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Recent Advances in Systems Metabolic Engineering Strategies

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 9997

Special Issue Editor


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Guest Editor
Synthetic Biology and Enzyme Engineering Laboratory, Department of Chemical and Biological Engineering (BK21 four), Korea University, Seoul 02481, Republic of Korea
Interests: synthetic biology; enzyme engineering; metabolic engineering; natural products; microbiome engineering

Special Issue Information

Dear Colleagues,

As a result of the ongoing climate crisis, there is growing interest in producing industrially important chemicals and materials from non-edible renewable resources or carbon dioxide instead of relying on traditional petrochemical refinery processes. Systems metabolic engineering, which integrates traditional metabolic engineering principles with modern technologies including synthetic biology, evolutionary engineering, and systems biology, has been playing a crucial role in constructing efficient microbial cell factories capable of industrially producing chemicals and materials. The field is rapidly advancing with the emergence of cutting-edge computational techniques, including genome-scale metabolic modeling, artificial-intelligence-based strain design, and computational enzyme design.

This Special Issue focuses on the recent tools and strategies for systems metabolic engineering. Original articles with significant advancements in the field and review papers that provide useful insights are both welcome. Potential topics include, but are not limited to, omics analysis, enzyme evolution, in silico pathway prediction and design, genome engineering, genome-scale metabolic modelling, natural-product biosynthesis, and fermentation techniques.

Dr. Dongsoo Yang
Guest Editor

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Keywords

  • systems metabolic engineering
  • synthetic biology
  • genome-scale metabolic modeling
  • microbial cell factory
  • enzyme engineering
  • metabolic pathway design

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Published Papers (3 papers)

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Research

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21 pages, 5974 KiB  
Article
The Construction of an Environmentally Friendly Super-Secreting Strain of Bacillus subtilis through Systematic Modulation of Its Secretory Pathway Using the CRISPR-Cas9 System
by Jordi Ferrando, David Miñana-Galbis and Pere Picart
Int. J. Mol. Sci. 2024, 25(13), 6957; https://doi.org/10.3390/ijms25136957 - 25 Jun 2024
Viewed by 1198
Abstract
Achieving commercially significant yields of recombinant proteins in Bacillus subtilis requires the optimization of its protein production pathway, including transcription, translation, folding, and secretion. Therefore, in this study, our aim was to maximize the secretion of a reporter α-amylase by overcoming potential bottlenecks [...] Read more.
Achieving commercially significant yields of recombinant proteins in Bacillus subtilis requires the optimization of its protein production pathway, including transcription, translation, folding, and secretion. Therefore, in this study, our aim was to maximize the secretion of a reporter α-amylase by overcoming potential bottlenecks within the secretion process one by one, using a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system. The strength of single and tandem promoters was evaluated by measuring the relative α-amylase activity of AmyQ integrated into the B. subtilis chromosome. Once a suitable promoter was selected, the expression levels of amyQ were upregulated through the iterative integration of up to six gene copies, thus boosting the α-amylase activity 20.9-fold in comparison with the strain harboring a single amyQ gene copy. Next, α-amylase secretion was further improved to a 26.4-fold increase through the overexpression of the extracellular chaperone PrsA and the signal peptide peptidase SppA. When the final expression strain was cultivated in a 3 L fermentor for 90 h, the AmyQ production was enhanced 57.9-fold. The proposed strategy allows for the development of robust marker-free plasmid-less super-secreting B. subtilis strains with industrial relevance. Full article
(This article belongs to the Special Issue Recent Advances in Systems Metabolic Engineering Strategies)
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Review

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25 pages, 1514 KiB  
Review
Biotechnological Plastic Degradation and Valorization Using Systems Metabolic Engineering
by Ga Hyun Lee, Do-Wook Kim, Yun Hui Jin, Sang Min Kim, Eui Seok Lim, Min Ji Cha, Ja Kyong Ko, Gyeongtaek Gong, Sun-Mi Lee, Youngsoon Um, Sung Ok Han and Jung Ho Ahn
Int. J. Mol. Sci. 2023, 24(20), 15181; https://doi.org/10.3390/ijms242015181 - 14 Oct 2023
Cited by 7 | Viewed by 4988
Abstract
Various kinds of plastics have been developed over the past century, vastly improving the quality of life. However, the indiscriminate production and irresponsible management of plastics have led to the accumulation of plastic waste, emerging as a pressing environmental concern. To establish a [...] Read more.
Various kinds of plastics have been developed over the past century, vastly improving the quality of life. However, the indiscriminate production and irresponsible management of plastics have led to the accumulation of plastic waste, emerging as a pressing environmental concern. To establish a clean and sustainable plastic economy, plastic recycling becomes imperative to mitigate resource depletion and replace non-eco-friendly processes, such as incineration. Although chemical and mechanical recycling technologies exist, the prevalence of composite plastics in product manufacturing complicates recycling efforts. In recent years, the biodegradation of plastics using enzymes and microorganisms has been reported, opening a new possibility for biotechnological plastic degradation and bio-upcycling. This review provides an overview of microbial strains capable of degrading various plastics, highlighting key enzymes and their role. In addition, recent advances in plastic waste valorization technology based on systems metabolic engineering are explored in detail. Finally, future perspectives on systems metabolic engineering strategies to develop a circular plastic bioeconomy are discussed. Full article
(This article belongs to the Special Issue Recent Advances in Systems Metabolic Engineering Strategies)
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12 pages, 1080 KiB  
Review
Metabolic Engineering and Synthetic Biology Approaches for the Heterologous Production of Aromatic Polyketides
by Dongsoo Yang, Hyunmin Eun and Cindy Pricilia Surya Prabowo
Int. J. Mol. Sci. 2023, 24(10), 8923; https://doi.org/10.3390/ijms24108923 - 18 May 2023
Cited by 5 | Viewed by 3068
Abstract
Polyketides are a diverse set of natural products with versatile applications as pharmaceuticals, nutraceuticals, and cosmetics, to name a few. Of several types of polyketides, aromatic polyketides comprising type II and III polyketides contain many chemicals important for human health such as antibiotics [...] Read more.
Polyketides are a diverse set of natural products with versatile applications as pharmaceuticals, nutraceuticals, and cosmetics, to name a few. Of several types of polyketides, aromatic polyketides comprising type II and III polyketides contain many chemicals important for human health such as antibiotics and anticancer agents. Most aromatic polyketides are produced from soil bacteria or plants, which are difficult to engineer and grow slowly in industrial settings. To this end, metabolic engineering and synthetic biology have been employed to efficiently engineer heterologous model microorganisms for enhanced production of important aromatic polyketides. In this review, we discuss the recent advancement in metabolic engineering and synthetic biology strategies for the production of type II and type III polyketides in model microorganisms. Future challenges and prospects of aromatic polyketide biosynthesis by synthetic biology and enzyme engineering approaches are also discussed. Full article
(This article belongs to the Special Issue Recent Advances in Systems Metabolic Engineering Strategies)
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