1
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Cheng B, Zhang D, Lin Q, Xi S, Ma J, Zan F, Biswal BK, Wang Z, Guo G. Short-chain fatty acid production and phosphorous recovery from waste activated sludge via anaerobic fermentation: A comparison of in-situ and ex-situ thiosulfate-assisted Fe 2+/persulfate pretreatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162172. [PMID: 36775172 DOI: 10.1016/j.scitotenv.2023.162172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Recently, increasing attention is given on the resource and energy recovery (e.g. short-chain fatty acids (SCFAs) and phosphorus (P)) from waste active sludge (WAS) under the "Dual carbon goals". This study compared four thiosulfate-assisted Fe2+/persulfate (TAFP) pretreatments of WAS, i.e. in-situ TAFP pretreatment (R1), ex-situ TAFP pretreatment (R2), in-situ TAFP pretreatment + pH adjustment (R3) and ex-situ TAFP pretreatment + pH adjustment (R4), followed by anaerobic fermentation over 20 days for SCFA production and P recovery. The results showed that the maximal SCFA yields in R1-4 were 730.2 ± 7.0, 1017.4 ± 13.9, 860.1 ± 40.8, and 1072.0 ± 33.2 mg COD/L, respectively, significantly higher than Control (365.2 ± 17.8 mg COD/L). The findings indicated that TAFP pretreatments (particularly ex-situ TAFP pretreatment) enhanced WAS disintegration and provided more soluble organics and subsequently promoted SCFA production. The P fractionation results showed the non-apatite inorganic P increased from 11.6 ± 0.2 mg P/g TSS in Control to 11.8 ± 0.5 (R1), 12.4 ± 0.3 (R2), 13.2 ± 0.7 (R3) and 12.7 ± 0.7 mg P/g TSS (R4), suggesting TAFP pretreatments improved P bioavailability due to formation of Fe-P mineral (Fe(H2PO4)2·2H2O), which could be recycled through magnetic separators. These findings were further strengthened by the analysis of microbial community and related marker genes that fermentative bacteria containing SCFA biosynthesis genes (e.g. pyk, pdhA, accA and accB) and iron-reducing bacteria containing iron-related proteins (e.g. feoA and feoB) were enriched in R1-4 (dominant in ex-situ pretreatment systems, R2 and R4). Economic evaluation further verified ex-situ TAFP pretreatment was cost-effective and a better strategy over other operations to treat WAS for SCFA production and P recovery.
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Affiliation(s)
- Boyi Cheng
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Da Zhang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Qingshan Lin
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Shihao Xi
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Jie Ma
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Basanta Kumar Biswal
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zongping Wang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China
| | - Gang Guo
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Wuhan 430074, China.
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2
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Feng L, Xu J, Ye C, Gao J, Huang L, Xu Z, Lian J. Metabolic Engineering of Pichia pastoris for the Production of Triacetic Acid Lactone. J Fungi (Basel) 2023; 9:jof9040494. [PMID: 37108948 PMCID: PMC10145311 DOI: 10.3390/jof9040494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Triacetic acid lactone (TAL) is a promising renewable platform polyketide with broad biotechnological applications. In this study, we constructed an engineered Pichia pastoris strain for the production of TAL. We first introduced a heterologous TAL biosynthetic pathway by integrating the 2-pyrone synthase encoding gene from Gerbera hybrida (Gh2PS). We then removed the rate-limiting step of TAL synthesis by introducing the posttranslational regulation-free acetyl-CoA carboxylase mutant encoding gene from S. cerevisiae (ScACC1*) and increasing the copy number of Gh2PS. Finally, to enhance intracellular acetyl-CoA supply, we focused on the introduction of the phosphoketolase/phosphotransacetylase pathway (PK pathway). To direct more carbon flux towards the PK pathway for acetyl-CoA generation, we combined it with a heterologous xylose utilization pathway or endogenous methanol utilization pathway. The combination of the PK pathway with the xylose utilization pathway resulted in the production of 825.6 mg/L TAL in minimal medium with xylose as the sole carbon source, with a TAL yield of 0.041 g/g xylose. This is the first report on TAL biosynthesis in P. pastoris and its direct synthesis from methanol. The present study suggests potential applications in improving the intracellular pool of acetyl-CoA and provides a basis for the construction of efficient cell factories for the production of acetyl-CoA derived compounds.
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Affiliation(s)
- Linjuan Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Junhao Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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3
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Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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4
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Cao M, Tran VG, Qin J, Olson A, Mishra S, Schultz JC, Huang C, Xie D, Zhao H. Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnol Bioeng 2022; 119:2529-2540. [PMID: 35701887 PMCID: PMC9540541 DOI: 10.1002/bit.28159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/16/2022] [Accepted: 06/12/2022] [Indexed: 12/19/2022]
Abstract
The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.
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Affiliation(s)
- Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Andrew Olson
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John C Schultz
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chunshuai Huang
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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5
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Lu S, Zhou C, Guo X, Du Z, Cheng Y, Wang Z, He X. Enhancing fluxes through the mevalonate pathway in
Saccharomyces cerevisiae
by engineering the HMGR and β‐alanine metabolism. Microb Biotechnol 2022; 15:2292-2306. [PMID: 35531990 PMCID: PMC9328733 DOI: 10.1111/1751-7915.14072] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022] Open
Abstract
Mevalonate (MVA) pathway is the core for terpene and sterol biosynthesis, whose metabolic flux influences the synthesis efficiency of such compounds. Saccharomyces cerevisiae is an attractive chassis for the native active MVA pathway. Here, the truncated form of Enterococcus faecalis MvaE with only 3‐Hydroxy‐3‐methylglutaryl coenzyme A reductase (HMGR) activity was found to be the most effective enzyme for MVA pathway flux using squalene as the metabolic marker, resulting in 431‐fold and 9‐fold increases of squalene content in haploid and industrial yeast strains respectively. Furthermore, a positive correlation between MVA metabolic flux and β‐alanine metabolic activity was found based on a metabolomic analysis. An industrial strain SQ3‐4 with high MVA metabolic flux was constructed by combined engineering HMGR activity, NADPH regeneration, cytosolic acetyl‐CoA supply and β‐alanine metabolism. The strain was further evaluated as the chassis for terpenoids production. Strain SQ3‐4‐CPS generated from expressing β‐caryophyllene synthase in SQ3‐4 produced 11.86 ± 0.09 mg l−1 β‐caryophyllene, while strain SQ3‐5 resulted from down‐regulation of ERG1 in SQ3‐4 produced 408.88 ± 0.09 mg l−1 squalene in shake flask cultivations. Strain SQ3‐5 produced 4.94 g l−1 squalene in fed‐batch fermentation in cane molasses medium, indicating the promising potential for cost‐effective production of squalene.
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Affiliation(s)
- Surui Lu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Chenyao Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Yanfei Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
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6
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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7
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Zhang X, Miao Q, Xu X, Ji B, Qu L, Wei Y. Developments in Fatty Acid-Derived Insect Pheromone Production Using Engineered Yeasts. Front Microbiol 2021; 12:759975. [PMID: 34858372 PMCID: PMC8632438 DOI: 10.3389/fmicb.2021.759975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The use of traditional chemical insecticides for pest control often leads to environmental pollution and a decrease in biodiversity. Recently, insect sex pheromones were applied for sustainable biocontrol of pests in fields, due to their limited adverse impacts on biodiversity and food safety compared to that of other conventional insecticides. However, the structures of insect pheromones are complex, and their chemical synthesis is not commercially feasible. As yeasts have been widely used for fatty acid-derived pheromone production in the past few years, using engineered yeasts may be promising and sustainable for the low-cost production of fatty acid-derived pheromones. The primary fatty acids produced by Saccharomyces cerevisiae and other yeasts are C16 and C18, and it is also possible to rewire/reprogram the metabolic flux for other fatty acids or fatty acid derivatives. This review summarizes the fatty acid biosynthetic pathway in S. cerevisiae and recent progress in yeast engineering in terms of metabolic engineering and synthetic biology strategies to produce insect pheromones. In the future, insect pheromones produced by yeasts might provide an eco-friendly pest control method in agricultural fields.
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Affiliation(s)
- Xiaoling Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Qin Miao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Xia Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lingbo Qu
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
- College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
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8
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Hayat IF, Plan M, Ebert BE, Dumsday G, Vickers CE, Peng B. Auxin-mediated induction of GAL promoters by conditional degradation of Mig1p improves sesquiterpene production in Saccharomyces cerevisiae with engineered acetyl-CoA synthesis. Microb Biotechnol 2021; 14:2627-2642. [PMID: 34499421 PMCID: PMC8601163 DOI: 10.1111/1751-7915.13880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase-bypass for acetyl-CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl-CoA-derived biochemical due to carbon loss and the cost of two high-energy phosphate bonds per molecule of acetyl-CoA. Here, we attempted to improve acetyl-CoA production efficiency by introducing heterologous acetylating aldehyde dehydrogenase and phosphoketolase pathways for acetyl-CoA synthesis to enhance production of the sesquiterpene trans-nerolidol. In addition, we introduced auxin-mediated degradation of the glucose-dependent repressor Mig1p to allow induced expression of GAL promoters on glucose so that production potential on glucose could be examined. The novel genes that we used to reconstruct the heterologous acetyl-CoA pathways did not sufficiently complement the loss of endogenous acetyl-CoA pathways, indicating that superior heterologous enzymes are necessary to establish fully functional synthetic acetyl-CoA pathways and properly explore their potential for nerolidol synthesis. Notwithstanding this, nerolidol production was improved twofold to a titre of ˜ 900 mg l-1 in flask cultivation using a combination of heterologous acetyl-CoA pathways and Mig1p degradation. Conditional Mig1p depletion is presented as a valuable strategy to improve the productivities in the strains engineered with GAL promoters-controlled pathways when growing on glucose.
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Affiliation(s)
- Irfan Farabi Hayat
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- School of Chemistry and Molecular Biosciences (SCMB)the University of QueenslandBrisbaneQld4072Australia
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
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9
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Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
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Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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10
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Wegner SA, Chen JM, Ip SS, Zhang Y, Dugar D, Avalos JL. Engineering acetyl-CoA supply and ERG9 repression to enhance mevalonate production in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2021; 48:6342157. [PMID: 34351398 PMCID: PMC8788843 DOI: 10.1093/jimb/kuab050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Mevalonate is a key precursor in isoprenoid biosynthesis and a promising commodity chemical. Although mevalonate is a native metabolite in Saccharomyces cerevisiae, its production is challenged by the relatively low flux toward acetyl-CoA in this yeast. In this study we explore different approaches to increase acetyl-CoA supply in S. cerevisiae to boost mevalonate production. Stable integration of a feedback-insensitive acetyl-CoA synthetase (Se-acsL641P) from Salmonella enterica and the mevalonate pathway from Enterococcus faecalis results in the production of 1,390 ± 10 mg/l of mevalonate from glucose. While bifid shunt enzymes failed to improve titers in high-producing strains, inhibition of squalene synthase (ERG9) results in a significant enhancement. Finally, increasing coenzyme A (CoA) biosynthesis by overexpression of pantothenate kinase (CAB1) and pantothenate supplementation further increased production to 3,830 ± 120 mg/l. Using strains that combine these strategies in lab-scale bioreactors results in the production of 13.3 ± 0.5 g/l, which is ∼360-fold higher than previously reported mevalonate titers in yeast. This study demonstrates the feasibility of engineering S. cerevisiae for high-level mevalonate production.
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Affiliation(s)
- Scott A Wegner
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jhong-Min Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Samantha S Ip
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yanfei Zhang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Deepak Dugar
- Visolis, Inc., 1488 Zephyr Ave. Hayward, CA 94544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA.,High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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11
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Li B, Cai D, Chen S. Metabolic Engineering of Central Carbon Metabolism of Bacillus licheniformis for Enhanced Production of Poly-γ-glutamic Acid. Appl Biochem Biotechnol 2021; 193:3540-3552. [PMID: 34312784 DOI: 10.1007/s12010-021-03619-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 01/17/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) is an anionic polymer with wide-ranging applications in the areas of medicine, light chemical industry, wastewater treatment, and agriculture. However, the production cost of γ-PGA is high for the requirement of adding the expensive precursor L-glutamic acid during fermentation, which hinders its widespread application. In this study, in order to improve γ-PGA yield, central carbon metabolism was engineered to enhance the carbon flux of tricarboxylic acid (TCA) cycle and glutamic acid synthesis in a γ-PGA production strain Bacillus licheniformis WX-02. Firstly, pyruvate dehydrogenase (PdhABCD) and citrate synthase (CitA) were overexpressed to strengthen the flux of pyruvate into TCA cycle, resulting in 34.93% and 11.14% increase of γ-PGA yield in B. licheniformis WX-02, respectively. Secondly, the carbon flux to glyoxylate shunt was rewired via varying the expression of isocitrate lyase (AceA), and a 23.24% increase of γ-PGA yield was obtained in AceA down-regulated strain WXPbacAaceBA. Thirdly, deletion of pyruvate formate-lyase gene pflB led to a 30.70% increase of γ-PGA yield. Finally, combinatorial metabolic engineering was applied, and γ-PGA titer was enhanced to 12.02 g/L via overexpressing pdhABCD and citA, repressing aceA, and deleting pflB, with a 69.30% improvement compared to WX-02. Collectively, metabolic engineering of central carbon metabolism is an effective strategy for enhanced γ-PGA production in B. licheniformis, and this research provided a promising strain for industrial production of γ-PGA.
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Affiliation(s)
- Bichan Li
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Shouwen Chen
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
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12
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Zhang Y, Su M, Qin N, Nielsen J, Liu Z. Expressing a cytosolic pyruvate dehydrogenase complex to increase free fatty acid production in Saccharomyces cerevisiae. Microb Cell Fact 2020; 19:226. [PMID: 33302960 PMCID: PMC7730738 DOI: 10.1186/s12934-020-01493-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is being exploited as a cell factory to produce fatty acids and their derivatives as biofuels. Previous studies found that both precursor supply and fatty acid metabolism deregulation are essential for enhanced fatty acid synthesis. A bacterial pyruvate dehydrogenase (PDH) complex expressed in the yeast cytosol was reported to enable production of cytosolic acetyl-CoA with lower energy cost and no toxic intermediate. RESULTS Overexpression of the PDH complex significantly increased cell growth, ethanol consumption and reduced glycerol accumulation. Furthermore, to optimize the redox imbalance in production of fatty acids from glucose, two endogenous NAD+-dependent glycerol-3-phosphate dehydrogenases were deleted, and a heterologous NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase was introduced. The best fatty acid producing strain PDH7 with engineering of precursor and co-factor metabolism could produce 840.5 mg/L free fatty acids (FFAs) in shake flask, which was 83.2% higher than the control strain YJZ08. Profile analysis of free fatty acid suggested the cytosolic PDH complex mainly resulted in the increases of unsaturated fatty acids (C16:1 and C18:1). CONCLUSIONS We demonstrated that cytosolic PDH pathway enabled more efficient acetyl-CoA provision with the lower ATP cost, and improved FFA production. Together with engineering of the redox factor rebalance, the cytosolic PDH pathway could achieve high level of FFA production at similar levels of other best acetyl-CoA producing pathways.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Mo Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Ning Qin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,BioInnovation Institute, Ole Maaløes Vej 3, 2200, Copenhagen N, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China.
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13
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Microbial production of limonene and its derivatives: Achievements and perspectives. Biotechnol Adv 2020; 44:107628. [DOI: 10.1016/j.biotechadv.2020.107628] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
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14
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Hellgren J, Godina A, Nielsen J, Siewers V. Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metab Eng 2020; 62:150-160. [DOI: 10.1016/j.ymben.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 01/31/2023]
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15
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Man Z, Guo J, Zhang Y, Cai Z. Regulation of intracellular ATP supply and its application in industrial biotechnology. Crit Rev Biotechnol 2020; 40:1151-1162. [PMID: 32862717 DOI: 10.1080/07388551.2020.1813071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Efficient cell factories are the core of industrial biotechnology. In recent years, synthetic biology develops rapidly, and more and more modified microbial cell factories are employed in industrial biotechnology. ATP plays vital roles in biosynthesis, metabolism regulation, and cellular maintenance. Regulating cellular ATP supply can effectively modify cellular metabolism. This paper presents a review of recent studies on the regulation of the intracellular ATP supply and its application in industrial biotechnology. Detailed strategies for regulating the ATP supply and the resulting impact on bioproduction are introduced. It is observed that regulating the cellular ATP supply can provide great possibilities for making microbial cells into efficient factories. Future perspectives for further understanding the function of ATP are also discussed.
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Affiliation(s)
- Zaiwei Man
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,Zaozhuang Key Laboratory of Corn Bioengineering, Zaozhuang Science and Technology Collaborative Innovation Center of Enzyme, Shandong Hengren Gongmao Co. Ltd, Zaozhuang, China
| | - Jing Guo
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Yingyang Zhang
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China
| | - Zhiqiang Cai
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
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16
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Abstract
Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.
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17
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Hu Y, Zhu Z, Nielsen J, Siewers V. Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals. Open Biol 2020; 9:190049. [PMID: 31088249 PMCID: PMC6544985 DOI: 10.1098/rsob.190049] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of S. cerevisiae for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.
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Affiliation(s)
- Yating Hu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Zhiwei Zhu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Jens Nielsen
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden.,3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , 2800 Kgs Lyngby , Denmark.,4 BioInnovation Institute , Ole Måløes Vej, 2200 Copenhagen N , Denmark
| | - Verena Siewers
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
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18
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Ku JT, Chen AY, Lan EI. Metabolic Engineering Design Strategies for Increasing Acetyl-CoA Flux. Metabolites 2020; 10:metabo10040166. [PMID: 32340392 PMCID: PMC7240943 DOI: 10.3390/metabo10040166] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 01/18/2023] Open
Abstract
Acetyl-CoA is a key metabolite precursor for the biosynthesis of lipids, polyketides, isoprenoids, amino acids, and numerous other bioproducts which are used in various industries. Metabolic engineering efforts aim to increase carbon flux towards acetyl-CoA in order to achieve higher productivities of its downstream products. In this review, we summarize the strategies that have been implemented for increasing acetyl-CoA flux and concentration, and discuss their effects. Furthermore, recent works have developed synthetic acetyl-CoA biosynthesis routes that achieve higher stoichiometric yield of acetyl-CoA from glycolytic substrates.
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Affiliation(s)
- Jason T. Ku
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan; (J.T.K.); (A.Y.C.)
| | - Arvin Y. Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan; (J.T.K.); (A.Y.C.)
| | - Ethan I. Lan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu City 300, Taiwan
- Correspondence:
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19
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Building cell factories for the production of advanced fuels. Biochem Soc Trans 2020; 47:1701-1714. [PMID: 31803925 DOI: 10.1042/bst20190168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Synthetic biology-based engineering strategies are being extensively employed for microbial production of advanced fuels. Advanced fuels, being comparable in energy efficiency and properties to conventional fuels, have been increasingly explored as they can be directly incorporated into the current fuel infrastructure without the need for reconstructing the pre-existing set-up rendering them economically viable. Multiple metabolic engineering approaches have been used for rewiring microbes to improve existing or develop newly programmed cells capable of efficient fuel production. The primary challenge in using these approaches is improving the product yield for the feasibility of the commercial processes. Some of the common roadblocks towards enhanced fuel production include - limited availability of flux towards precursors and desired pathways due to presence of competing pathways, limited cofactor and energy supply in cells, the low catalytic activity of pathway enzymes, obstructed product transport, and poor tolerance of host cells for end products. Consequently, despite extensive studies on the engineering of microbial hosts, the costs of industrial-scale production of most of these heterologously produced fuel compounds are still too high. Though considerable progress has been made towards successfully producing some of these biofuels, a substantial amount of work needs to be done for improving the titers of others. In this review, we have summarized the different engineering strategies that have been successfully used for engineering pathways into commercial hosts for the production of advanced fuels and different approaches implemented for tuning host strains and pathway enzymes for scaling up production levels.
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20
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Zhang C, Li M, Zhao GR, Lu W. Harnessing Yeast Peroxisomes and Cytosol Acetyl-CoA for Sesquiterpene α-Humulene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1382-1389. [PMID: 31944688 DOI: 10.1021/acs.jafc.9b07290] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic engineering of Saccharomyces cerevisiae focusing on the cytoplasm for sustainable terpenoid production is commonly practiced. However, engineering organelles for terpenoid production is rarely reported. Herein, peroxisomes, together with the cytoplasm, were engineered to boost sesquiterpene α-humulene synthesis in S. cerevisiae. The farnesyl diphosphate synthetic pathway and α-humulene synthase were successfully expressed inside yeast peroxisomes to enable high-level α-humulene production with glucose as the sole carbon source. With the combination of peroxisomal and cytoplasmic engineering, α-humulene production was increased by 2.5-fold compared to that in cytoplasm-engineered recombinant strains. Finally, the α-humulene titer of 1726.78 mg/L was achieved by fed-batch fermentation in a 5 L bioreactor. The strategy presented here offers an efficient method for terpenoid production in S. cerevisiae.
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Affiliation(s)
- Chuanbo Zhang
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300350 , People's Republic of China
| | - Man Li
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300350 , People's Republic of China
| | - Guang-Rong Zhao
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300350 , People's Republic of China
- Key Laboratory of System Bioengineering, Ministry of Education Tianjin University , Tianjin 300350 , People's Republic of China
- SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300350 , People's Republic of China
| | - Wenyu Lu
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300350 , People's Republic of China
- Key Laboratory of System Bioengineering, Ministry of Education Tianjin University , Tianjin 300350 , People's Republic of China
- SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300350 , People's Republic of China
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21
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Chen R, Yang S, Zhang L, Zhou YJ. Advanced Strategies for Production of Natural Products in Yeast. iScience 2020; 23:100879. [PMID: 32087574 PMCID: PMC7033514 DOI: 10.1016/j.isci.2020.100879] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022] Open
Abstract
Natural products account for more than 50% of all small-molecule pharmaceutical agents currently in clinical use. However, low availability often becomes problematic when a bioactive natural product is promising to become a pharmaceutical or leading compound. Advances in synthetic biology and metabolic engineering provide a feasible solution for sustainable supply of these compounds. In this review, we have summarized current progress in engineering yeast cell factories for production of natural products, including terpenoids, alkaloids, and phenylpropanoids. We then discuss advanced strategies in metabolic engineering at three different dimensions, including point, line, and plane (corresponding to the individual enzymes and cofactors, metabolic pathways, and the global cellular network). In particular, we comprehensively discuss how to engineer cofactor biosynthesis for enhancing the biosynthesis efficiency, other than the enzyme activity. Finally, current challenges and perspective are also discussed for future engineering direction.
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Affiliation(s)
- Ruibing Chen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Shan Yang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China; Biomedical Innovation R&D Center, School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
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22
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Gao S, Lyu Y, Zeng W, Du G, Zhou J, Chen J. Efficient Biosynthesis of (2 S)-Naringenin from p-Coumaric Acid in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1015-1021. [PMID: 31690080 DOI: 10.1021/acs.jafc.9b05218] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
(2S)-Naringenin, a (2S)-flavanone, is widely used in the food, chemical, and pharmaceutical industries because of its diverse physiological activities. The production of (2S)-naringenin in microorganisms provides an ideal source that reduces the cost of the flavonoid. To achieve efficient production of (2S)-naringenin in Saccharomyces cerevisiae (S. cerevisiae), we constructed a biosynthetic pathway from p-coumaric acid, a cost-effective and more efficient precursor. The (2S)-naringenin synthesis pathway genes were integrated into the yeast genome to obtain a (2S)-naringenin production strain. After gene dosage experiments, the genes negatively regulating the shikimate pathway and inefficient chalcone synthase activity were verified as factors limiting (2S)-naringenin biosynthesis. With fed-batch process optimization of the engineered strain, the titer of (2S)-naringenin reached 648.63 mg/L from 2.5 g/L p-coumaric acid. Our results indicate that the constitutive production of (2S)-naringenin from p-coumaric acid in S. cerevisiae is highly promising.
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23
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Park YK, Ledesma-Amaro R, Nicaud JM. De novo Biosynthesis of Odd-Chain Fatty Acids in Yarrowia lipolytica Enabled by Modular Pathway Engineering. Front Bioeng Biotechnol 2020; 7:484. [PMID: 32039184 PMCID: PMC6987463 DOI: 10.3389/fbioe.2019.00484] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/27/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial oils are regarded as promising alternatives to fossil fuels as concerns over environmental issues and energy production systems continue to mount. Odd-chain fatty acids (FAs) are a type of valuable lipid with various applications: they can serve as biomarkers, intermediates in the production of flavor and fragrance compounds, fuels, and plasticizers. Microorganisms naturally produce FAs, but such FAs are primarily even-chain; only negligible amounts of odd-chain FAs are generated. As a result, studies using microorganisms to produce odd-chain FAs have had limited success. Here, our objective was to biosynthesize odd-chain FAs de novo in Yarrowia lipolytica using inexpensive carbon sources, namely glucose, without any propionate supplementation. To achieve this goal, we constructed a modular metabolic pathway containing seven genes. In the engineered strain expressing this pathway, the percentage of odd-chain FAs out of total FAs was higher than in the control strain (3.86 vs. 0.84%). When this pathway was transferred into an obese strain, which had been engineered to accumulate large amounts of lipids, odd-chain fatty acid production was 7.2 times greater than in the control (0.05 vs. 0.36 g/L). This study shows that metabolic engineering research is making progress toward obtaining efficient cell factories that produce odd-chain FAs.
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Affiliation(s)
- Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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24
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Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae. Metab Eng 2019; 56:190-197. [DOI: 10.1016/j.ymben.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/23/2022]
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25
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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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Pyne ME, Narcross L, Martin VJJ. Engineering Plant Secondary Metabolism in Microbial Systems. PLANT PHYSIOLOGY 2019; 179:844-861. [PMID: 30643013 PMCID: PMC6393802 DOI: 10.1104/pp.18.01291] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/27/2018] [Indexed: 05/02/2023]
Abstract
An overview of common challenges and strategies underlying efforts to reconstruct plant isoprenoid, alkaloid, phenylpropanoid, and polyketide biosynthetic pathways in microbial systems.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Centre for Applied Synthetic Biology, Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Lauren Narcross
- Department of Biology, Centre for Applied Synthetic Biology, Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Vincent J J Martin
- Department of Biology, Centre for Applied Synthetic Biology, Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
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Bergman A, Hellgren J, Moritz T, Siewers V, Nielsen J, Chen Y. Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae. Microb Cell Fact 2019; 18:25. [PMID: 30709397 PMCID: PMC6359841 DOI: 10.1186/s12934-019-1072-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/23/2019] [Indexed: 12/05/2022] Open
Abstract
Introduction Phosphoketolases (Xfpk) are a non-native group of enzymes in yeast, which can be expressed in combination with other metabolic enzymes to positively influence the yield of acetyl-CoA derived products by reducing carbon losses in the form of CO2. In this study, a yeast strain expressing Xfpk from Bifidobacterium breve, which was previously found to have a growth defect and to increase acetate production, was characterized. Results Xfpk-expression was found to increase respiration and reduce biomass yield during glucose consumption in batch and chemostat cultivations. By cultivating yeast with or without Xfpk in bioreactors at different pHs, we show that certain aspects of the negative growth effects coupled with Xfpk-expression are likely to be explained by proton decoupling. At low pH, this manifests as a reduction in biomass yield and growth rate in the ethanol phase. Secondly, we show that intracellular sugar phosphate pools are significantly altered in the Xfpk-expressing strain. In particular a decrease of the substrates xylulose-5-phosphate and fructose-6-phosphate was detected (26% and 74% of control levels) together with an increase of the products glyceraldehyde-3-phosphate and erythrose-4-phosphate (208% and 542% of control levels), clearly verifying in vivo Xfpk enzymatic activity. Lastly, RNAseq analysis shows that Xfpk expression increases transcription of genes related to the glyoxylate cycle, the TCA cycle and respiration, while expression of genes related to ethanol and acetate formation is reduced. The physiological and transcriptional changes clearly demonstrate that a heterologous phosphoketolase flux in combination with endogenous hydrolysis of acetyl-phosphate to acetate increases the cellular demand for acetate assimilation and respiratory ATP-generation, leading to carbon losses. Conclusion Our study shows that expression of Xfpk in yeast diverts a relatively small part of its glycolytic flux towards acetate formation, which has a significant impact on intracellular sugar phosphate levels and on cell energetics. The elevated acetate flux increases the ATP-requirement for ion homeostasis and need for respiratory assimilation, which leads to an increased production of CO2. A majority of the negative growth effects coupled to Xfpk expression could likely be counteracted by preventing acetate accumulation via direct channeling of acetyl-phosphate towards acetyl-CoA. Electronic supplementary material The online version of this article (10.1186/s12934-019-1072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Bergman
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Hellgren
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Center (UPSC), 901 83, Umeå, Sweden.,Swedish Metabolomics Centre, Umeå Plant Science Center (UPSC), 901 83, Umeå, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
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Vavitsas K, Fabris M, Vickers CE. Terpenoid Metabolic Engineering in Photosynthetic Microorganisms. Genes (Basel) 2018; 9:E520. [PMID: 30360565 PMCID: PMC6266707 DOI: 10.3390/genes9110520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
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Wadhwa M, Srinivasan S, Bachhawat AK, Venkatesh KV. Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:152. [PMID: 30241525 PMCID: PMC6149198 DOI: 10.1186/s12934-018-1000-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Background Production of isoprenoids, a large and diverse class of commercially important chemicals, can be achieved through engineering metabolism in microorganisms. Several attempts have been made to reroute metabolic flux towards isoprenoid pathway in yeast. Most approaches have focused on the core isoprenoid pathway as well as on meeting the increased precursors and cofactor requirements. To identify unexplored genetic targets that positively influence the isoprenoid pathway activity, a carotenoid based genetic screen was previously developed and three novel mutants of a global TATA binding protein SPT15 was isolated for heightened isoprenoid flux in Saccharomyces cerevisiae. Results In this study, we investigated how one of the three spt15 mutants, spt15_Ala101Thr, was leading to enhanced isoprenoid pathway flux in S. cerevisiae. Metabolic flux analysis of the spt15_Ala101Thr mutant initially revealed a rerouting of the central carbon metabolism for the production of the precursor acetyl-CoA through activation of pyruvate-acetaldehyde-acetate cycle in the cytoplasm due to high flux in the reaction caused by pyruvate decarboxylase (PDC). This led to alternate routes of cytosolic NADPH generation, increased mitochondrial ATP production and phosphate demand in the mutant strain. Comparison of the transcriptomics of the spt15_Ala101Thr mutant cell with SPT15WT bearing cells shows upregulation of phosphate mobilization genes and pyruvate decarboxylase 6 (PDC6). Increasing the extracellular phosphate led to an increase in the growth rate and biomass but diverted flux away from the isoprenoid pathway. PDC6 is also shown to play a critical role in isoprenoid pathway flux under phosphate limitation conditions. Conclusion The study not only proposes a probable mechanism as to how a spt15_Ala101Thr mutant (a global TATA binding protein mutant) could increase flux towards the isoprenoid pathway, but also PDC as a new route of metabolic manipulation for increasing the isoprenoid flux in yeast. Electronic supplementary material The online version of this article (10.1186/s12934-018-1000-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manisha Wadhwa
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Mohali, India
| | - Sumana Srinivasan
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, India
| | - Anand K Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Mohali, India.
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, India.
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Huang YY, Jian XX, Lv YB, Nian KQ, Gao Q, Chen J, Wei LJ, Hua Q. Enhanced squalene biosynthesis in Yarrowia lipolytica based on metabolically engineered acetyl-CoA metabolism. J Biotechnol 2018; 281:106-114. [PMID: 29986837 DOI: 10.1016/j.jbiotec.2018.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
As a bioactive triterpenoid, squalene is widely used in the food industry, cosmetics, and pharmacology. Squalene's major commercial sources are the liver oil of deep-sea sharks and plant oils. In this study, we focused on the enhancement of squalene biosynthesis in Yarrowia lipolytica, with particular attention to the engineering of acetyl-CoA metabolism based on genome-scale metabolic reaction network analysis. Although the overexpression of the rate-limiting endogenous ylHMG1 (3-hydroxy-3-methylglutaryl-CoA reductase gene) could improve squalene synthesis by 3.2-fold over that by the control strain, the availability of the key intracellular precursor, acetyl-CoA, was found to play a more significant role in elevating squalene production. Analysis of metabolic networks with the newly constructed genome-scale metabolic model of Y. lipolytica iYL_2.0 showed that the acetyl-CoA pool size could be increased by redirecting carbon flux of pyruvate dehydrogenation towards the ligation of acetate and CoA or the cleavage of citrate to form oxaloacetate and acetyl-CoA. The overexpression of either acetyl-CoA synthetase gene from Salmonella enterica (acs*) or the endogenous ATP citrate lyase gene (ylACL1) resulted in a more than 50% increase in the cytosolic acetyl-CoA level. Moreover, iterative chromosomal integration of the ylHMG1, asc*, and ylACL1 genes resulted in a significant improvement in squalene production (16.4-fold increase in squalene content over that in the control strain). We also found that supplementation with 10 mM citrate in a flask culture further enhanced squalene production to 10 mg/g DCW. The information obtained in this study demonstrates that rationally engineering acetyl-CoA metabolism to ensure the supply of this key metabolic precursor is an efficient strategy for the enhancement of squalene biosynthesis.
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Affiliation(s)
- Yu-Ying Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Xing-Xing Jian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Yu-Bei Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Ke-Qing Nian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Qi Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, PR China
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Zhang Y, Nielsen J, Liu Z. Metabolic engineering ofSaccharomyces cerevisiaefor production of fatty acid–derived hydrocarbons. Biotechnol Bioeng 2018; 115:2139-2147. [DOI: 10.1002/bit.26738] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Yiming Zhang
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
| | - Jens Nielsen
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Hørsholm Denmark
| | - Zihe Liu
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- College of Life Science and Technology, Beijing University of Chemical TechnologyBeijing China
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Liu X, Liu X, Zhang Z, Sang M, Sun X, He C, Xin P, Zhang H. Functional Analysis of the FZF1 Genes of Saccharomyces uvarum. Front Microbiol 2018; 9:96. [PMID: 29467731 PMCID: PMC5808186 DOI: 10.3389/fmicb.2018.00096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/16/2018] [Indexed: 11/13/2022] Open
Abstract
Being a sister species of Saccharomyces cerevisiae, Saccharomyces uvarum shows great potential regarding the future of the wine industry. The sulfite tolerance of most S. uvarum strains is poor, however. This is a major flaw that limits its utility in the wine industry. In S. cerevisiae, FZF1 plays a positive role in the transcription of SSU1, which encodes a sulfite efflux transport protein that is critical for sulfite tolerance. Although FZF1 has previously been shown to play a role in sulfite tolerance in S. uvarum, there is little information about its action mechanism. To assess the function of FZF1, two over-expression vectors that contained different FZF1 genes, and one FZF1 silencing vector, were constructed and introduced into a sulfite-tolerant S. uvarum strain using electroporation. In addition, an FZF1-deletion strain was constructed. Both of the FZF1-over-expressing strains showed an elevated tolerance to sulfite, and the FZF1-deletion strain showed the opposite effect. Repression of FZF1 transcription failed, however, presumably due to the lack of alleles of DCR1 and AGO. The qRT-PCR analysis was used to examine changes in transcription in the strains. Surprisingly, neither over-expressing strain promoted SSU1 transcription, although MET4 and HAL4 transcripts significantly increased in both sulfite-tolerance increased strains. We conclude that FZF1 plays a different role in the sulfite tolerance of S. uvarum compared to its role in S. cerevisiae.
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Affiliation(s)
- Xiaozhen Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Xiaoping Liu
- College of Life Science, Jinggangshan University, Ji'an, China
| | - Zhiming Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Ming Sang
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Xiaodong Sun
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Chengzhong He
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Peiyao Xin
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Vickers CE, Williams TC, Peng B, Cherry J. Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Liu Z, Zhang Y, Jia X, Hu M, Deng Z, Xu Y, Liu T. In Vitro Reconstitution and Optimization of the Entire Pathway to Convert Glucose into Fatty Acid. ACS Synth Biol 2017; 6:701-709. [PMID: 28080041 DOI: 10.1021/acssynbio.6b00348] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glucose and fatty acids play essential physiological roles in nearly all living organisms, and the pathway that converts glucose into fatty acid is pivotal to the central metabolic network. We have successfully reconstituted a pathway that converts glucose to fatty acid in vitro using 30 purified proteins. Through systematic titration and optimization of the glycolytic pathway and pyruvate dehydrogenase, we increased the yield of free fatty acid from nondetectable to a level that exceeded 9% of the theoretical yield. We also reconstituted the entire pentose-phosphate pathway of Escherichia coli and established a pentose phosphate-glycolysis hybrid pathway, replacing GAPDH to enhance NADPH availability. Our efforts provide a useful platform for research involving these core biochemical transformations.
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Affiliation(s)
- Zheng Liu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuchen Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xiaoge Jia
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Mengzhu Hu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yancheng Xu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
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Takenaka M, Yoon KS, Matsumoto T, Ogo S. Acetyl-CoA production by encapsulated pyruvate ferredoxin oxidoreductase in alginate hydrogels. BIORESOURCE TECHNOLOGY 2017; 227:279-285. [PMID: 28040649 DOI: 10.1016/j.biortech.2016.12.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/10/2016] [Accepted: 12/12/2016] [Indexed: 05/08/2023]
Abstract
Pyruvate ferredoxin oxidoreductase from Citrobacter sp. S-77 (PFORS77) was purified in order to develop a method for acetyl-CoA production. Although the purified PFORS77 showed high O2-sensitivity, the activity could be remarkably stabilized in anaerobic conditions. PFORS77 was effectively immobilized on ceramic hydroxyapatite (PFORS77-HA) with an efficiency of more than 96%, however, after encapsulation of PFORS77-HA in alginate, the rate of catalytic acetyl-CoA production was highly reduced to 36% when compared to that of the free enzyme. However, the operational stability of the PFORS77-HA in alginate hydrogels was remarkable, retaining over 68% initial activity even after ten repeated cycles. The results suggested that the PFORS77-HA hydrogels have a high potential for biotechnological application.
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Affiliation(s)
- Makoto Takenaka
- International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ki-Seok Yoon
- International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Centre for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Centre for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I(2)CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Centre for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
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Raja V, Joshi AS, Li G, Maddipati KR, Greenberg ML. Loss of Cardiolipin Leads to Perturbation of Acetyl-CoA Synthesis. J Biol Chem 2016; 292:1092-1102. [PMID: 27941023 DOI: 10.1074/jbc.m116.753624] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/08/2016] [Indexed: 11/06/2022] Open
Abstract
Cardiolipin (CL), the signature phospholipid of mitochondrial membranes, plays an important role in mitochondrial processes and bioenergetics. CL is synthesized de novo and undergoes remodeling in the mitochondrial membranes. Perturbation of CL remodeling leads to the rare X-linked genetic disorder Barth syndrome, which shows disparities in clinical presentation. To uncover biochemical modifiers that exacerbate CL deficiency, we carried out a synthetic genetic array screen to identify synthetic lethal interactions with the yeast CL synthase mutant crd1Δ. The results indicated that crd1Δ is synthetically lethal with mutants in pyruvate dehydrogenase (PDH), which catalyzes the conversion of pyruvate to acetyl-CoA. Acetyl-CoA levels were decreased in the mutant. The synthesis of acetyl-CoA depends primarily on the PDH-catalyzed conversion of pyruvate in the mitochondria and on the PDH bypass in the cytosol, which synthesizes acetyl-CoA from acetate. Consistent with perturbation of the PDH bypass, crd1Δ cells grown on acetate as the sole carbon source exhibited decreased growth, decreased acetyl-CoA, and increased intracellular acetate levels resulting from decreased acetyl-CoA synthetase activity. PDH mRNA and protein levels were up-regulated in crd1Δ cells, but PDH enzyme activity was not increased, indicating that PDH up-regulation did not compensate for defects in the PDH bypass. These findings demonstrate for the first time that CL is required for acetyl-CoA synthesis, which is decreased in CL-deficient cells as a result of a defective PDH bypass pathway.
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Affiliation(s)
- Vaishnavi Raja
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| | - Amit S Joshi
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| | - Guiling Li
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| | - Krishna Rao Maddipati
- the Department of Pathology, Bioactive Lipids Research Program, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, Michigan 48202
| | - Miriam L Greenberg
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
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Bergman A, Siewers V, Nielsen J, Chen Y. Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae. AMB Express 2016; 6:115. [PMID: 27848233 PMCID: PMC5110461 DOI: 10.1186/s13568-016-0290-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/08/2016] [Indexed: 01/20/2023] Open
Abstract
Phosphoketolases catalyze an energy- and redox-independent cleavage of certain sugar phosphates. Hereby, the two-carbon (C2) compound acetyl-phosphate is formed, which enzymatically can be converted into acetyl-CoA—a key precursor in central carbon metabolism. Saccharomyces cerevisiae does not demonstrate efficient phosphoketolase activity naturally. In this study, we aimed to compare and identify efficient heterologous phosphoketolase enzyme candidates that in yeast have the potential to reduce carbon loss compared to the native acetyl-CoA producing pathway by redirecting carbon flux directly from C5 and C6 sugars towards C2-synthesis. Nine phosphoketolase candidates were expressed in S. cerevisiae of which seven produced significant amounts of acetyl-phosphate after provision of sugar phosphate substrates in vitro. The candidates showed differing substrate specificities, and some demonstrated activity levels significantly exceeding those of candidates previously expressed in yeast. The conducted studies also revealed that S. cerevisiae contains endogenous enzymes capable of breaking down acetyl-phosphate, likely into acetate, and that removal of the phosphatases Gpp1 and Gpp2 could largely prevent this breakdown. An evaluation of in vivo function of a subset of phosphoketolases was conducted by monitoring acetate levels during growth, confirming that candidates showing high activity in vitro indeed showed increased acetate accumulation, but expression also decreased cellular fitness. The study shows that expression of several bacterial phosphoketolase candidates in S. cerevisiae can efficiently divert intracellular carbon flux toward C2-synthesis, thus showing potential to be used in metabolic engineering strategies aimed to increase yields of acetyl-CoA derived compounds.
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Yuan J, Mishra P, Ching CB. Metabolically engineered Saccharomyces cerevisiae for branched-chain ester productions. J Biotechnol 2016; 239:90-97. [DOI: 10.1016/j.jbiotec.2016.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/17/2022]
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Diethard M, Gasser B, Egermeier M, Marx H, Sauer M. Industrial Microorganisms: Saccharomyces cerevisiaeand other Yeasts. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Mattanovich Diethard
- BOKU - University of Natural Resources and Life Sciences; Department of Biotechnology; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Muthgasse 18 1190 Vienna Austria
| | - Brigitte Gasser
- BOKU - University of Natural Resources and Life Sciences; Department of Biotechnology; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Muthgasse 18 1190 Vienna Austria
| | - Michael Egermeier
- BOKU - University of Natural Resources and Life Sciences; Department of Biotechnology; Muthgasse 18 1190 Vienna Austria
- BOKU - University of Natural Resources and Life Sciences; CD-Laboratory for Biotechnology of Glycerol; Muthgasse 18 1190 Vienna Austria
| | - Hans Marx
- BOKU - University of Natural Resources and Life Sciences; Department of Biotechnology; Muthgasse 18 1190 Vienna Austria
| | - Michael Sauer
- BOKU - University of Natural Resources and Life Sciences; Department of Biotechnology; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Muthgasse 18 1190 Vienna Austria
- BOKU - University of Natural Resources and Life Sciences; CD-Laboratory for Biotechnology of Glycerol; Muthgasse 18 1190 Vienna Austria
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de Las Heras AM, Portugal-Nunes DJ, Rizza N, Sandström AG, Gorwa-Grauslund MF. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact 2016; 15:197. [PMID: 27863495 PMCID: PMC5116212 DOI: 10.1186/s12934-016-0598-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
Background Poly-3-d-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. Results In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. Conclusions This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0598-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Diogo J Portugal-Nunes
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Nathasha Rizza
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Vattenhallen Science Center, John Ericssons väg 1, 223 63, Lund, Sweden
| | - Anders G Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.
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42
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Li M, Schneider K, Kristensen M, Borodina I, Nielsen J. Engineering yeast for high-level production of stilbenoid antioxidants. Sci Rep 2016; 6:36827. [PMID: 27833117 PMCID: PMC5105057 DOI: 10.1038/srep36827] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/21/2016] [Indexed: 01/07/2023] Open
Abstract
Stilbenoids, including resveratrol and its methylated derivatives, are natural potent antioxidants, produced by some plants in trace amounts as defense compounds. Extraction of stilbenoids from natural sources is costly due to their low abundance and often limited availability of the plant. Here we engineered the yeast Saccharomyces cerevisiae for production of stilbenoids on a simple mineral medium typically used for industrial production. We applied a pull-push-block strain engineering strategy that included overexpression of the resveratrol biosynthesis pathway, optimization of the electron transfer to the cytochrome P450 monooxygenase, increase of the precursors supply, and decrease of the pathway intermediates degradation. Fed-batch fermentation of the final strain resulted in a final titer of 800 mg l−1 resveratrol, which is by far the highest titer reported to date for production of resveratrol from glucose. We further integrated heterologous methyltransferases into the resveratrol platform strain and hereby demonstrated for the first time de novo biosynthesis of pinostilbene and pterostilbene, which have better stability and uptake in the human body, from glucose.
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Affiliation(s)
- Mingji Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Konstantin Schneider
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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43
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Ghosh A, Ando D, Gin J, Runguphan W, Denby C, Wang G, Baidoo EEK, Shymansky C, Keasling JD, García Martín H. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids. Front Bioeng Biotechnol 2016; 4:76. [PMID: 27761435 PMCID: PMC5050205 DOI: 10.3389/fbioe.2016.00076] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 11/24/2022] Open
Abstract
Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%.
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Affiliation(s)
- Amit Ghosh
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Indian Institute of Technology (IIT), School of Energy Science and Engineering, Kharagpur, India
| | - David Ando
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jennifer Gin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Weerawat Runguphan
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Charles Denby
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - George Wang
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Edward E K Baidoo
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Chris Shymansky
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Horsholm, Denmark
| | - Héctor García Martín
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
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44
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Biobased production of alkanes and alkenes through metabolic engineering of microorganisms. J Ind Microbiol Biotechnol 2016; 44:613-622. [PMID: 27565672 PMCID: PMC5408033 DOI: 10.1007/s10295-016-1814-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/30/2016] [Indexed: 12/02/2022]
Abstract
Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for sustainable production leading to reduced carbon dioxide emission there. One area that has attained much interest is microbial hydrocarbon biosynthesis, and in particular, alkanes and alkenes are important high-value chemicals as they can be utilized for a broad range of industrial purposes as well as ‘drop-in’ biofuels. Some microorganisms have the ability to biosynthesize alkanes and alkenes naturally, but their production level is extremely low. Therefore, there have been various attempts to recruit other microbial cell factories for production of alkanes and alkenes by applying metabolic engineering strategies. Here we review different pathways and involved enzymes for alkane and alkene production and discuss bottlenecks and possible solutions to accomplish industrial level production of these chemicals by microbial fermentation.
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45
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Jessop-Fabre MM, Jakočiūnas T, Stovicek V, Dai Z, Jensen MK, Keasling JD, Borodina I. EasyClone-MarkerFree: A vector toolkit for marker-less integration of genes into Saccharomyces cerevisiae via CRISPR-Cas9. Biotechnol J 2016; 11:1110-7. [PMID: 27166612 PMCID: PMC5094547 DOI: 10.1002/biot.201600147] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 03/14/2016] [Accepted: 05/03/2016] [Indexed: 11/08/2022]
Abstract
Saccharomyces cerevisiae is an established industrial host for production of recombinant proteins, fuels and chemicals. To enable stable integration of multiple marker-free overexpression cassettes in the genome of S. cerevisiae, we have developed a vector toolkit EasyClone-MarkerFree. The integration of linearized expression cassettes into defined genomic loci is facilitated by CRISPR/Cas9. Cas9 is recruited to the chromosomal location by specific guide RNAs (gRNAs) expressed from a set of gRNA helper vectors. Using our genome engineering vector suite, single and triple insertions are obtained with 90-100% and 60-70% targeting efficiency, respectively. We demonstrate application of the vector toolkit by constructing a haploid laboratory strain (CEN.PK113-7D) and a diploid industrial strain (Ethanol Red) for production of 3-hydroxypropionic acid, where we tested three different acetyl-CoA supply strategies, requiring overexpression of three to six genes each. Among the tested strategies was a bacterial cytosolic pyruvate dehydrogenase complex, which was integrated into the genome in a single transformation. The publicly available EasyClone-MarkerFree vector suite allows for facile and highly standardized genome engineering, and should be of particular interest to researchers working on yeast chassis with limited markers available.
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Affiliation(s)
- Mathew M Jessop-Fabre
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Zongjie Dai
- The Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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46
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Mitochondrial acetyl-CoA utilization pathway for terpenoid productions. Metab Eng 2016; 38:303-309. [PMID: 27471067 DOI: 10.1016/j.ymben.2016.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/25/2016] [Accepted: 07/25/2016] [Indexed: 12/26/2022]
Abstract
Acetyl-CoA is a central molecule in the metabolism of the cell, which is also a precursor molecule to a variety of value-added products such as terpenoids and fatty acid derived molecules. Considering subcellular compartmentalization of metabolic pathways allows higher concentrations of enzymes, substrates and intermediates, and bypasses competing pathways, mitochondrion-compartmentalized acetyl-CoA utilization pathways might offer better pathway activities with improved product yields. As a proof-of-concept, we sought to explore a mitochondrial farnesyl pyrophosphate (FPP) biosynthetic pathway for the biosynthesis of amorpha-4,11-diene in budding yeast. In the present study, the eight-gene FPP biosynthetic pathway was successfully expressed inside yeast mitochondria to enable high-level amorpha-4,11-diene production. In addition, we also found the mitochondrial compartment serves as a partial barrier for the translocation of FPP from mitochondria into the cytosol, which would potentially allow minimized loss of FPP to cytosolic competing pathways. To our best knowledge, this is the first report to harness yeast mitochondria for terpenoid productions from the mitochondrial acetyl-CoA pool. We envision subcellular metabolic engineering might also be employed for an efficient production of other bio-products from the mitochondrial acetyl-CoA in other eukaryotic organisms.
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47
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Yeast metabolic chassis designs for diverse biotechnological products. Sci Rep 2016; 6:29694. [PMID: 27430744 PMCID: PMC4949481 DOI: 10.1038/srep29694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, however, lagging behind, as it requires substantial engineering of the host metabolism. A chassis strain suitable for production of a range of molecules is therefore highly sought after but remains elusive. Here, we propose a genome-scale metabolic modeling approach to design chassis strains of Saccharomyces cerevisiae - a widely used microbial cell factory. For a group of 29 products covering a broad range of biochemistry and applications, we identified modular metabolic engineering strategies for re-routing carbon flux towards the desired product. We find distinct product families with shared targets forming the basis for the corresponding chassis cells. The design strategies include overexpression targets that group products by similarity in precursor and cofactor requirements, as well as gene deletion strategies for growth-product coupling that lead to non-intuitive product groups. Our results reveal the extent and the nature of flux re-routing necessary for producing a diverse range of products in a widely used cell factory and provide blueprints for constructing pre-optimized chassis strains.
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48
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Lian J, Zhao H. Functional Reconstitution of a Pyruvate Dehydrogenase in the Cytosol of Saccharomyces cerevisiae through Lipoylation Machinery Engineering. ACS Synth Biol 2016; 5:689-97. [PMID: 26991359 DOI: 10.1021/acssynbio.6b00019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acetyl-CoA is a key precursor for the biosynthesis of a wide range of fuels, chemicals, and value-added compounds, whose biosynthesis in Saccharomyces cerevisiae involves acetyl-CoA synthetase (ACS) and is energy intensive. Previous studies have demonstrated that functional expression of a pyruvate dehydrogenase (PDH) could fully replace the endogenous ACS-dependent pathway for cytosolic acetyl-CoA biosynthesis in an ATP-independent manner. However, the requirement for lipoic acid (LA) supplementation hinders its wide industrial applications. In the present study, we focus on the engineering of a de novo synthetic lipoylation machinery for reconstitution of a functional PDH in the cytosol of yeast. First, a LA auxotrophic yeast strain was constructed through the expression of the Escherichia coli PDH structural genes and a lipoate-protein ligase gene in an ACS deficient (acs1Δ acs2Δ) strain, based on which an in vivo acetyl-CoA reporter was developed for following studies. Then the de novo lipoylation pathway was reconstituted in the cytosol of yeast by coexpressing the yeast mitochondrial lipoylation machinery genes and the E. coli type II fatty acid synthase (FAS) genes. Alternatively, an unnatural de novo synthetic lipoylation pathway was constructed by combining the reversed β-oxidation pathway with an acyl-ACP synthetase gene. To the best of our knowledge, reconstitution of natural and unnatural de novo synthetic lipoylation pathways for functional expression of a PDH in the cytosol of yeast has never been reported. Our study has laid a solid foundation for the construction and further optimization of acetyl-CoA overproducing yeast strains.
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Affiliation(s)
- Jiazhang Lian
- Department of Chemical and Biomolecular Engineering,
Institute for
Genomic Biology, and ‡Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering,
Institute for
Genomic Biology, and ‡Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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49
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Requirements for Carnitine Shuttle-Mediated Translocation of Mitochondrial Acetyl Moieties to the Yeast Cytosol. mBio 2016; 7:mBio.00520-16. [PMID: 27143389 PMCID: PMC4959659 DOI: 10.1128/mbio.00520-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In many eukaryotes, the carnitine shuttle plays a key role in intracellular transport of acyl moieties. Fatty acid-grown Saccharomyces cerevisiae cells employ this shuttle to translocate acetyl units into their mitochondria. Mechanistically, the carnitine shuttle should be reversible, but previous studies indicate that carnitine shuttle-mediated export of mitochondrial acetyl units to the yeast cytosol does not occur in vivo. This apparent unidirectionality was investigated by constitutively expressing genes encoding carnitine shuttle-related proteins in an engineered S. cerevisiae strain, in which cytosolic acetyl coenzyme A (acetyl-CoA) synthesis could be switched off by omitting lipoic acid from growth media. Laboratory evolution of this strain yielded mutants whose growth on glucose, in the absence of lipoic acid, was l-carnitine dependent, indicating that in vivo export of mitochondrial acetyl units to the cytosol occurred via the carnitine shuttle. The mitochondrial pyruvate dehydrogenase complex was identified as the predominant source of acetyl-CoA in the evolved strains. Whole-genome sequencing revealed mutations in genes involved in mitochondrial fatty acid synthesis (MCT1), nuclear-mitochondrial communication (RTG2), and encoding a carnitine acetyltransferase (YAT2). Introduction of these mutations into the nonevolved parental strain enabled l-carnitine-dependent growth on glucose. This study indicates intramitochondrial acetyl-CoA concentration and constitutive expression of carnitine shuttle genes as key factors in enabling in vivo export of mitochondrial acetyl units via the carnitine shuttle. This study demonstrates, for the first time, that Saccharomyces cerevisiae can be engineered to employ the carnitine shuttle for export of acetyl moieties from the mitochondria and, thereby, to act as the sole source of cytosolic acetyl-CoA. Further optimization of this ATP-independent mechanism for cytosolic acetyl-CoA provision can contribute to efficient, yeast-based production of industrially relevant compounds derived from this precursor. The strains constructed in this study, whose growth on glucose depends on a functional carnitine shuttle, provide valuable models for further functional analysis and engineering of this shuttle in yeast and other eukaryotes.
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50
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Luo X, Zhao S, Huan T, Sun D, Friis RMN, Schultz MC, Li L. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res 2016; 15:1602-12. [PMID: 26947805 DOI: 10.1021/acs.jproteome.6b00070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types.
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Affiliation(s)
- Xian Luo
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Shuang Zhao
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Tao Huan
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Difei Sun
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - R Magnus N Friis
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Michael C Schultz
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Liang Li
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
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