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Chu LL, Tran CTB, Pham DTK, Nguyen HTA, Nguyen MH, Pham NM, Nguyen ATV, Phan DT, Do HM, Nguyen QH. Metabolic Engineering of Corynebacterium glutamicum for the Production of Flavonoids and Stilbenoids. Molecules 2024; 29:2252. [PMID: 38792114 PMCID: PMC11123965 DOI: 10.3390/molecules29102252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Flavonoids and stilbenoids, crucial secondary metabolites abundant in plants and fungi, display diverse biological and pharmaceutical activities, including potent antioxidant, anti-inflammatory, and antimicrobial effects. However, conventional production methods, such as chemical synthesis and plant extraction, face challenges in sustainability and yield. Hence, there is a notable shift towards biological production using microorganisms like Escherichia coli and yeast. Yet, the drawbacks of using E. coli and yeast as hosts for these compounds persist. For instance, yeast's complex glycosylation profile can lead to intricate protein production scenarios, including hyperglycosylation issues. Consequently, Corynebacterium glutamicum emerges as a promising alternative, given its adaptability and recent advances in metabolic engineering. Although extensively used in biotechnological applications, the potential production of flavonoid and stilbenoid in engineered C. glutamicum remains largely untapped compared to E. coli. This review explores the potential of metabolic engineering in C. glutamicum for biosynthesis, highlighting its versatility as a cell factory and assessing optimization strategies for these pathways. Additionally, various metabolic engineering methods, including genomic editing and biosensors, and cofactor regeneration are evaluated, with a focus on C. glutamicum. Through comprehensive discussion, the review offers insights into future perspectives in production, aiding researchers and industry professionals in the field.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi 12116, Vietnam
| | - Chau T. Bang Tran
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
| | - Duyen T. Kieu Pham
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
| | - Hoa T. An Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
| | - Mi Ha Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
| | - Nhung Mai Pham
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi 12116, Vietnam
| | - Anh T. Van Nguyen
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi 12116, Vietnam
| | - Dung T. Phan
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
| | - Ha Minh Do
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam
| | - Quang Huy Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam (Q.H.N.)
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, Hanoi (VNU), 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam
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Chu PH, Jenol MA, Phang LY, Ibrahim MF, Purkan P, Hadi S, Abd-Aziz S. Innovative approaches for amino acid production via consolidated bioprocessing of agricultural biomass. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33303-33324. [PMID: 38710845 DOI: 10.1007/s11356-024-33534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/27/2024] [Indexed: 05/08/2024]
Abstract
Agricultural plantations in Indonesia and Malaysia yield substantial waste, necessitating proper disposal to address environmental concerns. Yet, these wastes, rich in starch and lignocellulosic content, offer an opportunity for value-added product development, particularly amino acid production. Traditional methods often rely on costly commercial enzymes to convert biomass into fermentable sugars for amino acid production. An alternative, consolidated bioprocessing, enables the direct conversion of agricultural biomass into amino acids using selected microorganisms. This review provides a comprehensive assessment of the potential of agricultural biomass in Indonesia and Malaysia for amino acid production through consolidated bioprocessing. It explores suitable microorganisms and presents a case study on using Bacillus subtilis ATCC 6051 to produce 9.56 mg/mL of amino acids directly from pineapple plant stems. These findings contribute to the advancement of sustainable amino acid production methods using agricultural biomass especially in Indonesia and Malaysia through consolidated bioprocessing, reducing waste and enhancing environmental sustainability.
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Affiliation(s)
- Pei-Hsia Chu
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Azwan Jenol
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Lai-Yee Phang
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohamad Faizal Ibrahim
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Purkan Purkan
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - Sofijan Hadi
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - Suraini Abd-Aziz
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia.
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Yin L, Xi D, Shen Y, Ding N, Shao Q, Qian Y, Fang Y. Rewiring Metabolic Flux in Corynebacterium glutamicum Using a CRISPR/dCpf1-Based Bifunctional Regulation System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3077-3087. [PMID: 38303604 DOI: 10.1021/acs.jafc.3c08529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Corynebacterium glutamicum, a microorganism classified as generally recognized as safe for use in the industrial production of food raw materials and additives, has encountered challenges in achieving widespread adoption and popularization as microbial cell factories. These obstacles arise from the intricate nature of manipulating metabolic flux through conventional methods, such as gene knockout and enzyme overexpression. To address this challenge, we developed a CRISPR/dCpf1-based bifunctional regulation system to bidirectionally regulate the expression of multiple genes in C. glutamicum. Specifically, through fusing various transcription factors to the C-terminus of dCpf1, the resulting dCpf1-SoxS exhibited both CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) capabilities in C. glutamicum by altering the binding sites of crRNAs. The bifunctional regulation system was used to fine-tune metabolic flux from shikimic acid (SA) and l-serine biosynthesis, resulting in 27-fold and 10-fold increases in SA and l-serine production, respectively, compared to the original strain. These findings highlight the potential of the CRISPR/dCpf1-based bifunctional regulation system in effectively enhancing the yield of target products in C. glutamicum.
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Affiliation(s)
- Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Dandan Xi
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yuefeng Shen
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Nana Ding
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Qingsong Shao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Yongchang Qian
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yu Fang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
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Ferrer-Miralles N, Garcia-Fruitós E. Heterologous Expression of Difficult to Produce Proteins in Bacterial Systems. Int J Mol Sci 2024; 25:822. [PMID: 38255896 PMCID: PMC10815505 DOI: 10.3390/ijms25020822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Proteins play a crucial role in maintaining homeostasis, providing structure, and enabling various functions in biological systems [...].
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Affiliation(s)
- Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193 Bellaterra, Spain;
- Department of Genetics and Microbiology, Autonomous University of Barcelona, 08193 Bellaterra, Spain
- Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Elena Garcia-Fruitós
- Ruminant Production Group, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08140 Caldes de Montbui, Spain
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Roslan MAM, Omar MN, Sharif NAM, Raston NHA, Arzmi MH, Neoh HM, Ramzi AB. Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment. NPJ Biofilms Microbiomes 2023; 9:95. [PMID: 38065982 PMCID: PMC10709320 DOI: 10.1038/s41522-023-00463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.
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Affiliation(s)
| | - Mohd Norfikri Omar
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Nur Azlina Mohd Sharif
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Nurul Hanun Ahmad Raston
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd Hafiz Arzmi
- Department of Fundamental Dental & Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia
- Melbourne Dental School, The University of Melbourne, 3053, Melbourne, Victoria, Australia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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Zhang L, Lin Y, Yi X, Huang W, Hu Q, Zhang Z, Wu F, Ye JW, Chen GQ. Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution. Metab Eng 2023; 79:146-158. [PMID: 37543135 DOI: 10.1016/j.ymben.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023]
Abstract
Halophilic Halomonas bluephagenesis has been engineered to produce various added-value bio-compounds with reduced costs. However, the salt-stress regulatory mechanism remained unclear. H. bluephagenesis was randomly mutated to obtain low-salt growing mutants via atmospheric and room temperature plasma (ARTP). The resulted H. bluephagenesis TDH4A1B5 was constructed with the chromosomal integration of polyhydroxyalkanoates (PHA) synthesis operon phaCAB and deletion of phaP1 gene encoding PHA synthesis associated protein phasin, forming H. bluephagenesis TDH4A1B5P, which led to increased production of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-4-hydrobutyrate) (P34HB) by over 1.4-fold. H. bluephagenesis TDH4A1B5P also enhanced production of ectoine and threonine by 50% and 77%, respectively. A total 101 genes related to salinity tolerance was identified and verified via comparative genomic analysis among four ARTP mutated H. bluephagenesis strains. Recombinant H. bluephagenesis TDH4A1B5P was further engineered for PHA production utilizing sodium acetate or gluconate as sole carbon source. Over 33% cost reduction of PHA production could be achieved using recombinant H. bluephagenesis TDH4A1B5P. This study successfully developed a low-salt tolerant chassis H. bluephagenesis TDH4A1B5P and revealed salt-stress related genes of halophilic host strains.
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Affiliation(s)
- Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wuzhe Huang
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, Beijing, 101309, China
| | - Qitiao Hu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongnan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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