1
|
Wang S, Liu Y, Guo H, Meng Y, Xiong W, Liu R, Yang C. Establishment of low-cost production platforms of polyhydroxyalkanoate bioplastics from Halomonas cupida J9. Biotechnol Bioeng 2024; 121:2106-2120. [PMID: 38587130 DOI: 10.1002/bit.28694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 04/09/2024]
Abstract
Microbial production of polyhydroxyalkanoate (PHA) is greatly restricted by high production cost arising from high-temperature sterilization and expensive carbon sources. In this study, a low-cost PHA production platform was established from Halomonas cupida J9. First, a marker-less genome-editing system was developed in H. cupida J9. Subsequently, H. cupida J9 was engineered to efficiently utilize xylose for PHA biosynthesis by introducing a new xylose metabolism module and blocking xylonate production. The engineered strain J9UΔxylD-P8xylA has the highest PHA yield (2.81 g/L) obtained by Halomonas with xylose as the sole carbon source so far. This is the first report on the production of short- and medium-chain-length (SCL-co-MCL) PHA from xylose by Halomonas. Interestingly, J9UΔxylD-P8xylA was capable of efficiently utilizing glucose and xylose as co-carbon sources for PHA production. Furthermore, fed-batch fermentation of J9UΔxylD-P8xylA coupled to a glucose/xylose co-feeding strategy reached up to 12.57 g/L PHA in a 5-L bioreactor under open and unsterile condition. Utilization of corn straw hydrolysate as the carbon source by J9UΔxylD-P8xylA reached 7.0 g/L cell dry weight (CDW) and 2.45 g/L PHA in an open fermentation. In summary, unsterile production in combination with inexpensive feedstock highlights the potential of the engineered strain for the low-cost production of PHA from lignocellulose-rich agriculture waste.
Collapse
Affiliation(s)
- Siqi Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yujie Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Hongfu Guo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yan Meng
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Weini Xiong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ruihua Liu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
2
|
Jiang D, Wang M, Zhao X, Lu X, Zong H, Zhuge B. Glycerol Production from Undetoxified Lignocellulose Hydrolysate by a Multiresistant Engineered Candida glycerinogenes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1630-1639. [PMID: 38194497 DOI: 10.1021/acs.jafc.3c05818] [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: 01/11/2024]
Abstract
Glycerol is an important platform compound with multidisciplinary applications, and glycerol production using low-cost sugar cane bagasse hydrolysate is promising. Candida glycerinogenes, an industrial yeast strain known for its high glycerol production capability, has been found to thrive in bagasse hydrolysate obtained through a simple treatment without detoxification. The engineered C. glycerinogenes exhibited significant resistance to furfural, acetic acid, and 3,4-dimethylbenzaldehyde within undetoxified hydrolysates. To further enhance glycerol production, genetic modifications were made to Candida glycerinogenes to enhance the utilization of xylose. Fermentation of undetoxified bagasse hydrolysate by CgS45 resulted in a glycerol titer of 40.3 g/L and a yield of 40.4%. This process required only 1 kg of bagasse to produce 93.5 g of glycerol. This is the first report of glycerol production using lignocellulose, which presents a new way for environmentally friendly industrial production of glycerol.
Collapse
Affiliation(s)
- Dongqi Jiang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengying Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaohong Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
3
|
Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
Collapse
Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
| |
Collapse
|
4
|
Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [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: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
Collapse
Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
| |
Collapse
|
5
|
Sullivan SF, Shetty A, Bharadwaj T, Krishna N, Trivedi VD, Endalur Gopinarayanan V, Chappell TC, Sellers DM, Pravin Kumar R, Nair NU. Towards universal synthetic heterotrophy using a metabolic coordinator. Metab Eng 2023; 79:14-26. [PMID: 37406763 PMCID: PMC10529783 DOI: 10.1016/j.ymben.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/13/2023] [Accepted: 07/03/2023] [Indexed: 07/07/2023]
Abstract
Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as inputs to bioprocesses. We previously demonstrated that activation of the galactose (GAL) regulon, a regulatory structure used by this yeast to coordinate substrate utilization with biomass formation during growth on galactose, during growth on the non-native substrate xylose results in a vastly altered gene expression profile and faster growth compared with constitutive overexpression of the same heterologous catabolic pathway. However, this effort involved the creation of a xylose-inducible variant of Gal3p (Gal3pSyn4.1), the sensor protein of the GAL regulon, preventing this semi-synthetic regulon approach from being easily adapted to additional non-native substrates. Here, we report the construction of a variant Gal3pMC (metabolic coordinator) that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system. Multiple molecular modeling studies suggest that Gal3pMC occupies conformational states corresponding to galactose-bound Gal3p in an inducer-independent manner. Using Gal3pMC to test a regulon approach to the assimilation of the non-native lignocellulosic sugars xylose, arabinose, and cellobiose yields higher growth rates and final cell densities when compared with a constitutive overexpression of the same set of catabolic genes. The subsequent demonstration of rapid and complete co-utilization of all three non-native substrates suggests that Gal3pMC-mediated dynamic global gene expression changes by GAL regulon activation may be universally beneficial for engineering synthetic heterotrophy.
Collapse
Affiliation(s)
- Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Anuj Shetty
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Tharun Bharadwaj
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Naveen Krishna
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA; Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Todd C Chappell
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Daniel M Sellers
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - R Pravin Kumar
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA.
| |
Collapse
|
6
|
Liu J, Yang J, Yuan L, Wu C, Jiang Y, Zhuang W, Ying H, Yang S. Modulated Arabinose Uptake and cAMP Signaling Synergistically Improve Glucose and Arabinose Consumption in Recombinant Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12797-12806. [PMID: 37592391 DOI: 10.1021/acs.jafc.3c04386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
During the production of ethanol from lignocellulose-derived sugars, recombinant yeasts tend to utilize xylose and arabinose after glucose exhaustion. So far, many glucose-insensitive pentose transporters have been reported to counteract this phenomenon, but few studies have described intracellular factors. In this study, the combination of adaptive evolution, comparative genomics, and genetic complementation revealed that the hexokinase-deficient (Hxk0) arabinose-fermenting Saccharomyces cerevisiae requires the arabinose transporter variant Gal2-N376T and the mutations of guanine nucleotide exchange factor Cdc25 to overcome glucose restriction during arabinose assimilation. The results showed that the Hxk0 recombinant yeasts could lower the metabolic/physiological threshold of cell proliferation by downregulating the intracellular cAMP levels, resulting in smaller cells and increased arabinose assimilation under glucose restriction. In the medium containing 80 g/L glucose and 20 g/L arabinose, the evolved strain restoring the hexokinase activity completed fermentation at 22 h, compared to 24 h for the parental strain. Overall, the experimental results provide new insights into glucose repression of biorefinery yeasts.
Collapse
Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Junjie Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lihua Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunhua Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| |
Collapse
|
7
|
Chen S, Xu Z, Ding B, Zhang Y, Liu S, Cai C, Li M, Dale BE, Jin M. Big data mining, rational modification, and ancestral sequence reconstruction inferred multiple xylose isomerases for biorefinery. SCIENCE ADVANCES 2023; 9:eadd8835. [PMID: 36724227 PMCID: PMC9891696 DOI: 10.1126/sciadv.add8835] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/30/2022] [Indexed: 05/28/2023]
Abstract
The isomerization of xylose to xylulose is considered the most promising approach to initiate xylose bioconversion. Here, phylogeny-guided big data mining, rational modification, and ancestral sequence reconstruction strategies were implemented to explore new active xylose isomerases (XIs) for Saccharomyces cerevisiae. Significantly, 13 new active XIs for S. cerevisiae were mined or artificially created. Moreover, the importance of the amino-terminal fragment for maintaining basic XI activity was demonstrated. With the mined XIs, four efficient xylose-utilizing S. cerevisiae were constructed and evolved, among which the strain S. cerevisiae CRD5HS contributed to ethanol titers as high as 85.95 and 94.76 g/liter from pretreated corn stover and corn cob, respectively, without detoxifying or washing pretreated biomass. Potential genetic targets obtained from adaptive laboratory evolution were further analyzed by sequencing the high-performance strains. The combined XI mining methods described here provide practical references for mining other scarce and valuable enzymes.
Collapse
Affiliation(s)
- Sitong Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Boning Ding
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shuangmei Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Chenggu Cai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Muzi Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Bruce E. Dale
- Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Centre (GLBRC), Michigan State University, East Lansing, MI, 48824 USA
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| |
Collapse
|
8
|
Tan C, Xu P, Tao F. Carbon-negative synthetic biology: challenges and emerging trends of cyanobacterial technology. Trends Biotechnol 2022; 40:1488-1502. [PMID: 36253158 DOI: 10.1016/j.tibtech.2022.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
Global warming and climate instability have spurred interest in using renewable carbon resources for the sustainable production of chemicals. Cyanobacteria are ideal cellular factories for carbon-negative production of chemicals owing to their great potentials for directly utilizing light and CO2 as sole energy and carbon sources, respectively. However, several challenges in adapting cyanobacterial technology to industry, such as low productivity, poor tolerance, and product harvesting difficulty, remain. Synthetic biology may finally address these challenges. Here, we summarize recent advances in the production of value-added chemicals using cyanobacterial cell factories, particularly in carbon-negative synthetic biology and emerging trends in cyanobacterial applications. We also propose several perspectives on the future development of cyanobacterial technology for commercialization.
Collapse
Affiliation(s)
- Chunlin Tan
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
9
|
Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
Collapse
Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| |
Collapse
|
10
|
Lee YG, Kim C, Kuanyshev N, Kang NK, Fatma Z, Wu ZY, Cheng MH, Singh V, Yoshikuni Y, Zhao H, Jin YS. Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12085-12094. [PMID: 36103687 DOI: 10.1021/acs.jafc.2c04251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Issatchenkia orientalis, exhibiting high tolerance against harsh environmental conditions, is a promising metabolic engineering host for producing fuels and chemicals from cellulosic hydrolysates containing fermentation inhibitors under acidic conditions. Although genetic tools for I. orientalis exist, they require auxotrophic mutants so that the selection of a host strain is limited. We developed a drug resistance gene (cloNAT)-based genome-editing method for engineering any I. orientalis strains and engineered I. orientalis strains isolated from various sources for xylose fermentation. Specifically, xylose reductase, xylitol dehydrogenase, and xylulokinase from Scheffersomyces stipitis were integrated into an intended chromosomal locus in four I. orientalis strains (SD108, IO21, IO45, and IO46) through Cas9-based genome editing. The resulting strains (SD108X, IO21X, IO45X, and IO46X) efficiently produced ethanol from cellulosic and hemicellulosic hydrolysates even though the pH adjustment and nitrogen source were not provided. As they presented different fermenting capacities, selection of a host I. orientalis strain was crucial for producing fuels and chemicals using cellulosic hydrolysates.
Collapse
Affiliation(s)
- Ye-Gi Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, South Korea
| | - Chanwoo Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Nam Kyu Kang
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ming-Hsun Cheng
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| |
Collapse
|
11
|
Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
Collapse
Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
| |
Collapse
|
12
|
Gao J, Li Y, Yu W, Zhou YJ. Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol. Nat Metab 2022; 4:932-943. [PMID: 35817856 DOI: 10.1038/s42255-022-00601-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
Methanol is an ideal feedstock for biomanufacturing that can be beneficial for global carbon neutrality; however, the toxicity of methanol limits the efficiency of methanol metabolism toward biochemical production. We here show that engineering production of free fatty acids from sole methanol results in cell death with decreased cellular levels of phospholipids in the methylotrophic yeast Ogataea polymorpha, and cell growth is restored by adaptive laboratory evolution. Whole-genome sequencing of the adapted strains reveals that inactivation of LPL1 (encoding a putative lipase) and IZH3 (encoding a membrane protein related to zinc metabolism) preserve cell survival by restoring phospholipid metabolism. Engineering the pentose phosphate pathway and gluconeogenesis enables high-level production of free fatty acid (15.9 g l-1) from sole methanol. Preventing methanol-associated toxicity underscores the link between lipid metabolism and methanol tolerance, which should contribute to enhancing methanol-based biomanufacturing.
Collapse
Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
| |
Collapse
|
13
|
De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts. Nat Commun 2022; 13:3040. [PMID: 35650215 PMCID: PMC9160076 DOI: 10.1038/s41467-022-30826-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
High-sugar diet causes health problems, many of which can be addressed with the use of sugar substitutes. Rubusoside and rebaudiosides are interesting molecules, considered the next generation of sugar substitutes due to their low-calorie, superior sweetness and organoleptic properties. However, their low abundance in nature makes the traditional plant extraction process neither economical nor environmental-friendly. Here we engineer baker's yeast Saccharomyces cerevisiae as a chassis for the de novo production of rubusoside and rebaudiosides. In this process, we identify multiple issues that limit the production, including rate-liming steps, product stress on cellular fitness and unbalanced metabolic networks. We carry out a systematic engineering strategy to solve these issues, which produces rubusoside and rebaudiosides at titers of 1368.6 mg/L and 132.7 mg/L, respectively. The rubusoside chassis strain here constructed paves the way towards a sustainable, large-scale fermentation-based manufacturing of diverse rebaudiosides.
Collapse
|
14
|
Tan YS, Zhang RK, Liu ZH, Li BZ, Yuan YJ. Microbial Adaptation to Enhance Stress Tolerance. Front Microbiol 2022; 13:888746. [PMID: 35572687 PMCID: PMC9093737 DOI: 10.3389/fmicb.2022.888746] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 01/28/2023] Open
Abstract
Microbial cell factories have been widely used in the production of various chemicals. Although synthetic biology is useful in improving the cell factories, adaptation is still widely applied to enhance its complex properties. Adaptation is an important strategy for enhancing stress tolerance in microbial cell factories. Adaptation involves gradual modifications of microorganisms in a stressful environment to enhance their tolerance. During adaptation, microorganisms use different mechanisms to enhance non-preferred substrate utilization and stress tolerance, thereby improving their ability to adapt for growth and survival. In this paper, the progress on the effects of adaptation on microbial substrate utilization capacity and environmental stress tolerance are reviewed, and the mechanisms involved in enhancing microbial adaptive capacity are discussed.
Collapse
Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ren-Kuan Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| |
Collapse
|
15
|
Tan C, Xu P, Tao F. Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism. RESEARCH 2022. [DOI: 10.34133/research.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rationally controlling cellular metabolism is of great importance but challenging owing to its highly complex and chaotic nature. Natural existing sensory proteins like histidine kinases (HKs) are understood as “sensitive nodes” of biological networks that can trigger disruptive metabolic reprogramming (MRP) upon perceiving environmental fluctuation. Here, the “sensitive node” genes were adopted to devise a global MRP platform consisting of a CRISPR interference-mediated dual-gene combinational knockdown toolbox and survivorship-based metabolic interaction decoding algorithm. The platform allows users to decode the interfering effects of
n
×
n
gene pairs while only requiring the synthesis of
n
pairs of primers. A total of 35 HK genes and 24 glycine metabolic genes were selected as the targets to determine the effectiveness of our platform in a
Vibrio
sp. FA2. The platform was applied to decode the interfering impact of HKs on antibiotic resistance in strain FA2. A pattern of combined knockdown of HK genes (
sasA_8
and
04288
) was demonstrated to be capable of reducing antibiotic resistance of
Vibrio
by 108-fold. Patterns of combined knockdown of glycine pathway genes (e.g.,
gcvT
and
ltaE
) and several HK genes (e.g.,
cpxA
and
btsS
) were also revealed to increase glycine production. Our platform may enable an efficient and rational approach for global MRP based on the elucidation of high-order gene interactions. A web-based 1-stop service (
https://smrp.sjtu.edu.cn
) is also provided to simplify the implementation of this smart strategy in a broad range of cells.
Collapse
Affiliation(s)
- Chunlin Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|