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Wei X, Yang X, Hu C, Li Q, Liu Q, Wu Y, Xie L, Ning X, Li F, Cai T, Zhu Z, Zhang YHPJ, Zhang Y, Chen X, You C. ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA. Nat Commun 2024; 15:3267. [PMID: 38627361 PMCID: PMC11021460 DOI: 10.1038/s41467-024-46871-y] [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: 07/26/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
In vitro biotransformation (ivBT) facilitated by in vitro synthetic enzymatic biosystems (ivSEBs) has emerged as a highly promising biosynthetic platform. Several ivSEBs have been constructed to produce poly-3-hydroxybutyrate (PHB) via acetyl-coenzyme A (acetyl-CoA). However, some systems are hindered by their reliance on costly ATP, limiting their practicality. This study presents the design of an ATP-free ivSEB for one-pot PHB biosynthesis via acetyl-CoA utilizing starch-derived maltodextrin as the sole substrate. Stoichiometric analysis indicates this ivSEB can self-maintain NADP+/NADPH balance and achieve a theoretical molar yield of 133.3%. Leveraging simple one-pot reactions, our ivSEBs achieved a near-theoretical molar yield of 125.5%, the highest PHB titer (208.3 mM, approximately 17.9 g/L) and the fastest PHB production rate (9.4 mM/h, approximately 0.8 g/L/h) among all the reported ivSEBs to date, and demonstrated easy scalability. This study unveils the promising potential of ivBT for the industrial-scale production of PHB and other acetyl-CoA-derived chemicals from starch.
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Affiliation(s)
- Xinlei Wei
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Congcong Hu
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Qiangzi Li
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Qianqian Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yue Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Leipeng Xie
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Xiao Ning
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Fei Li
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Tao Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Zhiguang Zhu
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Yi-Heng P Job Zhang
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Xuejun Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Chun You
- In vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, People's Republic of China.
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Wang Q, Jin W, Zhou X, Chen C, Han W, Mahlia TMI, Li X, Jiang G, Liu H, Wang Q. Enhancing docosahexaenoic acid production in Aurantiochytrium species using atmospheric and room temperature plasma mutagenesis and comprehensive multi-omics analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169217. [PMID: 38081429 DOI: 10.1016/j.scitotenv.2023.169217] [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: 10/25/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Aurantiochytrium sp. belongs to marine heterotrophic single-cell protist, which is an important decomposer in marine ecosystem. Aurantiochytrium sp. has gained notoriety because of its ability to accumulate high-value docosahexaenoic acid (DHA), but the key factors of DHA synthesis were unclear at present. In this study, Atmospheric and Room Temperature Plasma technology was applied to the mutagenic breeding of Aurantiochytrium sp., and transcriptomics and proteomics were adopted to analyze the DHA-biosynthesis mechanism. According to the growth and DHA accumulation profiles, the mutant strain Aurantiochytrium sp. R2A35 was selected. The DHA content in total lipids was greatly improved from 49.39 % of the wild strain R2 to 63.69 % of the mutant strain. Moreover, the DHA content in the biomass of Aurantiochytrium sp. R2A35 as 39.72 % was the highest DHA productivity reported so far. The differentially expressed genes distinguished from transcriptome and the TMT-identified differential proteins distinguished from proteome confirmed that the expression of acetyl-CoA carboxylase and ketoacyl reductase was up-regulated by 4.78-fold and 6.95-fold, respectively and the fatty acid synthase was concurrently down-regulated by 2.79-fold, so that more precursor was transported to the polyketide synthase pathway, thereby increasing the DHA yield in Aurantiochytrium sp. R2A35. This research would provide reference for the DHA metabolism process and contribute to the understanding of the decomposer - Aurantiochytrium sp. in marine ecosystems.
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Affiliation(s)
- Qing Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgae Bioenergy, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, China
| | - Wenbiao Jin
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgae Bioenergy, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, China.
| | - Xu Zhou
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgae Bioenergy, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, China.
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Wei Han
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Shenzhen Engineering Laboratory of Microalgae Bioenergy, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, China
| | - T M Indra Mahlia
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, NSW 2522 Wollongong, Australia
| | - Huan Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Nie M, Wang J, Zhang K. Engineering a Novel Acetyl-CoA Pathway for Efficient Biosynthesis of Acetyl-CoA-Derived Compounds. ACS Synth Biol 2024; 13:358-369. [PMID: 38151239 DOI: 10.1021/acssynbio.3c00613] [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] [Indexed: 12/29/2023]
Abstract
Acetyl-CoA is an essential central metabolite in living organisms and a key precursor for various value-added products as well. However, the intracellular availability of acetyl-CoA limits the efficient production of these target products due to complex and strict regulation. Here, we proposed a new acetyl-CoA pathway, relying on two enzymes, threonine aldolase and acetaldehyde dehydrogenase (acetylating), which can convert one l-threonine into one acetyl-CoA, one glycine, and generate one NADH, without carbon loss. Introducing the acetyl-CoA pathway could increase the intracellular concentration of acetyl-CoA by 8.6-fold compared with the wild-type strain. To develop a cost-competitive and genetically stable acetyl-CoA platform strain, the new acetyl-CoA pathway, driven by the constitutive strong promoter, was integrated into the chromosome of Escherichia coli. We demonstrated the practical application of this new acetyl-CoA pathway by high titer production of β-alanine, mevalonate, and N-acetylglucosamine. At the same time, this pathway achieved a high-yield production of glycine, a value-added commodity chemical for the synthesis of glyphosate and thiamphenicol. This work shows the potential of this new acetyl-CoA pathway for the industrial production of acetyl-CoA-derived compounds.
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Affiliation(s)
- Mengzhen Nie
- Zhejiang University, Hangzhou, Zhejiang 310027, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Jingyu Wang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Kechun Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
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4
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Neves D, Meinen D, Alter TB, Blank LM, Ebert BE. Expanding Pseudomonas taiwanensis VLB120's acyl-CoA portfolio: Propionate production in mineral salt medium. Microb Biotechnol 2024; 17:e14309. [PMID: 37537795 PMCID: PMC10832534 DOI: 10.1111/1751-7915.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023] Open
Abstract
As one of the main precursors, acetyl-CoA leads to the predominant production of even-chain products. From an industrial biotechnology perspective, extending the acyl-CoA portfolio of a cell factory is vital to producing industrial relevant odd-chain alcohols, acids, ketones and polyketides. The bioproduction of odd-chain molecules can be facilitated by incorporating propionyl-CoA into the metabolic network. The shortest pathway for propionyl-CoA production, which relies on succinyl-CoA catabolism encoded by the sleeping beauty mutase operon, was evaluated in Pseudomonas taiwanensis VLB120. A single genomic copy of the sleeping beauty mutase genes scpA, argK and scpB combined with the deletion of the methylcitrate synthase PVLB_08385 was sufficient to observe propionyl-CoA accumulation in this Pseudomonas. The chassis' capability for odd-chain product synthesis was assessed by expressing an acyl-CoA hydrolase, which enabled propionate synthesis. Three fed-batch strategies during bioreactor fermentations were benchmarked for propionate production, in which a maximal propionate titre of 2.8 g L-1 was achieved. Considering that the fermentations were carried out in mineral salt medium under aerobic conditions and that a single genome copy drove propionyl-CoA production, this result highlights the potential of Pseudomonas to produce propionyl-CoA derived, odd-chain products.
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Affiliation(s)
- Dário Neves
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Daniel Meinen
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Tobias B. Alter
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Lars M. Blank
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Birgitta E. Ebert
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
- Australian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneQueenslandAustralia
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5
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Xu Z, Gao X, Li G, Nghiem LD, Luo W. Microbes from mature compost to promote bacterial chemotactic motility via tricarboxylic acid cycle-regulated biochemical metabolisms for enhanced composting performance. BIORESOURCE TECHNOLOGY 2023; 387:129633. [PMID: 37544546 DOI: 10.1016/j.biortech.2023.129633] [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: 06/30/2023] [Revised: 07/29/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
This study aims to reveal the underlying mechanisms of mature compost addition for improving organic waste composting. Composting experiments and metagenomic analysis were conducted to elucidate the role of mature compost addition to regulate microbial metabolisms and physiological behaviors for composting amelioration. Mature compost with or without inactivation pretreatment was added to the composting of kitchen and garden wastes at 0%, 5%, 10%, 15%, and 20% (by wet weight) for comparison. Results show that mature compost promoted pyruvate metabolism, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation to produce heat and energy to accelerate temperature increase for composting initiation and biological contaminant removal (>78%) for pasteurization. Energy requirement drives bacterial chemotactic motility towards nutrient-rich regions to sustain organic biodegradation. Nevertheless, when NADH formation exceeded NAD+ regeneration in oxidative phosphorylation, TCA cycle was restrained to limit continuous temperature increase and recover high intracellular NAD+/NADH ratio to secure stable oxidation reactions.
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Affiliation(s)
- Zhicheng Xu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Key Laboratory of Technology and Model for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Xingzu Gao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Wenhai Luo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Key Laboratory of Technology and Model for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing 100125, China.
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Li Z, Ren L, Wang X, Chen M, Wang T, Dai R, Wang Z. Anaerobic hydrolysis of recalcitrant tetramethylammonium from semiconductor wastewater: Performance and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132239. [PMID: 37567140 DOI: 10.1016/j.jhazmat.2023.132239] [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: 05/23/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The treatment of tetramethylammonium hydroxide (TMAH)-bearing wastewater, generated in the electronic and semiconductor industries, raises significant concerns due to the neurotoxic, recalcitrant, and bio-inhibiting effects of TMAH. In this study, we proposed the use of an anaerobic hydrolysis bioreactor (AHBR) for TMAH removal, achieving a high removal efficiency of approximately 85%, which greatly surpassed the performance of widely-used advanced oxidation processes (AOPs). Density functional theory calculations indicated that the unexpectedly poor efficiency (5.8-8.0%) of selected AOPs can be attributed to the electrostatic repulsion between oxidants and the tightly bound electrons of TMAH. Metagenomic analyses of the AHBR revealed that Proteobacteria and Euryarchaeota played a dominant role in the transformation of TMAH through processes such as methyl transfer, methanogenesis, and acetyl-coenzyme A synthesis, utilizing methyl-tetrahydromethanopterin as a substrate. Moreover, several potential functional genes (e.g., mprF, basS, bcrB, sugE) related to TMAH resistance have been identified. Molecular docking studies between five selected proteins and tetramethylammonium further provided evidence supporting the roles of these potential functional genes. This study demonstrates the superiority of AHBR as a pretreatment technology compared to several widely-researched AOPs, paving the way for the proper design of treatment processes to abate TMAH in semiconductor wastewater.
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Affiliation(s)
- Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lehui Ren
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xueye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tianlin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Gao J, Li Z, Zhu B, Wang L, Xu J, Wang B, Fu X, Han H, Zhang W, Deng Y, Wang Y, Zuo Z, Peng R, Tian Y, Yao Q. Creation of Environmentally Friendly Super "Dinitrotoluene Scavenger" Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303785. [PMID: 37715295 PMCID: PMC10602510 DOI: 10.1002/advs.202303785] [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: 06/09/2023] [Revised: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Pervasive environmental contamination due to the uncontrolled dispersal of 2,4-dinitrotoluene (2,4-DNT) represents a substantial global health risk, demanding urgent intervention for the removal of this detrimental compound from affected sites and the promotion of ecological restoration. Conventional methodologies, however, are energy-intensive, susceptible to secondary pollution, and may inadvertently increase carbon emissions. In this study, a 2,4-DNT degradation module is designed, assembled, and validated in rice plants. Consequently, the modified rice plants acquire the ability to counteract the phytotoxicity of 2,4-DNT. The most significant finding of this study is that these modified rice plants can completely degrade 2,4-DNT into innocuous substances and subsequently introduce them into the tricarboxylic acid cycle. Further, research reveals that the modified rice plants enable the rapid phytoremediation of 2,4-DNT-contaminated soil. This innovative, eco-friendly phytoremediation approach for dinitrotoluene-contaminated soil and water demonstrates significant potential across diverse regions, substantially contributing to carbon neutrality and sustainable development objectives by repurposing carbon and energy from organic contaminants.
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Liu J, Zhang S, Li W, Wang G, Xie Z, Cao W, Gao W, Liu H. Engineering a Phosphoketolase Pathway to Supplement Cytosolic Acetyl-CoA in Aspergillus niger Enables a Significant Increase in Citric Acid Production. J Fungi (Basel) 2023; 9:jof9050504. [PMID: 37233215 DOI: 10.3390/jof9050504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Citric acid is widely used in the food, chemical and pharmaceutical industries. Aspergillus niger is the workhorse used for citric acid production in industry. A canonical citrate biosynthesis that occurred in mitochondria was well established; however, some research suggested that the cytosolic citrate biosynthesis pathway may play a role in this chemical production. Here, the roles of cytosolic phosphoketolase (PK), acetate kinase (ACK) and acetyl-CoA synthetase (ACS) in citrate biosynthesis were investigated by gene deletion and complementation in A. niger. The results indicated that PK, ACK and ACS were important for cytosolic acetyl-CoA accumulation and had significant effects on citric acid biosynthesis. Subsequently, the functions of variant PKs and phosphotransacetylase (PTA) were evaluated, and their efficiencies were determined. Finally, an efficient PK-PTA pathway was reconstructed in A. niger S469 with Ca-PK from Clostridium acetobutylicum and Ts-PTA from Thermoanaerobacterium saccharolyticum. The resultant strain showed an increase of 96.4% and 88% in the citrate titer and yield, respectively, compared with the parent strain in the bioreactor fermentation. These findings indicate that the cytosolic citrate biosynthesis pathway is important for citric acid biosynthesis, and increasing the cytosolic acetyl-CoA level can significantly enhance citric acid production.
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Affiliation(s)
- Jiao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shanshan Zhang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenhao Li
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanyi Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Weixia Gao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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9
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Bachosz K, Zdarta J, Bilal M, Meyer AS, Jesionowski T. Enzymatic cofactor regeneration systems: A new perspective on efficiency assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161630. [PMID: 36657682 DOI: 10.1016/j.scitotenv.2023.161630] [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] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Nowadays, the specificity of enzymatic processes makes them more and more important every year, and their usage on an industrial scale seems to be necessary. Enzymatic cofactors, however, play a crucial part in the prospective applications of enzymes, because they are indispensable for conducting highly effective biocatalytic activities. Due to the relatively high cost of these compounds and their consumption during the processes carried out, it has become crucial to develop systems for cofactor regeneration. Therefore, in this review, an attempt was made to summarize current knowledge on enzymatic regeneration methods, which are characterized by high specificity, non-toxicity and reported to be highly efficient. The regeneration of cofactors, such as nicotinamide dinucleotides, coenzyme A, adenosine 5'-triphosphate and flavin nucleotides, which are necessary for the proper functioning of a large number of enzymes, is discussed, as well as potential directions for further development of these systems are highlighted. This review discusses a range of highly effective cofactor regeneration systems along with the productive synthesis of many useful chemicals, including the simultaneous renewal of several cofactors at the same time. Additionally, the impact of the enzyme immobilization process on improving the stability and the potential for multiple uses of the developed cofactor regeneration systems was also presented. Moreover, an attempt was made to emphasize the importance of the presented research, as well as the identification of research gaps, which mainly result from the lack of available literature on this topic.
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Affiliation(s)
- Karolina Bachosz
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland; Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Soltofts Plads 227, DK-2800 Kgs. Lyngby, Denmark.
| | - Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Soltofts Plads 227, DK-2800 Kgs. Lyngby, Denmark.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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10
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Sun J, Wang J, Bai C, Zhao J, Yun Y, Yu Z, Xue Y, Zhang T, Bao W. Natural fermentation quality, bacteria, and functional profiles of three cuttings of alfalfa silage in a year in Inner Mongolia, China. Front Microbiol 2023; 14:1083620. [PMID: 36970661 PMCID: PMC10033646 DOI: 10.3389/fmicb.2023.1083620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/16/2023] [Indexed: 03/11/2023] Open
Abstract
Alfalfa is harvested two or three times a year in central and western Inner Mongolia, China. However, the variations in bacterial communities as affected by wilting and ensiling, and the ensiling characteristics of alfalfa among the different cuttings, are not fully understood. To enable a more complete evaluation, alfalfa was harvested three times a year. At each time of cutting, alfalfa was harvested at early bloom, wilted for 6 h, and then ensiled in polyethylene bags for 60 days. The bacterial communities and nutritional components of fresh alfalfa(F), wilted alfalfa(W) and ensiled alfalfa(S), and the fermentation quality and functional profile of bacterial communities of the three cuttings alfalfa silage, were then analyzed. Functional characteristics of silage bacterial communities were evaluated according to the Kyoto Encyclopedia of Genes and Genomes. The results showed that all nutritional components, fermentation quality, bacterial communities, carbohydrate, amino acid metabolism and key enzymes of bacterial communities were influenced by cutting time. The species richness of F increased from the first cutting to the third cutting; it was not changed by wilting, but was decreased by ensiling. At phylum level, Proteobacteria were more predominant than other bacteria, followed by Firmicutes (0.063–21.39%) in F and W in the first and second cuttings. Firmicutes (96.66–99.79%) were more predominant than other bacteria, followed by Proteobacteria (0.13–3.19%) in S in the first and second cuttings. Proteobacteria, however, predominated over all other bacteria in F, W, or S in the third cutting. The third-cutting silage showed the highest levels of dry matter, pH and butyric acid (p < 0.05). Higher levels of pH and butyric acid were positively correlated with the most predominant genus in silage, and with Rosenbergiella and Pantoea. The third-cutting silage had the lowest fermentation quality as Proteobacteria were more predominant. This suggested that, compared with the first and second cutting, the third cutting is more likely to result in poorly preserved silage in the region studied.
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Affiliation(s)
- Juanjuan Sun
- Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- Inner Mongolia Academy of Grassland Science, Hohhot, China
- *Correspondence: Juanjuan Sun,
| | - Jing Wang
- College of Grassland, Resources and Environment,Inner Mongolia Agricultural University, Hohhot, China
| | - Chunsheng Bai
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jinmei Zhao
- Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- Inner Mongolia Academy of Grassland Science, Hohhot, China
| | - Ying Yun
- Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- Inner Mongolia Academy of Grassland Science, Hohhot, China
| | - Zhu Yu
- College of Grassland Science and Technology, China Agricultural University China, Beijing, China
| | - Yanlin Xue
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Tengwei Zhang
- Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- Inner Mongolia Academy of Grassland Science, Hohhot, China
| | - Wenlong Bao
- Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
- Inner Mongolia Academy of Grassland Science, Hohhot, China
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11
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Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metab Eng 2022; 74:83-97. [PMID: 36155822 DOI: 10.1016/j.ymben.2022.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/17/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolas Krink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980, Paterna, Spain
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Lorena Férnandez-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark.
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12
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Feng S, Ngo HH, Guo W, Chang SW, Nguyen DD, Liu Y, Zhang S, Phong Vo HN, Bui XT, Ngoc Hoang B. Volatile fatty acids production from waste streams by anaerobic digestion: A critical review of the roles and application of enzymes. BIORESOURCE TECHNOLOGY 2022; 359:127420. [PMID: 35690239 DOI: 10.1016/j.biortech.2022.127420] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Volatile fatty acids (VFAs) produced from organic-rich wastewater by anaerobic digestion attract attention due to the increasing volatile fatty acids market, sustainability and environmentally friendly characteristics. This review aims to give an overview of the roles and applications of enzymes, a biocatalyst which plays a significant role in anaerobic digestion, to enhance volatile fatty acids production. This paper systematically overviewed: (i) the enzymatic pathways of VFAs formation, competition, and consumption; (ii) the applications of enzymes in VFAs production; and (iii) feasible measures to boost the enzymatic processes. Furthermore, this review presents a critical evaluation on the major obstacles and feasible future research directions for the better applications of enzymatic processes to promote VFAs production from wastewater.
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Affiliation(s)
- Siran Feng
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia; Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
| | - Wenshan Guo
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia
| | - Soon Woong Chang
- Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Dinh Duc Nguyen
- Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Yi Liu
- Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200438, China
| | - Shicheng Zhang
- Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200438, China
| | - Hoang Nhat Phong Vo
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, Queensland 4102, Australia
| | - Xuan Thanh Bui
- Key Laboratory of Advanced Waste Treatment Technology, Faculty of Environment & Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Vietnam National University Ho Chi Minh (VNU-HCM), Ho Chi Minh City 70000, Viet Nam
| | - Bich Ngoc Hoang
- Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
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13
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Rang J, Cao L, Shuai L, Liu Y, Zhu Z, Xia Z, Jin D, Sun Y, Yu Z, Hu S, Xie Q, Xia L. Promoting Butenyl-spinosyn Production Based on Omics Research and Metabolic Network Construction in Saccharopolyspora pogona. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3557-3567. [PMID: 35245059 DOI: 10.1021/acs.jafc.2c00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the metabolism of Saccharopolyspora pogona on a global scale is essential for manipulating its metabolic capabilities to improve butenyl-spinosyn biosynthesis. Here, we combined multiomics analysis to parse S. pogona genomic information, construct a metabolic network, and mine important functional genes that affect the butenyl-spinosyn biosynthesis. This research not only elucidated the relationship between butenyl-spinosyn biosynthesis and the primary metabolic pathway but also showed that the low expression level and continuous downregulation of the bus cluster and the competitive utilization of acetyl-CoA were the main reasons for reduced butenyl-spinosyn production. Our framework identified 148 genes related to butenyl-spinosyn biosynthesis that were significantly differentially expressed, confirming that butenyl-spinosyn polyketide synthase (PKS) and succinic semialdehyde dehydrogenase (GabD) play an important role in regulating butenyl-spinosyn biosynthesis. Combined modification of these genes increased overall butenyl-spinosyn production by 6.38-fold to 154.1 ± 10.98 mg/L. Our results provide an important strategy for further promoting the butenyl-spinosyn titer.
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Affiliation(s)
- Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Duo Jin
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Ziquan Yu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (MOE of China), National & Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Development Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
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14
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Yao J, Wang J, Ju Y, Dong Z, Song X, Chen L, Zhang W. Engineering a Xylose-Utilizing Synechococcus elongatus UTEX 2973 Chassis for 3-Hydroxypropionic Acid Biosynthesis under Photomixotrophic Conditions. ACS Synth Biol 2022; 11:678-688. [PMID: 35119824 DOI: 10.1021/acssynbio.1c00364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photomixotrophic cultivation of cyanobacteria is considered a promising strategy to achieve both high cell density and product accumulation, since cyanobacteria can obtain carbon and energy sources from organic matter in addition to those obtained from CO2 and sunlight. Acetyl coenzyme A (acetyl-CoA) is a key precursor used for the biosynthesis of a wide variety of important value-added chemicals. However, the acetyl-CoA content in cyanobacteria is typically low under photomixotrophic conditions, which limits the productivity of the derived chemicals. In this study, a xylose utilization pathway from Escherichia coli was first engineered into fast-growing Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973), enabling the xylose based photomixotrophy. Metabolomics analysis of the engineered strain showed that the utilization of xylose enhanced the carbon flow to the oxidative pentose phosphate (OPP) pathway, along with an increase in the intracellular abundance of metabolites such as fructose-6-phosphate (F6P), fructose-1,6-bisphosphate (FBP), ribose-5-phosphate (R5P), erythrose-4-phosphate (E4P), and glyceraldehyde-3-phosphate (G3P). Then, the native glycolytic pathway was rewired via heterologous phosphoketolase (Pkt) gene expression, combined with phosphofructokinase (Pfk) gene knockout and fructose-1,6-bisphosphatase (Fbp) gene overexpression, to drive more carbon flux from xylose to acetyl-CoA. Finally, a heterologous 3-hydroxypropionic acid (3-HP) biosynthetic pathway was introduced. The results showed that 3-HP biosynthesis was improved by up to approximately 4.1-fold (from 22.5 mg/L to 91.3 mg/L) compared with the engineered strain without a rewired metabolism under photomixotrophic conditions and up to approximately 14-fold compared with the strain under photoautotrophic conditions. Using 3-HP as a "proof-of-molecule", our results demonstrated that this strategy could be applied to improve the intracellular pool of acetyl-CoA for the photomixotrophic production of value-added chemicals that require acetyl-CoA as a precursor in a cyanobacterial chassis.
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Affiliation(s)
- Jiaqi Yao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Jin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Yue Ju
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
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15
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Dokladny K, Crane JK, Kassicieh AJ, Kaper JB, Kovbasnjuk O. Cross-Talk between Probiotic Nissle 1917 and Human Colonic Epithelium Affects the Metabolite Composition and Demonstrates Host Antibacterial Effect. Metabolites 2021; 11:841. [PMID: 34940599 PMCID: PMC8706777 DOI: 10.3390/metabo11120841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/04/2022] Open
Abstract
Colonic epithelium-commensal interactions play a very important role in human health and disease development. Colonic mucus serves as an ecologic niche for a myriad of commensals and provides a physical barrier between the epithelium and luminal content, suggesting that communication between the host and microbes occurs mainly by soluble factors. However, the composition of epithelia-derived metabolites and how the commensal flora influences them is less characterized. Here, we used mucus-producing human adult stem cell-derived colonoid monolayers exposed apically to probiotic E. coli strain Nissle 1917 to characterize the host-microbial communication via small molecules. We measured the metabolites in the media from host and bacterial monocultures and from bacteria-colonoid co-cultures. We found that colonoids secrete amino acids, organic acids, nucleosides, and polyamines, apically and basolaterally. The metabolites from host-bacteria co-cultures markedly differ from those of host cells grown alone or bacteria grown alone. Nissle 1917 affects the composition of apical and basolateral metabolites. Importantly, spermine, secreted apically by colonoids, shows antibacterial properties, and inhibits the growth of several bacterial strains. Our data demonstrate the existence of a cross-talk between luminal bacteria and human intestinal epithelium via metabolites, which might affect the numbers of physiologic processes including the composition of commensal flora via bactericidal effects.
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Affiliation(s)
- Karol Dokladny
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA;
| | - John K. Crane
- Department of Medicine, Division of Infectious Diseases, University at Buffalo, Buffalo, NY 14206, USA;
| | - Alex J. Kassicieh
- University of New Mexico School of Medicine, Albuquerque, NM 87106, USA;
| | - James B. Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Olga Kovbasnjuk
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA;
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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16
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Li Q, Zhang J, Yang J, Jiang Y, Yang S. Recent progress on n-butanol production by lactic acid bacteria. World J Microbiol Biotechnol 2021; 37:205. [PMID: 34698975 DOI: 10.1007/s11274-021-03173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
n-Butanol is an essential chemical intermediate produced through microbial fermentation. However, its toxicity to microbial cells has limited its production to a great extent. The anaerobe lactic acid bacteria (LAB) are the most resistant to n-butanol, so it should be the first choice for improving n-butanol production. The present article aims to review the following aspects of n-butanol production by LAB: (1) the tolerance of LAB to n-butanol, including its tolerance level and potential tolerance mechanisms; (2) genome editing tools in the n-butanol-resistant LAB; (3) methods of LAB modification for n-butanol production and the production levels after modification. This review will provide a theoretical basis for further research on n-butanol production by LAB.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China
- Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China.
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17
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Microbial production of chemicals driven by CRISPR-Cas systems. Curr Opin Biotechnol 2021; 73:34-42. [PMID: 34303184 DOI: 10.1016/j.copbio.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Microorganisms have provided an attractive route for biosynthesis of various chemicals from renewable resources. CRISPR-Cas systems have served as powerful mechanisms for generating cell factories with desirable properties by manipulating nucleic acids quickly and efficiently. The CRISPR-Cas system provides a toolbox with excellent opportunities for identifying better biocatalysts, multiplexed fine-tuning of metabolic flux, efficient utilization of low-cost substrates, and improvement of metabolic robustness. The overall goal of this review highlights recent advances in the development of microbial cell factories for chemical production using various CRISPR-Cas systems. The perspectives for further development or applications of CRISPR-Cas systems for strain improvement are also discussed.
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