Cited by Engineered autonomous dynamic regulation of metabolic flux

Deep-learning-enhanced metal-organic framework e-skin for health monitoring DOI

Xinyi Ke,

Yifan Duan,

Duan Yun-feng

et al.

Device, Journal Year: 2025, Volume and Issue: unknown, P. 100650 - 100650

Published: Jan. 1, 2025

Language: Английский

Citations

Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast DOI

Charlotte Cautereels, Jolien Smets, Peter W. Bircham

et al.

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

Published: Feb. 7, 2024

Abstract Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up (toxic) intermediates requires balanced every pathway gene. However, despite progress metabolic modeling, optimization gene still heavily relies on trial-and-error. Here, we report an approach for vivo, multiplexed G ene E xpression M odification b y L oxPsym-Cr e R ecombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites independently shuffle promoter terminator modules at distinct genomic loci. facilitates creation large strain libraries, which ranges over 120-fold each harbors a unique profile. When applied biosynthetic astaxanthin, industrially relevant antioxidant, single round improved flux doubled production titers. Together, this shows that allows rapid efficient pathways, offering possibilities enhancing performance microbial factories.

Language: Английский

Citations

A New‐Generation Base Editor with an Expanded Editing Window for Microbial Cell Evolution In Vivo Based on CRISPR‒Cas12b Engineering DOI

Wenliang Hao, Wenjing Cui,

Zhongmei Liu

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(22)

Published: April 11, 2024

Abstract Base editors (BEs) are widely used as revolutionary genome manipulation tools for cell evolution. To screen the targeted individuals, it is often necessary to expand editing window ensure highly diverse variant library. However, current BEs suffer from a limited of 5–6 bases, corresponding only 2–3 amino acids. Here, by engineering CRISPR‒Cas12b, study develops dCas12b‐based CRISPRi system, which can efficiently repress gene expression blocking initiation and elongation transcription. Further, based on dCas12b, new‐generation with an expanded established, covering entire protospacer or more. The results smaller steric hindrance compared other Cas proteins. universality new BE successfully validated in Bacillus subtilis Escherichia coli . As proof concept, spectinomycin‐resistant E. strain (BL21) 6.49‐fold increased protein secretion efficiency JM109 obtained using BE. study, tremendously expanding BEs, capacity library exponentially, greatly increasing screening microbial

Language: Английский

Citations

Genetic circuits for metabolic flux optimization DOI

Xianhao Xu, Xueqin Lv,

Xinyu Bi

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(8), P. 791 - 806

Published: March 12, 2024

Language: Английский

Citations

Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics DOI

Brett A. Graver, Namrata Chakravarty, Kevin Solomon

et al.

Trends in biotechnology, Journal Year: 2023, Volume and Issue: 42(1), P. 61 - 73

Published: July 12, 2023

Language: Английский

Citations

Synthetic Genes For Dynamic Regulation Of DNA‐Based Receptors DOI

Daniela Sorrentino, Simona Ranallo, E. Nakamura

et al.

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(17)

Published: March 8, 2024

We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. demonstrate this by engineering three model DNA-based receptors: triplex-forming DNA complex, an ATP-binding aptamer, hairpin strand, whose ability bind their specific can be cotranscriptionally regulated (activated or inhibited) through RNA molecules produced rationally designed genes. The kinetics our sensors genetically generated inputs captured differential equation models, corroborating predictability approach used. This shows that highly programmable controlled with instructions provided dynamic transcriptional systems, illustrating promise context coupling nanotechnology biological signaling.

Language: Английский

Citations

Reshaping Phosphatase Substrate Preference for Controlled Biosynthesis Using a “Design–Build–Test–Learn” Framework DOI

Jiangong Lu,

Xueqin Lv,

Wenwen Yu

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(22)

Published: March 19, 2024

Abstract Biosynthesis is the application of enzymes in microbial cell factories and has emerged as a promising alternative to chemical synthesis. However, natural with limited catalytic performance often need be engineered meet specific needs through time‐consuming trial‐and‐error process. This study presents quantum mechanics (QM)‐incorporated design–build–test–learn (DBTL) framework rationally design phosphatase BT4131, an enzyme ambiguous substrate spectrum involved N ‐acetylglucosamine (GlcNAc) biosynthesis. First, mutant M1 (L129Q) designed using force field‐based methods, resulting 1.4‐fold increase preference ( k cat / K m ) toward GlcNAc‐6‐phosphate (GlcNAc6P). QM calculations indicate that shift caused by 13.59 kcal mol −1 reduction activation energy. Furthermore, iterative computer‐aided conducted stabilize transition state. As result, M4 (I49Q/L129Q/G172L) 9.5‐fold cat‐GlcNAc6P m‐GlcNAc6P 59% decrease cat‐Glc6P m‐Glc6P highly desirable compared wild type GlcNAc‐producing chassis. The GlcNAc titer increases 217.3 g L yield 0.597 (g glucose) 50‐L bioreactor, representing highest reported level. Collectively, this DBTL provides easy yet fascinating approach rational for industrially viable biocatalysts.

Language: Английский

Citations

Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor DOI

Yaokang Wu, Yang Li, Yanfeng Liu

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(8), P. 4739 - 4755

Published: April 3, 2024

Abstract Mutagenesis driving genetic diversity is vital for understanding and engineering biological systems. However, the lack of effective methods to generate in-situ mutagenesis in multiple genomic loci combinatorially limits study complex functions. Here, we design construct MultiduBE, a dCas12a-based multiplexed dual-function base editor, an all-in-one plasmid performing combinatorial mutagenesis. Two synthetic effectors, duBE-1a duBE-2b, are created by amalgamating functionalities cytosine deaminase (from hAPOBEC3A or hAID*Δ ), adenine TadA9), crRNA array processing dCas12a). Furthermore, introducing separator Sp4 minimizes interference array, thereby facilitating both Escherichia coli Bacillus subtilis. Guided corresponding arrays, MultiduBE successfully employed cell physiology reprogramming metabolic regulation. A novel mutation conferring streptomycin resistance has been identified B. subtilis incorporated into mutant strains with antibiotic resistance. Moreover, surfactin riboflavin titers improved 42% 15-fold, respectively, compared control single gene mutation. Overall, provides convenient efficient way perform

Language: Английский

Citations

Recent advances in genome mining and synthetic biology for discovery and biosynthesis of natural products DOI

Mingpeng Wang,

Lei Chen, Zhaojie Zhang

et al.

Critical Reviews in Biotechnology, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 21

Published: Aug. 12, 2024

Natural products have long served as critical raw materials in chemical and pharmaceutical manufacturing, primarily which can provide superior scaffolds or intermediates for drug discovery development. Over the last century, natural contributed to more than a third of therapeutic production. However, traditional methods producing drugs from become less efficient expensive over past few decades. The combined utilization genome mining synthetic biology based on sequencing, bioinformatics tools, big data analytics, genetic engineering, metabolic systems promises counter this trend. Here, we reviewed recent (2020–2023) examples used resolve challenges production products, such variety, poor efficiency, low yield. Additionally, emerging design principles, building strategies its application prospects NPs synthesis also been discussed.

Language: Английский

Citations

Efficient Protein Expression and Biosynthetic Gene Cluster Regulation in Bacillus subtilis Driven by a T7-BOOST System DOI

Yaokang Wu, Yang Li, Yuting Zhang

et al.

ACS Synthetic Biology, Journal Year: 2023, Volume and Issue: 12(11), P. 3328 - 3339

Published: Oct. 27, 2023

Bacillus subtilis is a generally recognized as safe microorganism that widely used for protein expression and chemical production, but has limited number of genetic regulatory components compared with the Gram-negative model Escherichia coli. In this study, two-module plug-and-play T7-based optimized output strategy transcription (T7-BOOST) systems low leakage wide dynamic range was constructed based on inducible promoters Phy-spank PxylA. The first T7 RNA polymerase-driven module seamlessly integrated into genome CRISPR/Cpf1 system, while second control introduced low, medium, high copy plasmids characterization. As proof concept, T7-BOOST were successfully employed whole-cell catalysis production γ-aminobutyric acid (109.8 g/L 98.0% conversion rate), human αS1 casein lactoferrin, regulation exogenous lycopene biosynthetic gene cluster endogenous riboflavin cluster. Overall, system serves stringent, controllable, effective tool regulating in B. subtilis.

Language: Английский

Citations