1
|
Kaushal M, Upton DJ, Gupta JK, Wood AJ, Srivastava S. Reconstruction of a genome-scale metabolic model and in-silico flux analysis of Aspergillus tubingensis: a non-mycotoxinogenic citric acid-producing fungus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:70. [PMID: 38807234 PMCID: PMC11134751 DOI: 10.1186/s13068-024-02506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/20/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Aspergillus tubingensis is a citric acid-producing fungus that can utilize sugars in hydrolysate of lignocellulosic biomass such as sugarcane bagasse and, unlike A. niger, does not produce mycotoxins. To date, no attempt has been made to model its metabolism at genome scale. RESULTS Here, we utilized the whole-genome sequence (34.96 Mb length) and the measured biomass composition to reconstruct a genome-scale metabolic model (GSMM) of A. tubingensis DJU120 strain. The model, named iMK1652, consists of 1652 genes, 1657 metabolites and 2039 reactions distributed over four cellular compartments. The model has been extensively curated manually. This included removal of dead-end metabolites and generic reactions, addition of secondary metabolite pathways and several transporters. Several mycotoxin synthesis pathways were either absent or incomplete in the genome, providing a genomic basis for the non-toxinogenic nature of this species. The model was further refined based on the experimental phenotypic microarray (Biolog) data. The model closely captured DJU120 fermentative data on glucose, xylose, and phosphate consumption, as well as citric acid and biomass production, showing its applicability to capture citric acid fermentation of lignocellulosic biomass hydrolysate. CONCLUSIONS The model offers a framework to conduct metabolic systems biology investigations and can act as a scaffold for integrative modelling of A. tubingensis.
Collapse
Affiliation(s)
- Mehak Kaushal
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Perfect Day India Pvt. Ltd., Bangalore, India
| | - Daniel J Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jai K Gupta
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
- JKG: Zero Cow Factory, Surat, India
| | - A Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
| | - Shireesh Srivastava
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
2
|
Xu J, Cheng S, Zhang R, Cai F, Zhu Z, Cao J, Wang J, Yu Q. Study on the mechanism of sodium ion inhibiting citric acid fermentation in Aspergillus niger. BIORESOURCE TECHNOLOGY 2024; 394:130245. [PMID: 38145764 DOI: 10.1016/j.biortech.2023.130245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Excessive sodium significantly inhibits citric acid fermentation by Aspergillus niger during the recycling of citric acid wastewater. This study aimed to elucidate the inhibition mechanism at the interface of physiology and transcriptomics. The results showed that excessive sodium caused a 22.3 % increase in oxalic acid secretion and a 147.6 % increase in H+-ATPase activity at the 4 h fermentation compared to the control. Meanwhile, a 13.1 % reduction in energy charge level and a 15.2 % decline in NADH content were found, which implied the effects on carbon metabolism and redox balance. In addition, transcriptomic analysis revealed that excessive sodium altered the gene expression profiles related to ATPase, hydrolase, and oxidoreductase, as well as pathways like glyoxylate metabolism, and transmembrane transport. These findings gained insights into the metabolic regulation of A. niger response to environmental stress and provided theoretical guidance for the construction of sodium-tolerant A. niger for industrial application.
Collapse
Affiliation(s)
- Jian Xu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Sulian Cheng
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Ruijing Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Fengjiao Cai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Zhengjun Zhu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Jinghua Cao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Jiangbo Wang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China
| | - Qi Yu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, 28 Nanli Road, Wuhan 430068, China.
| |
Collapse
|
3
|
Unnikrishnan BV, Binitha NK. Positive effect of inoculation with an Aspergillus strain on phosphorus and iron nutrition plus volatile organic compounds in rice. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01129-4. [PMID: 38200388 DOI: 10.1007/s12223-024-01129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
We explored the potential of a fungal strain Aspergillus costaricensis KS1 for modulating growth and nutrient mobilization in rice. At laboratory conditions, there was a decline in pH of the medium on inoculation with the strain and the production of citric acid was observed under broth conditions. Similarly, there was higher solubilization of tricalcium phosphate and siderophore production in liquid medium on inoculation with the strain. The effect of inoculation of KS1 was studied in rice and higher growth and yield were observed on inoculation compared to control. The content of phosphorus and iron in stem and roots of KS1 inoculated plants was higher in comparison with uninoculated control. There was also increased availability of phosphorus and iron content in soil grown with KS1 inoculated plants. In addition, inoculation with strain resulted in a higher content of volatile organic compounds such as linoleic acid, linolenic acid, and ethyl isoallocholate in stem of rice. A. costaricensis KS1 can be used for improving phosphorus and iron nutrition and impart tolerance against stresses in rice.
Collapse
Affiliation(s)
| | - Nadayi Karayi Binitha
- Department of Soil Science and Agricultural Chemistry, College of Agriculture, Kerala Agricultural University, Kasaragod, Kerala, India
| |
Collapse
|
4
|
Han Y, Tafur Rangel A, Pomraning KR, Kerkhoven EJ, Kim J. Advances in genome-scale metabolic models of industrially important fungi. Curr Opin Biotechnol 2023; 84:103005. [PMID: 37797483 DOI: 10.1016/j.copbio.2023.103005] [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: 08/01/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Many fungal species have been used industrially for production of biofuels and bioproducts. Developing strains with better performance in biomanufacturing contexts requires a systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated for several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. Here, we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test-learn cycles, ultimately advancing the field of fungal biomanufacturing.
Collapse
Affiliation(s)
- Yichao Han
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Albert Tafur Rangel
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kyle R Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Joonhoon Kim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Joint BioEnergy Institute, Department of Energy, Emeryville, CA, USA.
| |
Collapse
|
5
|
Zhou S, Ding N, Han R, Deng Y. Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories. BIORESOURCE TECHNOLOGY 2023; 379:128986. [PMID: 37001700 DOI: 10.1016/j.biortech.2023.128986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.
Collapse
Affiliation(s)
- Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Nana Ding
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
6
|
Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022; 123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.
Collapse
Affiliation(s)
- Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aashutosh Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hongxiang Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
7
|
Liu D, Xu Z, Li J, Liu Q, Yuan Q, Guo Y, Ma H, Tian C. Reconstruction and analysis of genome-scale metabolic model for thermophilic fungus Myceliophthora thermophila. Biotechnol Bioeng 2022; 119:1926-1937. [PMID: 35257374 DOI: 10.1002/bit.28080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 03/03/2022] [Indexed: 11/11/2022]
Abstract
Myceliophthora thermophila, a thermophilic fungus that can degrade and utilize all major polysaccharides in plant biomass, has great potential in biotechnological industries. Here, the first manually curated genome-scale metabolic model iDL1450 for M. thermophila was reconstructed using an auto-generating pipeline with thorough manual curation. The model contains 1450 genes, 2592 reactions and 1784 unique metabolites. High accuracy was shown in predictions related to carbon and nitrogen source utilization based on data obtained from Biolog experiments. Besides, metabolism profiles were analyzed using iDL1450 integrated with transcriptomics data of M. thermophila at various growth temperatures. The refined model provides new insights into thermophilic fungi metabolism and sheds light on model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zixiang Xu
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| |
Collapse
|
8
|
Upton DJ, Kaushal M, Whitehead C, Faas L, Gomez LD, McQueen-Mason SJ, Srivastava S, Wood AJ. Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:4. [PMID: 35418297 PMCID: PMC8756645 DOI: 10.1186/s13068-021-02099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Citric acid is typically produced industrially by Aspergillus niger-mediated fermentation of a sucrose-based feedstock, such as molasses. The fungus Aspergillus niger has the potential to utilise lignocellulosic biomass, such as bagasse, for industrial-scale citric acid production, but realising this potential requires strain optimisation. Systems biology can accelerate strain engineering by systematic target identification, facilitated by methods for the integration of omics data into a high-quality metabolic model. In this work, we perform transcriptomic analysis to determine the temporal expression changes during fermentation of bagasse hydrolysate and develop an evolutionary algorithm to integrate the transcriptomic data with the available metabolic model to identify potential targets for strain engineering. RESULTS The novel integrated procedure matures our understanding of suboptimal citric acid production and reveals potential targets for strain engineering, including targets consistent with the literature such as the up-regulation of citrate export and pyruvate carboxylase as well as novel targets such as the down-regulation of inorganic diphosphatase. CONCLUSIONS In this study, we demonstrate the production of citric acid from lignocellulosic hydrolysate and show how transcriptomic data across multiple timepoints can be coupled with evolutionary and metabolic modelling to identify potential targets for further engineering to maximise productivity from a chosen feedstock. The in silico strategies employed in this study can be applied to other biotechnological goals, assisting efforts to harness the potential of microorganisms for bio-based production of valuable chemicals.
Collapse
Affiliation(s)
- Daniel J Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
| | - Mehak Kaushal
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Caragh Whitehead
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Laura Faas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Leonardo D Gomez
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Shireesh Srivastava
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - A Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| |
Collapse
|
9
|
Wei Z, Xu Y, Xu Q, Cao W, Huang H, Liu H. Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects. Front Bioeng Biotechnol 2021; 9:765685. [PMID: 34660563 PMCID: PMC8511312 DOI: 10.3389/fbioe.2021.765685] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Malic acid, a four-carbon dicarboxylic acid, is widely used in the food, chemical and medical industries. As an intermediate of the TCA cycle, malic acid is one of the most promising building block chemicals that can be produced from renewable sources. To date, chemical synthesis or enzymatic conversion of petrochemical feedstocks are still the dominant mode for malic acid production. However, with increasing concerns surrounding environmental issues in recent years, microbial fermentation for the production of L-malic acid was extensively explored as an eco-friendly production process. The rapid development of genetic engineering has resulted in some promising strains suitable for large-scale bio-based production of malic acid. This review offers a comprehensive overview of the most recent developments, including a spectrum of wild-type, mutant, laboratory-evolved and metabolically engineered microorganisms for malic acid production. The technological progress in the fermentative production of malic acid is presented. Metabolic engineering strategies for malic acid production in various microorganisms are particularly reviewed. Biosynthetic pathways, transport of malic acid, elimination of byproducts and enhancement of metabolic fluxes are discussed and compared as strategies for improving malic acid production, thus providing insights into the current state of malic acid production, as well as further research directions for more efficient and economical microbial malic acid production.
Collapse
Affiliation(s)
- Zhen Wei
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yongxue Xu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, China
| |
Collapse
|
10
|
Williams T, Parker D, Taubman B. Characterization of Unmalted Barley Treated with Aspergillus oryzae. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1978045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Tom Williams
- A.R. Smith Department of Chemistry and Fermentation Sciences, Appalachian State University, Boone, NC, U.S.A
| | - Daniel Parker
- A.R. Smith Department of Chemistry and Fermentation Sciences, Appalachian State University, Boone, NC, U.S.A
| | - Brett Taubman
- A.R. Smith Department of Chemistry and Fermentation Sciences, Appalachian State University, Boone, NC, U.S.A
| |
Collapse
|
11
|
Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.
Collapse
|
12
|
Adeoye AO, Lateef A. Biotechnological valorization of cashew apple juice for the production of citric acid by a local strain of Aspergillus niger LCFS 5. JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2021; 19:137. [PMID: 34533689 PMCID: PMC8448800 DOI: 10.1186/s43141-021-00232-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/21/2021] [Indexed: 01/22/2023]
Abstract
Background This work investigates the production of citric acid from cashew apple juice, an abundant waste in the processing of cashew, using a local strain of Aspergillus niger and the application of the citric acid as a coagulant for the production of soy cheese. Fungal isolates were obtained from a cashew plantation in Ogbomoso, Nigeria, using potato dextrose agar. Further screening was undertaken to determine the qualitative strength of acid production by the fungi on Czapek-Dox agar supplemented with bromocresol green, with the development of yellow zone taken as an indication of citric acid production. Thereafter, the best producing strain was cultivated in a cashew apple juice medium. Results Out of 150 fungal isolates generated from the cashew plantation, 92 (61.3%), 44 (29.3%) and 14 (9.3%) were obtained from cashew fruits, soil and cashew tree surfaces, respectively. Different strains of fungi isolated include Aspergillus niger, A. flavus, A. foetidus, A. heteromorphus, A. nidulans and A. viridinutans. The isolates produced yellow zonation of 0.4–5.5 cm on modified Czapek-Dox agar; the highest was observed for a strain of A. niger LCFS 5, which was identified using molecular tools. In the formulated cashew apple juice medium, the citric acid yield of LCFS 5 ranged 16.0–92.8 g/l with the peak obtained on the 10th day of fermentation. The citric acid produced was recovered using the double precipitation method with Ca(OH)2 and H2SO4 having ≈ 70% purity of citric acid on HPLC. The citric acid acted as a coagulant to produce soy cheese with 66.67% acceptability by panelists. Conclusion This work has extended the frontiers of valorization of cashew waste by a strain of A. niger to produce citric acid in high yield, with potential application in food industries.
Collapse
Affiliation(s)
- Adekunle Olusegun Adeoye
- Department of Food Science, Ladoke Akintola University of Technology, PMB, 4000, Ogbomoso, Nigeria
| | - Agbaje Lateef
- Laboratory of Industrial Microbiology and Nanobiotechnology, Department of Pure and Applied Biology, Ladoke Akintola University of Technology, PMB, 4000, Ogbomoso, Nigeria.
| |
Collapse
|
13
|
Zhou J, Zhuang Y, Xia J. Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions. Microb Cell Fact 2021; 20:125. [PMID: 34193117 PMCID: PMC8247156 DOI: 10.1186/s12934-021-01614-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level. Results Based on the basic GSMM model iHL1210 of Aspergillus niger, we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of A. niger by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$k_{{cat}}$$\end{document}kcat values, predicting the differential expression of enzymes under different growth conditions. Conclusions This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with A. niger. Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of A. niger by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for A. niger, the enzyme-constrained GSMM model will show greater application space on the system level. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01614-2.
Collapse
Affiliation(s)
- Jingru Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China.
| |
Collapse
|