ReaL-MGE is a tool for enhanced multiplex genome engineering and application to malonyl-CoA anabolism DOI Creative Commons
Wentao Zheng, Yuxuan Wang, Jie Cui

et al.

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

Published: Nov. 12, 2024

The complexities encountered in microbial metabolic engineering continue to elude prediction and design. Unravelling these requires strategies that go beyond conventional genetics. Using multiplex mutagenesis with double stranded (ds) DNA, we extend the repertoire previously pioneered using single strand (ss) oligonucleotides. We present ReaL-MGE (Recombineering Linear CRISPR/Cas9 assisted Multiplex Genome Engineering). enables precise manipulation of numerous large DNA sequences as demonstrated by simultaneous insertion multiple kilobase-scale into E. coli, Schlegelella brevitalea Pseudomonas putida genomes without any off-target errors. applications enhance intracellular malonyl-CoA levels three achieved 26-, 20-, 13.5-fold elevations respectively, thereby promoting target polyketide yields more than an order magnitude. In a further round ReaL-MGE, adapt S. elevation utilizing restricted carbon source (lignocellulose from straw) realize production anti-cancer secondary metabolite, epothilone lignocellulose. dsDNA incorporation lengthy segments can fully encode additional functions. Additionally, utilization PCR generate dsDNAs brings flexible design advantages. presents strategic options engineering. Engineering) species. Here, authors demonstrate its utility enhancing producing valuable compounds like

Language: Английский

CRISPR/Cas13X-assisted programmable and multiplexed translation regulation for controlled biosynthesis DOI Creative Commons
X. Xu, Xueqin Lv, Yanfeng Liu

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(1)

Published: Jan. 7, 2025

Abstract Developing efficient gene regulation tools is essential for optimizing microbial cell factories, but most existing only modulate expression at the transcriptional level. Regulation translational level provides a faster dynamic response, whereas developing programmable, and multiplexed tool remains challenge. Here, we have developed CRISPRi CRISPRa systems based on hfCas13X that can regulate translation in Bacillus subtilis. First, constructed system to catalytically deactivated (dhfCas13X). Second, designed unique mRNA–crRNA pairs construct DiCRISPRa (degradation-inhibited CRISPRa) TsCRISPRa (translation-started systems, which activate downstream by enhancing mRNA stability or initiating translation. In addition, found fusing dhfCas13X with RNA-binding chaperone BHfq significantly improved activation efficiency of (43.2-fold). Finally, demonstrated CRISPR could be used optimize metabolic networks two biotechnologically relevant compounds, riboflavin 2′-fucosyllactose, increasing their titers 3- 1.2-fold, respectively. The here provide new offer ideas construction systems.

Language: Английский

Citations

2
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research DOI Creative Commons
Hui Zhao, Yuan Yang, Shuaiqi Wang

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D621 - D628

Published: Nov. 29, 2022

Abstract Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, microbial investigations. Activity values NPs against specific targets useful discovering targeted therapeutic agents investigating the mechanism plants. Composition/concentration in individual facilitate assessments investigations quality herbs phenotypes microbes. Here, we describe an update NPASS product database previously featured NAR. This includes: (i) new ∼95 000 records composition/concentration ∼1 490 NPs/NP clusters ∼390 species, (ii) extended ∼43 200 ∼7 700 (∼40% ∼32% increase, respectively), (iii) ∼31 600 sources ∼94 400 (∼26% (iv) types ∼440 co-cultured microbes ∼420 engineered microbes, (v) ∼66 without experimental but with estimated profiles from established chemical similarity tool Chemical Checker, (vi) computed drug-likeness properties absorption, distribution, metabolism, excretion toxicity (ADMET) all NPs. version is freely accessible at http://bidd.group/NPASS.

Language: Английский

Citations

43
Microbial recycling of lithium-ion batteries: Challenges and outlook DOI Creative Commons
Joseph Jegan Roy, Norazean Zaiden, Minh Phuong

et al.

Joule, Journal Year: 2023, Volume and Issue: 7(3), P. 450 - 456

Published: Feb. 7, 2023

Language: Английский

Citations

30
Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters DOI Creative Commons
Hanne Put, Hans Gerstmans, Hanne Vande Capelle

et al.

Natural Product Reports, Journal Year: 2024, Volume and Issue: 41(7), P. 1113 - 1151

Published: Jan. 1, 2024

Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that either difficult or impossible cultivate under laboratory conditions, produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms more easily cultured and engineered, larger quantities can be obtained new analogues with potentially improved biological activity other desirable properties generated. Moreover, expression cryptic BGCs in a suitable facilitate identification characterization novel products. Heterologous therefore represents valuable tool for product discovery engineering as it allows study manipulation their pathways controlled setting, enabling innovative applications.

Language: Английский

Citations

12
Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites DOI Creative Commons

Taotao Han,

Guopeng Miao

Molecules, Journal Year: 2024, Volume and Issue: 29(9), P. 2106 - 2106

Published: May 2, 2024

Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest disease problems. Additionally, multi-step demanding nature chemical synthesis adds production costs, limiting widespread application. In vitro metabolic engineering significantly enhanced successful industrial cases. As synthetic biology advances, more research focusing on heterologous using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating performance various types from perspectives yield strategies. It also discusses challenges they face offers insights into future efforts directions.

Language: Английский

Citations

10
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

9
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

9
Engineering Saccharomyces cerevisiae for medical applications DOI Creative Commons
Carla Maneira,

Alexandre Chamas,

Gerald Lackner

et al.

Microbial Cell Factories, Journal Year: 2025, Volume and Issue: 24(1)

Published: Jan. 9, 2025

Abstract Background During the last decades, advancements in synthetic biology opened doors for a profusion of cost-effective, fast, and ecologically friendly medical applications priorly unimaginable. Following trend, genetic engineering baker’s yeast, Saccharomyces cerevisiae , propelled its status from an instrumental ally food industry to therapy prophylaxis aid. Main text In this review, we scrutinize main engineered S. field focusing on use as cell factory pharmaceuticals vaccines, biosensor diagnostic biomimetic assays, live biotherapeutic product smart situ treatment intestinal ailments. An extensive view these fields' academic commercial developments well hindrances is presented. Conclusion Although still faces challenges, development yeast-based often considered success story. The rapid advances strongly support case future where yeasts play important role medicine.

Language: Английский

Citations

1
Engineering oleaginous red yeasts as versatile chassis for the production of olechemicals and valuable compounds: Current advances and perspectives DOI
Guiping Gong, Bo Wu,

Linpei Liu

et al.

Biotechnology Advances, Journal Year: 2024, Volume and Issue: 76, P. 108432 - 108432

Published: Aug. 18, 2024

Language: Английский

Citations

7
Genetic manipulation and tools in myxobacteria for the exploitation of secondary metabolism DOI Creative Commons
Xin‐jing Yue, Duohong Sheng, Zhuo Li

et al.

Engineering Microbiology, Journal Year: 2023, Volume and Issue: 3(2), P. 100075 - 100075

Published: Jan. 20, 2023

Myxobacteria are famous for their capacity social behavior and natural product biosynthesis. The unique sociality of myxobacteria is not only an intriguing scientific topic but also the main limiting factor manipulation. After more than half a century research, series genetic techniques have been developed, rendering these mysterious bacteria manipulable. Here, we review advances in manipulation myxobacteria, with particular focus on exploitation secondary metabolism. We emphasize necessity urgency constructing myxobacterial chassis synthetic biology research untapped

Language: Английский

Citations

16