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Guo Q, Xu J, Li J, Tang S, Cheng Y, Gao B, Xiong LB, Xiong J, Wang FQ, Wei DZ. Synergistic increase in coproporphyrin III biosynthesis by mitochondrial compartmentalization in engineered Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 9:834-841. [PMID: 39113689 PMCID: PMC11305229 DOI: 10.1016/j.synbio.2024.07.001] [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: 05/15/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Coproporphyrin III (CP III), a natural porphyrin derivative, has extensive applications in the biomedical and material industries. S. cerevisiae has previously been engineered to highly accumulate the CP III precursor 5-aminolevulinic acid (ALA) through the C4 pathway. In this study, a combination of cytoplasmic metabolic engineering and mitochondrial compartmentalization was used to enhance CP III production in S. cerevisiae. By integrating pathway genes into the chromosome, the CP III titer gradually increased to 32.5 ± 0.5 mg/L in shake flask cultivation. Nevertheless, increasing the copy number of pathway genes did not consistently enhance CP III synthesis. Hence, the partial synthesis pathway was compartmentalized in mitochondria to evaluate its effectiveness in increasing CP III production. Subsequently, by superimposing the mitochondrial compartmentalization strategy on cytoplasmic metabolic engineered strains, the CP III titer was increased to 64.3 ± 1.9 mg/L. Furthermore, augmenting antioxidant pathway genes to reduce reactive oxygen species (ROS) levels effectively improved the growth of engineered strains, resulting in a further increase in the CP III titer to 82.9 ± 1.4 mg/L. Fed-batch fermentations in a 5 L bioreactor achieved a titer of 402.8 ± 9.3 mg/L for CP III. This study provides a new perspective on engineered yeast for the microbial production of porphyrins.
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Affiliation(s)
- Qidi Guo
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaqi Xu
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jiacun Li
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuyan Tang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuhui Cheng
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bei Gao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Liang-Bin Xiong
- Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jie Xiong
- Department of Gastroenterology, Tongji Institute of Digestive Disease, Tongji Hospital, School of Medicine, TongJi University, Shanghai, 200065, China
| | - Feng-Qing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Dong-Zhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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Shimazaki S, Yamada R, Yamamoto Y, Matsumoto T, Ogino H. Building a machine-learning model to predict optimal mevalonate pathway gene expression levels for efficient production of a carotenoid in yeast. Biotechnol J 2024; 19:e2300285. [PMID: 37953664 DOI: 10.1002/biot.202300285] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Simultaneous modification of the expression levels of many metabolic enzyme genes results in diverse expression ratios of these genes; however, the relationship between gene expression levels and chemical productivity remains unclear. However, clarification of this relationship is expected to improve the productivity of useful chemicals. Supervised machine learning is considered to be an effective means to clarify this relationship. In this study, to improve the productivity of carotenoids in yeast Saccharomyces cerevisiae, we aimed to build a machine-learning model that can predict the optimal gene expression level for carotenoid production. First, we obtained data on the expression levels of mevalonate pathway enzyme genes and carotenoid production. Then, based on these data, we built a machine-learning model to predict carotenoid productivity based on gene expression levels. The prediction accuracy of 0.6292 (coefficient of determination) was achieved using the test data. The maximum predicted carotenoid productivity was 4.3 times higher in the engineered strain than in the parental strain, suggesting that the expression levels of the mevalonate pathway enzyme genes tHMG1 and ERG8 have a particularly large impact on carotenoid productivity. This study could be one of the important achievements in addressing the uncertainty of genotype-phenotype correlations, which is one of the challenges facing metabolic engineering strategies.
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Affiliation(s)
- Shun Shimazaki
- Department of Chemical Engineering, Osaka Metropolitan University, Sakai, Osaka, Japan
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, Sakai, Osaka, Japan
| | - Yoshiki Yamamoto
- Department of Chemical Engineering, Osaka Metropolitan University, Sakai, Osaka, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, Sakai, Osaka, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, Sakai, Osaka, Japan
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3
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Feng Q, Ning X, Qin L, Li J, Li C. Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2023; 11:1218832. [PMID: 38026848 PMCID: PMC10666755 DOI: 10.3389/fbioe.2023.1218832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs. Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP64-p65-Rta) and inhibiting effector proteins (KRAB, MeCP2, and KRAB-MeCP2), along with RNA scaffolds of MS2, PP7 and crRNA arrays were implemented in different combinations to investigate quantitative promoter strength. In the CRISPR/dCas9 system, the regulation rate ranged from 81.9% suppression to 627% activation in the mCherry gene reporter system. Studies on crRNA point mutations and crRNA arrays were conducted in the CRISPR/dCpf1 system, with the highest transcriptional inhibitory rate reaching up to 530% higher than the control. Furthermore, the orthogonal CRISPR/dCas9-dCpf1 inhibition system displayed distinct dual functions, simultaneously regulating the mCherry gene by dCas9/gRNA (54.6% efficiency) and eGFP gene by dCpf1/crRNA (62.4% efficiency) without signal crosstalk. Results and discussion: Finally, we established an engineered yeast cell factory for β-carotene production using the CRISPR/dCas9-dCpf1 bifunctional system to achieve targeted modulation of both heterologous and endogenous metabolic pathways in Saccharomyces cerevisiae. The system includes an activation module of CRISPRa/dCas9 corresponding to a gRNA-protein complex library of 136 plasmids, and an inhibition module of CRISPRi/dCpf1 corresponding to a small crRNA array library. Results show that this CRISPR/dCas9-dCpf1 bifunctional orthogonal system is more quantitatively effective and expandable for simultaneous CRISPRa/i network control compared to single-guide edition, demonstrating higher potential of future application in yeast biotechnology.
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Affiliation(s)
- Qing Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Xiaoyu Ning
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Jun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Lab for Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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4
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Yamamoto Y, Yamada R, Matsumoto T, Ogino H. Construction of a machine-learning model to predict the optimal gene expression level for efficient production of D-lactic acid in yeast. World J Microbiol Biotechnol 2023; 39:69. [PMID: 36607503 DOI: 10.1007/s11274-022-03515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
The modification of gene expression is being researched in the production of useful chemicals by metabolic engineering of the yeast Saccharomyces cerevisiae. When the expression levels of many metabolic enzyme genes are modified simultaneously, the expression ratio of these genes becomes diverse; the relationship between the gene expression ratio and chemical productivity remains unclear. In other words, it is challenging to predict phenotypes from genotypes. However, the productivity of useful chemicals can be improved if this relationship is clarified. In this study, we aimed to construct a machine-learning model that can be used to clarify the relationship between gene expression levels and D-lactic acid productivity and predict the optimal gene expression level for efficient D-lactic acid production in yeast. A machine-learning model was constructed using data on D-lactate dehydrogenase and glycolytic genes expression (13 dimensions) and D-lactic acid productivity. The coefficient of determination of the completed machine-learning model was 0.6932 when using the training data and 0.6628 when using the test data. Using the constructed machine-learning model, we predicted the optimal gene expression level for high D-lactic acid production. We successfully constructed a machine-learning model to predict both D-lactic acid productivity and the suitable gene expression ratio for the production of D-lactic acid. The technique established in this study could be key for predicting phenotypes from genotypes, a problem faced by recent metabolic engineering strategies.
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Affiliation(s)
- Yoshiki Yamamoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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Chaturvedi S, Bhattacharya A, Rout PK, Nain L, Khare SK. An Overview of Enzymes and Rate-Limiting Steps Responsible for Lipid Production in Oleaginous Yeast. Ind Biotechnol (New Rochelle N Y) 2022. [DOI: 10.1089/ind.2021.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Prasant K. Rout
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Lata Nain
- Division of Microbiology, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
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6
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Pereira H, Azevedo F, Domingues L, Johansson B. Expression of Yarrowia lipolytica acetyl-CoA carboxylase in Saccharomyces cerevisiae and its effect on in-vivo accumulation of Malonyl-CoA. Comput Struct Biotechnol J 2022; 20:779-787. [PMID: 36284710 PMCID: PMC9582701 DOI: 10.1016/j.csbj.2022.01.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Novel S. cerevisiae strain with tetracycline repressible ACC1 promoter. Functional expression of Y. lipolytica ACC1 in S. cerevisiae. Higher malonyl-CoA concentration achieved with Y. lipolytica ACC1 gene. S. cerevisiae Acc1p seems to interact with the heterologous Y. lipolytica Acc1p.
Malonyl-CoA is an energy-rich molecule formed by the ATP-dependent carboxylation of acetyl coenzyme A catalyzed by acetyl-CoA carboxylase. This molecule is an important precursor for many biotechnologically interesting compounds such as flavonoids, polyketides, and fatty acids. The yeast Saccharomyces cerevisiae remains one of the preferred cell factories, but has a limited capacity to produce malonyl-CoA compared to oleaginous organisms. We developed a new S. cerevisiae strain with a conditional allele of ACC1, the essential acetyl-CoA carboxylase (ACC) gene, as a tool to test heterologous genes for complementation. Yarrowia lipolytica is an oleaginous yeast with a higher capacity for lipid production than S. cerevisiae, possibly due to a higher capacity to produce malonyl-CoA. Measuring relative intracellular malonyl-CoA levels with an in-vivo biosensor confirmed that expression of Y. lipolytica ACC in S. cerevisiae leads to a higher accumulation of malonyl-CoA compared with overexpression of the native gene from an otherwise identical vector. The higher accumulation was generally accompanied by a decreased growth rate. Concomitant expression of both the homologous and heterologous ACC1 genes eliminated the growth defect, with a marginal reduction of malonyl-CoA accumulation.
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Affiliation(s)
- Humberto Pereira
- CBMA - Center of Molecular and Environmental Biology Engineering
| | - Flávio Azevedo
- CBMA - Center of Molecular and Environmental Biology Engineering
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology Engineering
- Corresponding author.
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7
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Zhang Q, Yu S, Lyu Y, Zeng W, Zhou J. Systematically Engineered Fatty Acid Catabolite Pathway for the Production of (2 S)-Naringenin in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:1166-1175. [PMID: 33877810 DOI: 10.1021/acssynbio.1c00002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The (2S)-naringenin is an important natural flavonoid with several bioactive effects on human health. It is also a key precursor in the biosynthesis of other high value compounds. The production of (2S)-naringenin is significantly influenced by the acetyl-CoA available in the cytosol. In this study, we increased the acetyl-CoA supply via the β-oxidation of fatty acids in the peroxisomes of Saccharomyces cerevisiae. Several lipases from different sources and PEX11, FOX1, FOX2, and FOX3, the key genes of the fatty acid β-oxidation pathway, were overexpressed during the production of (2S)-naringenin in yeast. The level of acetyl-CoA was 0.205 nmol higher than that in the original strain and the production of (2S)-naringenin increased to 286.62 mg/g dry cell weight when PEX11 was overexpressed in S. cerevisiae strain L07. Remarkable (2S)-naringenin production (1129.44 mg/L) was achieved with fed-batch fermentation, with the highest titer reported in any microorganism. Our results demonstrated the use of fatty acid β-oxidation to increase the level of cytoplasmic acetyl-CoA and the production of its derivatives.
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Affiliation(s)
- Qian Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunbin Lyu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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8
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Li S, Zhang Q, Wang J, Liu Y, Zhao Y, Deng Y. Recent progress in metabolic engineering of Saccharomyces cerevisiae for the production of malonyl-CoA derivatives. J Biotechnol 2020; 325:83-90. [PMID: 33278463 DOI: 10.1016/j.jbiotec.2020.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 02/08/2023]
Abstract
To reduce dependence on petroleum, the biosynthesis of important chemicals from simple substrates using industrial microorganisms has attracted increased attention. Metabolic engineering of Saccharomyces cerevisiae offers a sustainable and flexible alternative for the production of various chemicals. As a key metabolic intermediate, malonyl-CoA is a precursor for many useful compounds. However, the productivity of malonyl-CoA derivatives is restricted by the low cellular level of malonyl-CoA and enzymatic performance. In this review, we focused on how to increase the intracellular malonyl-CoA level and summarize the recent advances in different metabolic engineering strategies for directing intracellular malonyl-CoA to the desired malonyl-CoA derivatives, including strengthening the malonyl-CoA supply, reducing malonyl-CoA consumption, and precisely controlling the intracellular malonyl-CoA level. These strategies provided new insights for further improving the synthesis of malonyl-CoA derivatives in microorganisms.
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Affiliation(s)
- Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Qiyue Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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9
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Discovering Low Toxicity Ionic Liquids for Saccharomyces cerevisiae by Using the Agar Well Diffusion Test. Processes (Basel) 2020. [DOI: 10.3390/pr8091163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Ionic liquids (ILs) are new solvents widely used in many technologies due to their unique and advantageous physicochemical properties. In biotechnological applications, ILs can be used along with microorganisms such as Saccharomyces cerevisiae. Due to the enormous number of ILs that can be synthesized through the combination of different anions and cations, it is necessary to have an easy and quick tool for the preliminary screening of their biocompatibility for being used in biotechnological applications. In this work, the agar well diffusion test was successfully applied as a rapid method to identify toxic/nontoxic ILs toward S. cerevisiae. Sixty-three ILs containing a diverse set of cations and anions were used. Through this methodology, nine fully biocompatible ILs toward S. cerevisiae were identified, including: [Bmim+] [NO3−], [HOPmim+] [NO3−], [Bmim+] [NTf2−], [N8,8,8,1+] [NTf2−], [S2,2,2+] [NTf2−], [EMPyr+] [NTf2−], [BMPi+] [NTf2−], [Moxa+] [MeSO4−] and [Chol+] [H2PO4−]. The analysis of the results also provides preliminary rules to enable the design of biocompatible ILs with S. cerevisiae. In this context, the toxicity was mainly determined by the cation nature although some anions can also display a strong influence on the IL biocompatibility as the bistriflimide anion. Besides, it was observed that an increase in the alkyl chain length of cations, such as imidazolium or pyridinium, involves an increase in the IL toxicity.
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10
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Cunha JT, Soares PO, Baptista SL, Costa CE, Domingues L. Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production. Bioengineered 2020; 11:883-903. [PMID: 32799606 PMCID: PMC8291843 DOI: 10.1080/21655979.2020.1801178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biorefinery concept, consisting in using renewable biomass with economical and energy goals, appeared in response to the ongoing exhaustion of fossil reserves. Bioethanol is the most prominent biofuel and has been considered one of the top chemicals to be obtained from biomass. Saccharomyces cerevisiae, the preferred microorganism for ethanol production, has been the target of extensive genetic modifications to improve the production of this alcohol from renewable biomasses. Additionally, S. cerevisiae strains from harsh industrial environments have been exploited due to their robust traits and improved fermentative capacity. Nevertheless, there is still not an optimized strain capable of turning second generation bioprocesses economically viable. Considering this, and aiming to facilitate and guide the future development of effective S. cerevisiae strains, this work reviews genetic engineering strategies envisioning improvements in 2nd generation bioethanol production, with special focus in process-related traits, xylose consumption, and consolidated bioprocessing. Altogether, the genetic toolbox described proves S. cerevisiae to be a key microorganism for the establishment of a bioeconomy, not only for the production of lignocellulosic bioethanol, but also having potential as a cell factory platform for overall valorization of renewable biomasses.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
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11
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Zhou S, Hao T, Xu S, Deng Y. Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds. Biotechnol Adv 2020; 43:107575. [PMID: 32512221 DOI: 10.1016/j.biotechadv.2020.107575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shumin Xu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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12
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Engineering Yarrowia lipolytica towards food waste bioremediation: Production of fatty acid ethyl esters from vegetable cooking oil. J Biosci Bioeng 2020; 129:31-40. [DOI: 10.1016/j.jbiosc.2019.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/22/2022]
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13
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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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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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15
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Microbial conversion of xylose into useful bioproducts. Appl Microbiol Biotechnol 2018; 102:9015-9036. [PMID: 30141085 DOI: 10.1007/s00253-018-9294-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023]
Abstract
Microorganisms can produce a number of different bioproducts from the sugars in plant biomass. One challenge is devising processes that utilize all of the sugars in lignocellulosic hydrolysates. D-xylose is the second most abundant sugar in these hydrolysates. The microbial conversion of D-xylose to ethanol has been studied extensively; only recently, however, has conversion to bioproducts other than ethanol been explored. Moreover, in the case of yeast, D-xylose may provide a better feedstock for the production of bioproducts other than ethanol, because the relevant pathways are not subject to glucose-dependent repression. In this review, we discuss how different microorganisms are being used to produce novel bioproducts from D-xylose. We also discuss how D-xylose could be potentially used instead of glucose for the production of value-added bioproducts.
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16
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Chaturvedi S, Bhattacharya A, Khare SK. Trends in Oil Production from Oleaginous Yeast Using Biomass: Biotechnological Potential and Constraints. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s000368381804004x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Lian J, HamediRad M, Zhao H. Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System. Biotechnol J 2018; 13:e1700601. [PMID: 29436783 DOI: 10.1002/biot.201700601] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/22/2018] [Indexed: 12/20/2022]
Abstract
Thanks to its ease of use, modularity, and scalability, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been increasingly used in the design and engineering of Saccharomyces cerevisiae, one of the most popular hosts for industrial biotechnology. This review summarizes the recent development of this disruptive technology for metabolic engineering applications, including CRISPR-mediated gene knock-out and knock-in as well as transcriptional activation and interference. More importantly, multi-functional CRISPR systems that combine both gain- and loss-of-function modulations for combinatorial metabolic engineering are highlighted.
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Affiliation(s)
- Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana,IL 61801, United States
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18
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Fan Y, Meng HM, Hu GR, Li FL. Biosynthesis of nervonic acid and perspectives for its production by microalgae and other microorganisms. Appl Microbiol Biotechnol 2018; 102:3027-3035. [PMID: 29478140 DOI: 10.1007/s00253-018-8859-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 12/15/2022]
Abstract
Nervonic acid (NA) is a major very long-chain monounsaturated fatty acid found in the white matter of mammalian brains, which plays a critical role in the treatment of psychotic disorders and neurological development. In the nature, NA has been synthesized by a handful plants, fungi, and microalgae. Although the metabolism of fatty acid has been studied for decades, the biosynthesis of NA has yet to be illustrated. Generally, the biosynthesis of NA is considered starting from oleic acid through fatty acid elongation, in which malonyl-CoA and long-chain acyl-CoA are firstly condensed by a rate-limiting enzyme 3-ketoacyl-CoA synthase (KCS). Heterologous expression of kcs gene from high NA producing species in plants and yeast has led to synthesis of NA. Nevertheless, it has also been reported that desaturases in a few plants can catalyze very long-chain saturated fatty acid into NA. This review highlights recent advances in the biosynthesis, the sources, and the biotechnological aspects of NA.
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Affiliation(s)
- Yong Fan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, People's Republic of China
| | - Hui-Min Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, People's Republic of China
| | - Guang-Rong Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, People's Republic of China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, People's Republic of China.
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19
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Lian J, HamediRad M, Hu S, Zhao H. Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system. Nat Commun 2017; 8:1688. [PMID: 29167442 PMCID: PMC5700065 DOI: 10.1038/s41467-017-01695-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/10/2017] [Indexed: 12/24/2022] Open
Abstract
Designing an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We demonstrate the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner. Metaboli engineering through gene overexpression, knock-down and knock-out is often carried out sequentially in a high labor, low-throughput manner. Here, the authors use CRISPR-mediated gene activation, interference and deletion to rapidly rewire S. cerevisiae metabolism in a single step.
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Affiliation(s)
- Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sumeng Hu
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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20
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Shi S, Zhao H. Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals. Front Microbiol 2017; 8:2185. [PMID: 29167664 PMCID: PMC5682390 DOI: 10.3389/fmicb.2017.02185] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/25/2017] [Indexed: 01/23/2023] Open
Abstract
Oleaginous yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.
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Affiliation(s)
- Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Huimin Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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21
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Yuzbasheva EY, Mostova EB, Andreeva NI, Yuzbashev TV, Fedorov AS, Konova IA, Sineoky SP. A metabolic engineering strategy for producing free fatty acids by the Yarrowia lipolytica yeast based on impairment of glycerol metabolism. Biotechnol Bioeng 2017; 115:433-443. [PMID: 28832949 DOI: 10.1002/bit.26402] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/04/2017] [Accepted: 08/14/2017] [Indexed: 12/23/2022]
Abstract
In recent years, bio-based production of free fatty acids from renewable resources has attracted attention for their potential as precursors for the production of biofuels and biochemicals. In this study, the oleaginous yeast Yarrowia lipolytica was engineered to produce free fatty acids by eliminating glycerol metabolism. Free fatty acid production was monitored under lipogenic conditions with glycerol as a limiting factor. Firstly, the strain W29 (Δgpd1), which is deficient in glycerol synthesis, was obtained. However, W29 (Δgpd1) showed decreased biomass accumulation and glucose consumption in lipogenic medium containing a limiting supply of glycerol. Analysis of substrate utilization from a mixture of glucose and glycerol by the parental strain W29 revealed that glycerol was metabolized first and glucose utilization was suppressed. Thus, the Δgpd1Δgut2 double mutant, which is deficient also in glycerol catabolism, was constructed. In this genetic background, growth was repressed by glycerol. Oleate toxicity was observed in the Δgpd1Δgut2Δpex10 triple mutant strain which is deficient additionally in peroxisome biogenesis. Consequently, two consecutive rounds of selection of spontaneous mutants were performed. A mutant released from growth repression by glycerol was able to produce 136.8 mg L-1 of free fatty acids in a test tube, whereas the wild type accumulated only 30.2 mg L-1 . Next, an isolated oleate-resistant strain produced 382.8 mg L-1 of free fatty acids. Finely, acyl-CoA carboxylase gene (ACC1) over-expression resulted to production of 1436.7 mg L-1 of free fatty acids. The addition of dodecane promoted free fatty acid secretion and enhanced the level of free fatty acids up to 2033.8 mg L-1 during test tube cultivation.
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Affiliation(s)
- Evgeniya Y Yuzbasheva
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | - Elizaveta B Mostova
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | - Natalia I Andreeva
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | - Tigran V Yuzbashev
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | - Alexander S Fedorov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
| | - Irina A Konova
- National Research Centre "Kurchatov Institute," NBICS-Centre, Biotechnology and Bioenergy Laboratory, Moscow, Russia
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), Moscow, Russia
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22
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Menendez-Bravo S, Comba S, Gramajo H, Arabolaza A. Metabolic engineering of microorganisms for the production of structurally diverse esters. Appl Microbiol Biotechnol 2017; 101:3043-3053. [PMID: 28275821 DOI: 10.1007/s00253-017-8179-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 11/25/2022]
Abstract
Conventional petroleum-based chemical industry, although economically still thriving, is now facing great socio-political challenges due to the increasing concerns on climate change and limited availability of fossil resources. In this context, microbial production of fuels and commodity oleochemicals from renewable biomass is being considered a promising sustainable alternative. The increasing understanding of cellular systems has enabled the redesign of microbial metabolism for the production of compounds present in many daily consumer products such as esters, waxes, fatty acids (FA) and fatty alcohols. Small aliphatic esters are important flavour and fragrance elements while long-chain esters, composed of FA esterified to fatty alcohols, are widely used in lubricant formulas, paints, coatings and cosmetics. Here, we review recent advances in the biosynthesis of these types of mono alkyl esters in vivo. We focus on the critical ester bond-forming enzymes and the latest metabolic engineering strategies employed for the biosynthesis of a wide range of products ranging from low-molecular-weight esters to waxy compounds.
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Affiliation(s)
- Simón Menendez-Bravo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Santiago Comba
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Hugo Gramajo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (2000), Rosario, Argentina.
| | - Ana Arabolaza
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda (2000), Rosario, Argentina.
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23
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Liu W, Zhang B, Jiang R. Improving acetyl-CoA biosynthesis in Saccharomyces cerevisiae via the overexpression of pantothenate kinase and PDH bypass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:41. [PMID: 28239413 PMCID: PMC5316175 DOI: 10.1186/s13068-017-0726-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/09/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Acetyl-CoA is an important precursor in Saccharomyces cerevisiae. Various approaches have been adopted to improve its cytosolic level previously with the emphasis on engineering the "acetyl-" part of acetyl-CoA. To the best of our knowledge, there have been no reports on engineering the "-CoA" part so far. RESULTS In this study, we had tried to engineer S. cerevisiae from both the "-CoA" part via pantothenate kinase overexpression (PanK from S. cerevisiae, the rate-limiting enzyme for CoA synthesis) and the "acetyl-"part through PDH bypass introduction (ALD6 from S. cerevisiae and SeAcsL641P from Salmonella enteric). A naringenin-producing reporter strain had been constructed to reflect cytosolic acetyl-CoA level as acetyl-CoA is the precursor of naringenin. It was found that PanK overexpression or PDH bypass introduction alone only led to a twofold or 6.74-fold increase in naringenin titer, but the combination of both (strain CENFPAA01) had resulted in 24.4-fold increase as compared to the control (strain CENF09) in the presence of 0.5 mM substrate p-coumaric acid. The supplement of PanK substrate pantothenate resulted in another 19% increase in naringenin production. CONCLUSIONS To greatly enhance acetyl-CoA level in yeast cytosol, it is feasible to engineer both the "acetyl-" part and the "-CoA" part simultaneously. Insufficient CoA supply might aggravate acetyl-CoA shortage and cause low yield of target product.
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Affiliation(s)
- Wenshan Liu
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Bo Zhang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
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Jiménez-Díaz L, Caballero A, Pérez-Hernández N, Segura A. Microbial alkane production for jet fuel industry: motivation, state of the art and perspectives. Microb Biotechnol 2016; 10:103-124. [PMID: 27723249 PMCID: PMC5270751 DOI: 10.1111/1751-7915.12423] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 11/27/2022] Open
Abstract
Bio‐jet fuel has attracted a lot of interest in recent years and has become a focus for aircraft and engine manufacturers, oil companies, governments and researchers. Given the global concern about environmental issues and the instability of oil market, bio‐jet fuel has been identified as a promising way to reduce the greenhouse gas emissions from the aviation industry, while also promoting energy security. Although a number of bio‐jet fuel sources have been approved for manufacture, their commercialization and entry into the market is still a far way away. In this review, we provide an overview of the drivers for intensified research into bio‐jet fuel technologies, the type of chemical compounds found in bio‐jet fuel preparations and the current state of related pre‐commercial technologies. The biosynthesis of hydrocarbons is one of the most promising approaches for bio‐jet fuel production, and thus we provide a detailed analysis of recent advances in the microbial biosynthesis of hydrocarbons (with a focus on alkanes). Finally, we explore the latest developments and their implications for the future of research into bio‐jet fuel technologies.
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Affiliation(s)
- Lorena Jiménez-Díaz
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | - Antonio Caballero
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain
| | | | - Ana Segura
- Abengoa Research, Campus Palmas Altas, C/Energía Solar, 41014, Sevilla, Spain.,Estación Experimental del Zaidín-CSIC, C/Profesor Albareda s/n, 18008, Granada, Spain
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25
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Improved ethyl caproate production of Chinese liquor yeast by overexpressing fatty acid synthesis genes with OPI1 deletion. J Ind Microbiol Biotechnol 2016; 43:1261-70. [PMID: 27344573 DOI: 10.1007/s10295-016-1795-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
During yeast fermentation, ethyl esters play a key role in the development of the flavor profiles of Chinese liquor. Ethyl caproate, an ethyl ester eliciting apple-like flavor, is the characteristic flavor of strong aromatic liquor, which is the best selling liquor in China. In the traditional fermentation process, ethyl caproate is mainly produced at the later fermentation stage by aroma-producing yeast, bacteria, and mold in a mud pit instead of Saccharomyces cerevisiae at the expense of grains and fermentation time. To improve the production of ethyl caproate by Chinese liquor yeast (S. cerevisiae) with less food consumption and shorter fermentation time, we constructed three recombinant strains, namely, α5-ACC1ΔOPI1, α5-FAS1ΔOPI1, and α5-FAS2ΔOPI1 by overexpressing acetyl-CoA carboxylase (ACC1), fatty acid synthase 1 (FAS1), and fatty acid synthase 2 (FAS2) with OPI1 (an inositol/choline-mediated negative regulatory gene) deletion, respectively. In the liquid fermentation of corn hydrolysate, the contents of ethyl caproate produced by α5-ACC1ΔOPI1, α5-FAS1ΔOPI1, and α5-FAS2ΔOPI1 increased by 0.40-, 1.75-, and 0.31-fold, correspondingly, compared with the initial strain α5. The contents of other fatty acid ethyl esters (FAEEs) (C8:0, C10:0, C12:0) also increased. In comparison, the content of FAEEs produced by α5-FAS1ΔOPI1 significantly improved. Meanwhile, the contents of acetyl-CoA and ethyl acetate were enhanced by α5-FAS1ΔOPI1. Overall, this study offers a promising platform for the development of pure yeast culture fermentation of Chinese strong aromatic liquor without the use of a mud pit.
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26
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van Rossum HM, Kozak BU, Pronk JT, van Maris AJA. Engineering cytosolic acetyl-coenzyme A supply in Saccharomyces cerevisiae: Pathway stoichiometry, free-energy conservation and redox-cofactor balancing. Metab Eng 2016; 36:99-115. [PMID: 27016336 DOI: 10.1016/j.ymben.2016.03.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/20/2016] [Accepted: 03/21/2016] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae is an important industrial cell factory and an attractive experimental model for evaluating novel metabolic engineering strategies. Many current and potential products of this yeast require acetyl coenzyme A (acetyl-CoA) as a precursor and pathways towards these products are generally expressed in its cytosol. The native S. cerevisiae pathway for production of cytosolic acetyl-CoA consumes 2 ATP equivalents in the acetyl-CoA synthetase reaction. Catabolism of additional sugar substrate, which may be required to generate this ATP, negatively affects product yields. Here, we review alternative pathways that can be engineered into yeast to optimize supply of cytosolic acetyl-CoA as a precursor for product formation. Particular attention is paid to reaction stoichiometry, free-energy conservation and redox-cofactor balancing of alternative pathways for acetyl-CoA synthesis from glucose. A theoretical analysis of maximally attainable yields on glucose of four compounds (n-butanol, citric acid, palmitic acid and farnesene) showed a strong product dependency of the optimal pathway configuration for acetyl-CoA synthesis. Moreover, this analysis showed that combination of different acetyl-CoA production pathways may be required to achieve optimal product yields. This review underlines that an integral analysis of energy coupling and redox-cofactor balancing in precursor-supply and product-formation pathways is crucial for the design of efficient cell factories.
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Affiliation(s)
- Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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27
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van Rossum HM, Kozak BU, Niemeijer MS, Duine HJ, Luttik MAH, Boer VM, Kötter P, Daran JMG, van Maris AJA, Pronk JT. Alternative reactions at the interface of glycolysis and citric acid cycle in Saccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow017. [PMID: 26895788 PMCID: PMC5815053 DOI: 10.1093/femsyr/fow017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2016] [Indexed: 11/14/2022] Open
Abstract
Pyruvate and acetyl-coenzyme A, located at the interface between glycolysis and TCA cycle, are important intermediates in yeast metabolism and key precursors for industrially relevant products. Rational engineering of their supply requires knowledge of compensatory reactions that replace predominant pathways when these are inactivated. This study investigates effects of individual and combined mutations that inactivate the mitochondrial pyruvate-dehydrogenase (PDH) complex, extramitochondrial citrate synthase (Cit2) and mitochondrial CoA-transferase (Ach1) in Saccharomyces cerevisiae. Additionally, strains with a constitutively expressed carnitine shuttle were constructed and analyzed. A predominant role of the PDH complex in linking glycolysis and TCA cycle in glucose-grown batch cultures could be functionally replaced by the combined activity of the cytosolic PDH bypass and Cit2. Strongly impaired growth and a high incidence of respiratory deficiency in pda1Δ ach1Δ strains showed that synthesis of intramitochondrial acetyl-CoA as a metabolic precursor requires activity of either the PDH complex or Ach1. Constitutive overexpression of AGP2, HNM1, YAT2, YAT1, CRC1 and CAT2 enabled the carnitine shuttle to efficiently link glycolysis and TCA cycle in l-carnitine-supplemented, glucose-grown batch cultures. Strains in which all known reactions at the glycolysis-TCA cycle interface were inactivated still grew slowly on glucose, indicating additional flexibility at this key metabolic junction.
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Affiliation(s)
- Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Matthijs S Niemeijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Hendrik J Duine
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Viktor M Boer
- DSM Biotechnology Center, Alexander Fleminglaan 1, NL-2613 AX Delft, The Netherlands
| | - Peter Kötter
- Institute for Molecular Bio Sciences, Goethe University, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
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Pérez-Torrado R, Gamero E, Gómez-Pastor R, Garre E, Aranda A, Matallana E. Yeast biomass, an optimised product with myriad applications in the food industry. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Teo WS, Ling H, Yu AQ, Chang MW. Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid short- and branched-chain alkyl esters biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:177. [PMID: 26543501 PMCID: PMC4634726 DOI: 10.1186/s13068-015-0361-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/22/2015] [Indexed: 06/01/2023]
Abstract
BACKGROUND Biodiesel is a mixture of fatty acid short-chain alkyl esters of different fatty acid carbon chain lengths. However, while fatty acid methyl or ethyl esters are useful biodiesel produced commercially, fatty acid esters with branched-chain alcohol moieties have superior fuel properties. Crucially, this includes improved cold flow characteristics, as one of the major problems associated with biodiesel use is poor low-temperature flow properties. Hence, microbial production as a renewable, nontoxic and scalable method to produce fatty acid esters with branched-chain alcohol moieties from biomass is critical. RESULTS We engineered Saccharomyces cerevisiae to produce fatty acid short- and branched-chain alkyl esters, including ethyl, isobutyl, isoamyl and active amyl esters using endogenously synthesized fatty acids and alcohols. Two wax ester synthase genes (ws2 and Maqu_0168 from Marinobacter sp.) were cloned and expressed. Both enzymes were found to catalyze the formation of fatty acid esters, with different alcohol preferences. To boost the ability of S. cerevisiae to produce the aforementioned esters, negative regulators of the INO1 gene in phospholipid metabolism, Rpd3 and Opi1, were deleted to increase flux towards fatty acyl-CoAs. In addition, five isobutanol pathway enzymes (Ilv2, Ilv5, Ilv3, Aro10, and Adh7) targeted into the mitochondria were overexpressed to enhance production of alcohol precursors. By combining these engineering strategies with high-cell-density fermentation, over 230 mg/L fatty acid short- and branched-chain alkyl esters were produced, which is the highest titer reported in yeast to date. CONCLUSIONS In this work, we engineered the metabolism of S. cerevisiae to produce biodiesels in the form of fatty acid short- and branched-chain alkyl esters, including ethyl, isobutyl, isoamyl and active amyl esters. To our knowledge, this is the first report of the production of fatty acid isobutyl and active amyl esters in S. cerevisiae. Our findings will be useful for engineering S. cerevisiae strains toward high-level and sustainable biodiesel production.
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Affiliation(s)
- Wei Suong Teo
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117597 Singapore
- />NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Hua Ling
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117597 Singapore
- />NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Ai-Qun Yu
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117597 Singapore
- />NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
| | - Matthew Wook Chang
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117597 Singapore
- />NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456 Singapore
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Petrovič U. Next-generation biofuels: a new challenge for yeast. Yeast 2015; 32:583-93. [DOI: 10.1002/yea.3082] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 11/11/2022] Open
Affiliation(s)
- Uroš Petrovič
- Jožef Stefan Institute; Department of Molecular and Biomedical Sciences; Ljubljana Slovenia
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31
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Sheng J, Feng X. Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions. Front Microbiol 2015; 6:554. [PMID: 26106371 PMCID: PMC4459083 DOI: 10.3389/fmicb.2015.00554] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/20/2015] [Indexed: 12/14/2022] Open
Abstract
Fatty acid-derived biofuels can be a better solution than bioethanol to replace petroleum fuel, since they have similar energy content and combustion properties as current transportation fuels. The environmentally friendly microbial fermentation process has been used to synthesize advanced biofuels from renewable feedstock. Due to their robustness as well as the high tolerance to fermentation inhibitors and phage contamination, yeast strains such as Saccharomyces cerevisiae and Yarrowia lipolytica have attracted tremendous attention in recent studies regarding the production of fatty acid-derived biofuels, including fatty acids, fatty acid ethyl esters, fatty alcohols, and fatty alkanes. However, the native yeast strains cannot produce fatty acids and fatty acid-derived biofuels in large quantities. To this end, we have summarized recent publications in this review on metabolic engineering of yeast strains to improve the production of fatty acid-derived biofuels, identified the bottlenecks that limit the productivity of biofuels, and categorized the appropriate approaches to overcome these obstacles.
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Affiliation(s)
- Jiayuan Sheng
- Biomolecular Engineering Lab, Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Xueyang Feng
- Biomolecular Engineering Lab, Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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