focus strategies manipulating traits plants.

Language: Английский

Citations

56
Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants DOI Creative Commons

Erum Yasmeen,

Jin Wang, Muhammad Riaz

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: 4(4), P. 100558 - 100558

Published: Feb. 9, 2023

With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design construct biological parts, modules, circuits, even whole systems. To overcome limitations native promoters in controlling gene expression, promoter aims synthesize short, inducible, conditionally controlled coordinate expression multiple genes diverse plant metabolic signaling pathways. Synthetic are versatile can drive accurately with smart responses; they show potential for enhancing desirable traits crops, thereby improving crop yield, nutritional quality, food security. This review first illustrates importance synthetic promoters, then introduces architecture thoroughly summarizes advances construction. Restrictions future applications such improvement also discussed.

Language: Английский

Citations

34
Customizing cellular signal processing by synthetic multi-level regulatory circuits DOI Creative Commons
Yuanli Gao, Lei Wang, Baojun Wang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Dec. 18, 2023

As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic with unprecedented complexity have been implemented over past decade. These mechanisms, such as transcription translation control, could integrated into hybrid termed "multi-level circuits". The multi-level circuit design will tremendously benefit current paradigm, from modifying basic dynamics facilitating real-world applications, unleashing our capabilities customize cellular address global challenges through biology.

Language: Английский

Citations

29
Synthetic biology for plant genetic engineering and molecular farming DOI
Yunqing Wang, Gözde S. Demirer

Trends in biotechnology, Journal Year: 2023, Volume and Issue: 41(9), P. 1182 - 1198

Published: April 1, 2023

Language: Английский

Citations

24