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Liang Z, Huang C, Xia Y, Ye Z, Fan S, Zeng J, Guo S, Ma X, Sun L, Huo YX. Identification of functional sgRNA mutants lacking canonical secondary structure using high-throughput FACS screening. Cell Rep 2024; 43:114290. [PMID: 38823012 DOI: 10.1016/j.celrep.2024.114290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/22/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Coexpressing multiple identical single guide RNAs (sgRNAs) in CRISPR-dependent engineering triggers genetic instability and phenotype loss. To provide sgRNA derivatives for efficient DNA digestion, we design a high-throughput digestion-activity-dependent positive screening strategy and astonishingly obtain functional nonrepetitive sgRNA mutants with up to 48 out of the 61 nucleotides mutated, and these nonrepetitive mutants completely lose canonical secondary sgRNA structure in simulation. Cas9-sgRNA complexes containing these noncanonical sgRNAs maintain wild-type level of digestion activities in vivo, indicating that the Cas9 protein is compatible with or is able to adjust the secondary structure of sgRNAs. Using these noncanonical sgRNAs, we achieve multiplex genetic engineering for gene knockout and base editing in microbial cell factories. Libraries of strains with rewired metabolism are constructed, and overproducers of isobutanol or 1,3-propanediol are identified by biosensor-based fluorescence-activated cell sorting (FACS). This work sheds light on the remarkable flexibility of the secondary structure of functional sgRNA.
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Affiliation(s)
- Zeyu Liang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yan Xia
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zhaojin Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shunhua Fan
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Junwei Zeng
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China
| | - Lichao Sun
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China.
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2
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Sjöberg G, Reķēna A, Fornstad M, Lahtvee PJ, van Maris AJA. Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae. Metab Eng 2024; 82:49-59. [PMID: 38309619 DOI: 10.1016/j.ymben.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Enzyme-constrained genome-scale models (ecGEMs) have potential to predict phenotypes in a variety of conditions, such as growth rates or carbon sources. This study investigated if ecGEMs can guide metabolic engineering efforts to swap anaerobic redox-neutral ATP-providing pathways in yeast from alcoholic fermentation to equimolar co-production of 2,3-butanediol and glycerol. With proven pathways and low product toxicity, the ecGEM solution space aligned well with observed phenotypes. Since this catabolic pathway provides only one-third of the ATP of alcoholic fermentation (2/3 versus 2 ATP per glucose), the ecGEM predicted a growth decrease from 0.36 h-1 in the reference to 0.175 h-1 in the engineered strain. However, this <3-fold decrease would require the specific glucose consumption rate to increase. Surprisingly, after the pathway swap the engineered strain immediately grew at 0.15 h-1 with a glucose consumption rate of 29 mmol (g CDW)-1 h-1, which was indeed higher than reference (23 mmol (g CDW)-1 h-1) and one of the highest reported for S. cerevisiae. The accompanying 2,3-butanediol- (15.8 mmol (g CDW)-1 h-1) and glycerol (19.6 mmol (g CDW)-1 h-1) production rates were close to predicted values. Proteomics confirmed that this increased consumption rate was facilitated by enzyme reallocation from especially ribosomes (from 25.5 to 18.5 %) towards glycolysis (from 28.7 to 43.5 %). Subsequently, 200 generations of sequential transfer did not improve growth of the engineered strain, showing the use of ecGEMs in predicting opportunity space for laboratory evolution. The observations in this study illustrate both the current potential, as well as future improvements, of ecGEMs as a tool for both metabolic engineering and laboratory evolution.
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Affiliation(s)
- Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alīna Reķēna
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Matilda Fornstad
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petri-Jaan Lahtvee
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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3
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Meliawati M, Volke DC, Nikel PI, Schmid J. Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production. Microb Biotechnol 2024; 17:e14438. [PMID: 38529712 DOI: 10.1111/1751-7915.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next-generation biofuel. A CRISPR-Cas9-based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3-butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L-1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network-wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose-6-phosphate 1-dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation.
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Affiliation(s)
- Meliawati Meliawati
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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4
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Li ZM, Hu Z, Wang X, Chen S, Yu W, Liu J, Li Z. Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843. Int J Mol Sci 2023; 24:12198. [PMID: 37569577 PMCID: PMC10418658 DOI: 10.3390/ijms241512198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
α-Ketoglutarate decarboxylase is a crucial enzyme in the tricarboxylic acid cycle of cyanobacteria, catalyzing the non-oxidative decarboxylation of α-ketoglutarate to produce succinate semialdehyde and CO2. The decarboxylation process is reliant on the cofactor of thiamine diphosphate. However, this enzyme's biochemical and structural properties have not been well characterized. In this work, two α-ketoglutarate decarboxylases encoded by MAE_06010 and MiAbw_01735 genes from Microcystis aeruginosa NIES-843 (MaKGD) and NIES-4325 (MiKGD), respectively, were overexpressed and purified by using an Escherichia coli expression system. It was found that MaKGD exhibited 9.2-fold higher catalytic efficiency than MiKGD, which may be attributed to the absence of glutamate decarboxylase in Microcystis aeruginosa NIES-843. Further biochemical investigation of MaKGD demonstrated that it displayed optimum activity at pH 6.5-7.0 and was most activated by Mg2+. Additionally, MaKGD showed substrate specificity towards α-ketoglutarate. Structural modeling and autodocking results revealed that the active site of MaKGD contained a distinct binding pocket where α-ketoglutarate and thiamine diphosphate interacted with specific amino acid residues via hydrophobic interactions, hydrogen bonds and salt bridges. Furthermore, the mutagenesis study provided strong evidence supporting the importance of certain residues in the catalysis of MaKGD. These findings provide new insights into the structure-function relationships of α-ketoglutarate decarboxylases from cyanobacteria.
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Affiliation(s)
- Zhi-Min Li
- College of Chemistry and Materials, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Ziwei Hu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Suhang Chen
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiyan Yu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Liu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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Jo YY, Park S, Gong G, Roh S, Yoo J, Ahn JH, Lee SM, Um Y, Kim KH, Ko JK. Enhanced production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) with modulated 3-hydroxyvalerate fraction by overexpressing acetolactate synthase in Cupriavidus necator H16. Int J Biol Macromol 2023:125166. [PMID: 37270139 DOI: 10.1016/j.ijbiomac.2023.125166] [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: 03/28/2023] [Revised: 05/16/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Abstract
The elastomeric properties of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a biodegradable copolymer, strongly depend on the molar composition of 3-hydroxyvalerate (3 HV). This paper reports an improved artificial pathway for enhancing the 3HV component during PHBV biosynthesis from a structurally unrelated carbon source by Cupriavidus necator H16. To increase the intracellular accumulation of propionyl-CoA, a key precursor of the 3HV monomer, we developed a recombinant strain by genetically manipulating the branched-chain amino acid (e.g., valine, isoleucine) pathways. Overexpression of the heterologous feedback-resistant acetolactate synthase (alsS), (R)-citramalate synthase (leuA), homologous 3-ketothiolase (bktB), and the deletion of 2-methylcitrate synthase (prpC) resulted in biosynthesis of 42.5 % (g PHBV/g dry cell weight) PHBV with 64.9 mol% 3 HV monomer from fructose as the sole carbon source. This recombinant strain also accumulated the highest PHBV content of 54.5 % dry cell weight (DCW) with 24 mol% 3HV monomer from CO2 ever reported. The lithoautotrophic cell growth and PHBV production by the recombinant C. necator were promoted by oxygen stress. The thermal properties of PHBV showed a decreasing trend of the glass transition and melting temperatures with increasing 3 HV fraction. The average molecular weights of PHBV with modulated 3 HV fractions were between 20 and 26 × 104 g/mol.
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Affiliation(s)
- Young Yun Jo
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Soyoung Park
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Soonjong Roh
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jin Yoo
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jung Ho Ahn
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea.
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Moxley WC, Brown RE, Eiteman MA. Escherichia coli aceE variants coding pyruvate dehydrogenase improve the generation of pyruvate-derived acetoin. Eng Life Sci 2023; 23:e2200054. [PMID: 36874610 PMCID: PMC9978916 DOI: 10.1002/elsc.202200054] [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: 09/23/2022] [Revised: 11/23/2022] [Accepted: 01/07/2023] [Indexed: 02/04/2023] Open
Abstract
Several chromosomally expressed AceE variants were constructed in Escherichia coli ΔldhA ΔpoxB ΔppsA and compared using glucose as the sole carbon source. These variants were examined in shake flask cultures for growth rate, pyruvate accumulation, and acetoin production via heterologous expression of the budA and budB genes from Enterobacter cloacae ssp. dissolvens. The best acetoin-producing strains were subsequently studied in controlled batch culture at the one-liter scale. PDH variant strains attained up to four-fold greater acetoin than the strain expressing the wild-type PDH. In a repeated batch process, the H106V PDH variant strain attained over 43 g/L of pyruvate-derived products, acetoin (38.5 g/L) and 2R,3R-butanediol (5.0 g/L), corresponding to an effective concentration of 59 g/L considering the dilution. The acetoin yield from glucose was 0.29 g/g with a volumetric productivity of 0.9 g/L·h (0.34 g/g and 1.0 g/L·h total products). The results demonstrate a new tool in pathway engineering, the modification of a key metabolic enzyme to improve the formation of a product via a kinetically slow, introduced pathway. Direct modification of the pathway enzyme offers an alternative to promoter engineering in cases where the promoter is involved in a complex regulatory network.
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Affiliation(s)
- W Chris Moxley
- Department of Microbiology University of Georgia Athens Georgia USA
| | - Rachel E Brown
- School of Chemical Materials and Biomedical Engineering University of Georgia Athens Georgia USA
| | - Mark A Eiteman
- Department of Microbiology University of Georgia Athens Georgia USA.,School of Chemical Materials and Biomedical Engineering University of Georgia Athens Georgia USA
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Wen A, Yang Z, Liu N, Zeng H, Qin L. Dynamic correlation between tetramethylpyrazine and influencing factors in Bacillus subtilis-fermented dehulled adlay. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hui X, Tian JM, Wang X, Zhang ZQ, Zhao YM, Gao WY, Li H. Overall analyses of the reactions catalyzed by acetohydroxyacid synthase/acetolactate synthase using a precolumn derivatization-HPLC method. Anal Biochem 2023; 660:114980. [PMID: 36368345 DOI: 10.1016/j.ab.2022.114980] [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: 10/09/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
A precolumn derivatization-HPLC method using 2,4-dinitrophenylhydrazine and 4-nitro-o-phenylenediamine as respective labeling reagents for comprehensive analyses of the reactions catalyzed by acetohydroxyacid synthase (AHAS)/acetolactate synthase (ALS) is developed and evaluated in this research. Comparison with the classic Bauerle' UV assay which can analyze the enzymes only through measurement of acetoin production, the HPLC method shows advantages because it can analyze the enzymes not only via determination of consumption of the substrate pyruvate, but also via measurement of formation of the products including acetoin, 2,3-butanedione, and acetaldehyde in the enzymatic reactions. Thus the results deduced from the HPLC method can reflect the trait of each enzyme in a more precise manner. As far as we know, this is the first time that the reactions mediated by AHAS/ALS using pyruvate as a single substrate are globally analyzed and the features of the enzymes are properly discussed.
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Affiliation(s)
- Xian Hui
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Jin-Meng Tian
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Xin Wang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhen-Qian Zhang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Ya-Mei Zhao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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9
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Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:41. [PMID: 35501883 PMCID: PMC9063327 DOI: 10.1186/s13068-022-02144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2022] [Indexed: 11/15/2022]
Abstract
Background Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. Results Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. Conclusions This research provides a new way to improve the efficiency of the biological route of isobutanol production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02144-8. Kp-IpdC is more efficient than KivD for 2-ketoisovalerate decarboxylation. Pyruvate decarboxylase activity is a limitation of Kp-IpdC. T290L variant exhibits a decreased pyruvate decarboxylase activity. Isobutanol production by K. pneumoniae T290L was improved.
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Evaluation of Metabolic Engineering Strategies on 2-Ketoisovalerate Production by Escherichia coli. Appl Environ Microbiol 2022; 88:e0097622. [PMID: 35980178 PMCID: PMC9469723 DOI: 10.1128/aem.00976-22] [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] [Indexed: 11/20/2022] Open
Abstract
As an important metabolic intermediate, 2-ketoisovalerate has significant potential in the pharmaceutical and biofuel industries. However, a low output through microbial fermentation inhibits its industrial application. The microbial production of 2-ketoisovalerate is representative whereby redox imbalance is generated with two molecules of NADH accumulated and an extra NADPH required to produce one 2-ketoisovalerate from glucose. To achieve efficient 2-ketoisovalerate production, metabolic engineering strategies were evaluated in Escherichia coli. After deleting the competing routes, overexpressing the key enzymes for 2-ketoisovalerate production, tuning the supply of NADPH, and recycling the excess NADH through enhancing aerobic respiration, a 2-ketoisovalerate titer and yield of 46.4 g/L and 0.644 mol/mol glucose, respectively, were achieved. To reduce the main by-product of isobutanol, the activity and expression of acetolactate synthase were modified. Additionally, a protein degradation tag was fused to pyruvate dehydrogenase (PDH) to curtail the conversion of pyruvate precursor into acetyl-CoA and the generation of NADH. The resulting strain, 050TY/pCTSDTQ487S-RBS55, was initially incubated under aerobic conditions to attain sufficient cell mass and then transferred to a microaerobic condition to degrade PDH and inhibit the remaining activity of PDH. Intracellular redox imbalance was relieved with titer, productivity and yield of 2-ketoisovalerate improved to 55.8 g/L, 2.14 g/L h and 0.852 mol/mol glucose. These results revealed metabolic engineering strategies for the production of a redox-imbalanced fermentative metabolite with high titer, productivity, and yield. IMPORTANCE An efficient microbial strain was constructed for 2-ketoisovalerate synthesis. The positive effect of the leuA deletion on 2-ketoisovalerate production was found. An optimal combination of overexpressing the target genes was obtained by adjusting the positions of the multiple enzymes on the plasmid frame and the presence of terminators, which could also be useful for the production of downstream products such as isobutanol and l-valine. Reducing the isobutanol by-product by engineering the acetolactate synthase called for special attention to decreasing the promiscuous activity of the enzymes involved. Redox-balancing strategies such as tuning the expression of the chromosomal pyridine nucleotide transhydrogenase, recycling NADH under aerobic cultivation, switching off PDH by degradation, and inhibiting the expression and activity under microaerobic conditions were proven effective for improving 2-ketoisovalerate production. The degradation of PDH and inhibiting this enzyme's expression would serve as a means to generate a wide range of products from pyruvate.
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Tian J, Xing B, Li M, Xu C, Huo YX, Guo S. Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers. Int J Mol Sci 2022; 23:ijms23094853. [PMID: 35563243 PMCID: PMC9099979 DOI: 10.3390/ijms23094853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable host strains. Herein, we develop an efficient CRISPR-Cas9 method for large-scale and scarless genome engineering in the Bacillus subtilis genome, which can delete up to 134.3 kb DNA fragments, 3.5 times as long as the previous report, with a positivity rate of 100%. The effects of using a heterologous NHEJ system, linear donor DNA, and various donor DNA length on the engineering efficiencies were also investigated. The CRISPR-Cas9 method was then utilized for Bacillus subtilis genome simplification and construction of a series of individual and cumulative deletion mutants, which are further screened for overproducer of isobutanol, a new generation biofuel. These results suggest that the method is a powerful genome engineering tool for constructing and screening engineered host strains with enhanced capabilities, highlighting the potential for synthetic biology and metabolic engineering.
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12
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Xie H, Lindblad P. Expressing 2-keto acid pathway enzymes significantly increases photosynthetic isobutanol production. Microb Cell Fact 2022; 21:17. [PMID: 35105340 PMCID: PMC8805274 DOI: 10.1186/s12934-022-01738-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Background Cyanobacteria, photosynthetic microorganisms, are promising green cell factories for chemical production, including biofuels. Isobutanol, a four-carbon alcohol, is considered as a superior candidate as a biofuel for its high energy density with suitable chemical and physical characteristics. The unicellular cyanobacterium Synechocystis PCC 6803 has been successfully engineered for photosynthetic isobutanol production from CO2 and solar energy in a direct process. Results Heterologous expression of α-ketoisovalerate decarboxylase (KivdS286T) is sufficient for isobutanol synthesis via the 2-keto acid pathway in Synechocystis. With additional expression of acetolactate synthase (AlsS), acetohydroxy-acid isomeroreductase (IlvC), dihydroxy-acid dehydratase (IlvD), and alcohol dehydrogenase (Slr1192OP), the Synechocystis strain HX42, with a functional 2-keto acid pathway, showed enhanced isobutanol production reaching 98 mg L−1 in short-term screening experiments. Through modulating kivdS286T copy numbers as well as the composition of the 5′-region, a final Synechocystis strain HX47 with three copies of kivdS286T showed a significantly improved isobutanol production of 144 mg L−1, an 177% increase compared to the previously reported best producing strain under identical conditions. Conclusions This work demonstrates the feasibility to express heterologous genes with a combination of self-replicating plasmid-based system and genome-based system in Synechocystis cells. Obtained isobutanol-producing Synechocystis strains form the base for further investigation of continuous, long-term-photosynthetic isobutanol production from solar energy and carbon dioxide. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01738-z.
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Affiliation(s)
- Hao Xie
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120, Uppsala, Sweden.
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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14
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Metabolic engineering of Escherichia coli for the production of isobutanol: a review. World J Microbiol Biotechnol 2021; 37:168. [PMID: 34487256 DOI: 10.1007/s11274-021-03140-0] [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: 07/23/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
With the ongoing depletion of fossil fuel resources and emerging environmental issues, increasing research effort is being dedicated to producing biofuels from renewable substrates. With its advantages over ethanol in terms of energy density, octane number, and hygroscopicity, isobutanol is considered a potential alternative to traditional gasoline. However, as wild-type microorganisms cannot achieve the production of isobutanol with high titers and yields, rational genetic engineering has been employed to enhance its production. Herein, we review the latest developments in the metabolic engineering of Escherichia coli for the production of isobutanol, including those related to the utilization of diverse carbon sources, balancing the redox state, improving isobutanol tolerance, and application of synthetic biology circuits and tools.
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15
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Sirohi R, Joun J, Choi HI, Gaur VK, Sim SJ. Algal glycobiotechnology: omics approaches for strain improvement. Microb Cell Fact 2021; 20:163. [PMID: 34419059 PMCID: PMC8379821 DOI: 10.1186/s12934-021-01656-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
Microalgae has the capability to replace petroleum-based fuels and is a promising option as an energy feedstock because of its fast growth, high photosynthetic capacity and remarkable ability to store energy reserve molecules in the form of lipids and starch. But the commercialization of microalgae based product is difficult due to its high processing cost and low productivity. Higher accumulation of these molecules may help to cut the processing cost. There are several reports on the use of various omics techniques to improve the strains of microalgae for increasing the productivity of desired products. To effectively use these techniques, it is important that the glycobiology of microalgae is associated to omics approaches to essentially give rise to the field of algal glycobiotechnology. In the past few decades, lot of work has been done to improve the strain of various microalgae such as Chlorella, Chlamydomonas reinhardtii, Botryococcus braunii etc., through genome sequencing and metabolic engineering with major focus on significantly increasing the productivity of biofuels, biopolymers, pigments and other products. The advancements in algae glycobiotechnology have highly significant role to play in innovation and new developments for the production algae-derived products as above. It would be highly desirable to understand the basic biology of the products derived using -omics technology together with biochemistry and biotechnology. This review discusses the potential of different omic techniques (genomics, transcriptomics, proteomics, metabolomics) to improve the yield of desired products through algal strain manipulation.
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Affiliation(s)
- Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Jaemin Joun
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Hong Ii Choi
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Vivek Kumar Gaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226 001, India
| | - Sang Jun Sim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea.
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16
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Moxley WC, Eiteman MA. Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants. Appl Environ Microbiol 2021; 87:e0048721. [PMID: 33863707 PMCID: PMC8315933 DOI: 10.1128/aem.00487-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/10/2021] [Indexed: 11/20/2022] Open
Abstract
Altering metabolic flux at a key branch point in metabolism has commonly been accomplished through gene knockouts or by modulating gene expression. An alternative approach to direct metabolic flux preferentially toward a product is decreasing the activity of a key enzyme through protein engineering. In Escherichia coli, pyruvate can accumulate from glucose when carbon flux through the pyruvate dehydrogenase complex is suppressed. Based on this principle, 16 chromosomally expressed AceE variants were constructed in E. coli C and compared for growth rate and pyruvate accumulation using glucose as the sole carbon source. To prevent conversion of pyruvate to other products, the strains also contained deletions in two nonessential pathways: lactate dehydrogenase (ldhA) and pyruvate oxidase (poxB). The effect of deleting phosphoenolpyruvate synthase (ppsA) on pyruvate assimilation was also examined. The best pyruvate-accumulating strains were examined in controlled batch and continuous processes. In a nitrogen-limited chemostat process at steady-state growth rates of 0.15 to 0.28 h-1, an engineered strain expressing the AceE[H106V] variant accumulated pyruvate at a yield of 0.59 to 0.66 g pyruvate/g glucose with a specific productivity of 0.78 to 0.92 g pyruvate/g cells·h. These results provide proof of concept that pyruvate dehydrogenase complex variants can effectively shift carbon flux away from central carbon metabolism to allow pyruvate accumulation. This approach can potentially be applied to other key enzymes in metabolism to direct carbon toward a biochemical product. IMPORTANCE Microbial production of biochemicals from renewable resources has become an efficient and cost-effective alternative to traditional chemical synthesis methods. Metabolic engineering tools are important for optimizing a process to perform at an economically feasible level. This study describes an additional tool to modify central metabolism and direct metabolic flux to a product. We have shown that variants of the pyruvate dehydrogenase complex can direct metabolic flux away from cell growth to increase pyruvate production in Escherichia coli. This approach could be paired with existing strategies to optimize metabolism and create industrially relevant and economically feasible processes.
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Affiliation(s)
- W. Chris Moxley
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Mark A. Eiteman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
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17
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Liu H, Liu S, Osire T, Zhang X, Xu M, Yang ST, Yang T, Rao Z. Engineering the 2,3-BD pathway in Bacillus subtilis by shifting the carbon flux in favor of 2,3-BD synthesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Zhao T, Li Y, Yuan S, Ye Y, Peng Z, Zhou R, Liu J. Structure-Based Design of Acetolactate Synthase From Bacillus licheniformis Improved Protein Stability Under Acidic Conditions. Front Microbiol 2020; 11:582909. [PMID: 33193222 PMCID: PMC7652814 DOI: 10.3389/fmicb.2020.582909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
Catabolic acetolactate synthase (cALS) plays a crucial role in the quality of liquor because of its ability to catalyze the synthesis of the endogenous precursor product α-acetolactate of the aromatic compound tetramethylpyrazine (TTMP) and acetoin. However, the vulnerability of cALS to acidic conditions limits its application in the Chinese liquor brewing industry. Here we report the biochemical characterization of cALS from B. licheniformis T2 (BlALS) that was screened from Chinese liquor brewing microorganisms. BlALS showed optimal activity levels at pH 7.0, and the values of Km and Vmax were 27.26 mM and 6.9 mM⋅min–1, respectively. Through site-directed mutagenesis, we improved the stability of BlALS under acidic conditions. Replacing the two basic residues of BlALS with acidic mutations (N210D and H399D) significantly improved the acid tolerance of the enzyme with a prolonged half-life of 2.2 h (compared with wild-type BlALS of 0.8 h) at pH 4.0. Based on the analysis of homologous modeling, the positive charge area of the electrostatic potential on the protein surface and the number of hydrogen bonds near the active site increased, which helped BlALSN210D–H399D to withstand the acidic environment; this could extend its application in the food fermentation industry.
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Affiliation(s)
- Ting Zhao
- Faculty of Bioengineering, Wuliangye Liquor College, Sichuan University of Science and Engineering, Yibin, China
| | - Yuan Li
- Faculty of Bioengineering, Wuliangye Liquor College, Sichuan University of Science and Engineering, Yibin, China
| | - Siqi Yuan
- Faculty of Bioengineering, Wuliangye Liquor College, Sichuan University of Science and Engineering, Yibin, China
| | - Yang Ye
- Faculty of Bioengineering, Wuliangye Liquor College, Sichuan University of Science and Engineering, Yibin, China
| | | | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jun Liu
- Faculty of Bioengineering, Wuliangye Liquor College, Sichuan University of Science and Engineering, Yibin, China.,Wuliangye Group Co. Ltd., Yibin, China.,College of Biomass Science and Engineering, Sichuan University, Chengdu, China
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19
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Novak K, Baar J, Freitag P, Pflügl S. Metabolic engineering of Escherichia coli W for isobutanol production on chemically defined medium and cheese whey as alternative raw material. J Ind Microbiol Biotechnol 2020; 47:1117-1132. [PMID: 33068182 PMCID: PMC7728641 DOI: 10.1007/s10295-020-02319-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
The aim of this study was to establish isobutanol production on chemically defined medium in Escherichia coli. By individually expressing each gene of the pathway, we constructed a plasmid library for isobutanol production. Strain screening on chemically defined medium showed successful production in the robust E. coli W strain, and expression vector IB 4 was selected as the most promising construct due to its high isobutanol yields and efficient substrate uptake. The investigation of different aeration strategies in combination with strain improvement and the implementation of a pulsed fed-batch were key for the development of an efficient production process. E. coli W ΔldhA ΔadhE Δpta ΔfrdA enabled aerobic isobutanol production at 38% of the theoretical maximum. Use of cheese whey as raw material resulted in longer process stability, which allowed production of 20 g l−1 isobutanol. Demonstrating isobutanol production on both chemically defined medium and a residual waste stream, this study provides valuable information for further development of industrially relevant isobutanol production processes.
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Affiliation(s)
- Katharina Novak
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Juliane Baar
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Philipp Freitag
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
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20
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Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
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21
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Kulyashov M, Peltek SE, Akberdin IR. A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. Microorganisms 2020; 8:E1002. [PMID: 32635563 PMCID: PMC7409357 DOI: 10.3390/microorganisms8071002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022] Open
Abstract
The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.
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Affiliation(s)
- Mikhail Kulyashov
- Biosoft.ru, 630058 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Department of Molecular Biotechnology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Ilya R. Akberdin
- Biosoft.ru, 630058 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of Molecular Biotechnology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
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22
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Hasegawa S, Jojima T, Suda M, Inui M. Isobutanol production in Corynebacterium glutamicum: Suppressed succinate by-production by pckA inactivation and enhanced productivity via the Entner–Doudoroff pathway. Metab Eng 2020; 59:24-35. [DOI: 10.1016/j.ymben.2020.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
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23
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Ma L, Guo L, Yang Y, Guo K, Yan Y, Ma X, Huo YX. Protein-based biorefining driven by nitrogen-responsive transcriptional machinery. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:29. [PMID: 32127916 PMCID: PMC7045595 DOI: 10.1186/s13068-020-1667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Protein-based bioconversion has been demonstrated as a sustainable approach to produce higher alcohols and ammonia fertilizers. However, owing to the switchover from transcription mediated by the bacterial RNA polymerase σ70 to that mediated by alternative σ factors, the biofuel production driven by σ70-dependent promoters declines rapidly once cells enter the stationary phase or encounter stresses. To enhance biofuel production, in this study the growth phase-independent and nitrogen-responsive transcriptional machinery mediated by the σ54 is exploited to drive robust protein-to-fuel conversion. RESULTS We demonstrated that disrupting the Escherichia coli ammonia assimilation pathways driven by glutamate dehydrogenase and glutamine synthetase could sustain the activity of σ54-mediated transcription under ammonia-accumulating conditions. In addition, two σ54-dependent promoters, argTp and glnAp2, were identified as suitable candidates for driving pathway expression. Using these promoters, biofuel production from proteins was shown to persist to the stationary phase, with the net production in the stationary phase being 1.7-fold higher than that derived from the optimal reported σ70-dependent promoter P LlacO1. Biofuel production reaching levels 1.3- to 3.4-fold higher than those of the σ70-dependent promoters was also achieved by argTp and glnAp2 under stressed conditions. Moreover, the σ54-dependent promoters realized more rapid and stable production than that of σ70-dependent promoters during fed-batch fermentation, producing up to 4.78 g L - 1 of total biofuels. CONCLUSIONS These results suggested that the nitrogen-responsive transcriptional machinery offers the potential to decouple production from growth, highlighting this system as a novel candidate to realize growth phase-independent and stress-resistant biofuel production.
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Affiliation(s)
- Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Yunpeng Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Kai Guo
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA 30602 USA
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
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24
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Zhang X, Han R, Bao T, Zhao X, Li X, Zhu M, Yang T, Xu M, Shao M, Zhao Y, Rao Z. Synthetic engineering of Corynebacterium crenatum to selectively produce acetoin or 2,3-butanediol by one step bioconversion method. Microb Cell Fact 2019; 18:128. [PMID: 31387595 PMCID: PMC6683508 DOI: 10.1186/s12934-019-1183-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acetoin (AC) and 2,3-butanediol (2,3-BD) as highly promising bio-based platform chemicals have received more attentions due to their wide range of applications. However, the non-efficient substrate conversion and mutually transition between AC and 2,3-BD in their natural producing strains not only led to a low selectivity but also increase the difficulty of downstream purification. Therefore, synthetic engineering of more suitable strains should be a reliable strategy to selectively produce AC and 2,3-BD, respectively. RESULTS In this study, the respective AC (alsS and alsD) and 2,3-BD biosynthesis pathway genes (alsS, alsD, and bdhA) derived from Bacillus subtilis 168 were successfully expressed in non-natural AC and 2,3-BD producing Corynebacterium crenatum, and generated recombinant strains, C. crenatum SD and C. crenatum SDA, were proved to produce 9.86 g L-1 of AC and 17.08 g L-1 of 2,3-BD, respectively. To further increase AC and 2,3-BD selectivity, the AC reducing gene (butA) and lactic acid dehydrogenase gene (ldh) in C. crenatum were then deleted. Finally, C. crenatumΔbutAΔldh SD produced 76.93 g L-1 AC in one-step biocatalysis with the yield of 0.67 mol mol-1. Meanwhile, after eliminating the lactic acid production and enhancing 2,3-butanediol dehydrogenase activity, C. crenatumΔldh SDA synthesized 88.83 g L-1 of 2,3-BD with the yield of 0.80 mol mol-1. CONCLUSIONS The synthetically engineered C. crenatumΔbutAΔldh SD and C. crenatumΔldh SDA in this study were proved as an efficient microbial cell factory for selective AC and 2,3-BD production. Based on the insights from this study, further synthetic engineering of C. crenatum for AC and 2,3-BD production is suggested.
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Affiliation(s)
- Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Rumeng Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Teng Bao
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210 China
| | - Xiangfei Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Manchi Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Minglong Shao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Youxi Zhao
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, 10023 People’s Republic of China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
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Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metab Eng 2019; 52:324-340. [DOI: 10.1016/j.ymben.2018.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/25/2018] [Indexed: 10/27/2022]
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Acedos MG, de la Torre I, Santos VE, Garcia-Ochoa F. Kinetic Modeling of the Isobutanol Production from Glucose Using Shimwellia blattae (p424IbPSO) Strain: Effect of Initial Substrate Concentration. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel G. Acedos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Isabel de la Torre
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Victoria E. Santos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Felix Garcia-Ochoa
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
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Acedos MG, Santos VE, Garcia-Ochoa F. Resting cells isobutanol production by Shimwellia blattae (p424IbPSO): Influence of growth culture conditions. Biotechnol Prog 2018; 34:1073-1080. [PMID: 30281946 DOI: 10.1002/btpr.2705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
Abstract
Isobutanol is a promising gasoline additive and could even be a potential substitute used directly as combustible. In this work, the production of isobutanol from glucose by Shimwellia blattae (p424IbPSO) in resting cell cultures is studied. This production has two stages, involving a resting cell phase that has not been studied before. The cell growth was carried out under different operating conditions: temperature and medium composition (YE, ammonium, and IPTG concentrations), looking for the highest isobutanol production. Moreover, the cells were collected at three different growth times checking their isobutanol production capacity. The best operating conditions have been determined as: 30°C of temperature, a medium containing 1.5 g L-1 YE and 1.4 g L-1 of ammonium as nitrogen sources, adding 0.5 mM IPTG as inducer. The cells collected at early growth times are significantly more active. The use of S. blattae (p424IbPSO) in resting cells is a good strategy for the production of isobutanol from glucose yielding better results than in batch growth cultures, a yield of 60% attainment of theoretical maximum yield is obtained under optimal conditions. In addition, it has been demonstrated that if the cells are cultured at higher temperatures and with high IPTG concentrations, inclusion bodies are formed in the cytoplasm inhibiting the isobutanol production in the resting cell stage.
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Affiliation(s)
- Miguel G Acedos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Victoria E Santos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Felix Garcia-Ochoa
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
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A synthetic pathway for the production of 2-hydroxyisovaleric acid in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:579-588. [DOI: 10.1007/s10295-018-2005-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/02/2018] [Indexed: 11/25/2022]
Abstract
Abstract
Synthetic biology, encompassing the design and construction of novel artificial biological pathways and organisms and the redesign of existing natural biological systems, is rapidly expanding the number of applications for which biological systems can play an integral role. In the context of chemical production, the combination of synthetic biology and metabolic engineering approaches continues to unlock the ability to biologically produce novel and complex molecules from a variety of feedstocks. Here, we utilize a synthetic approach to design and build a pathway to produce 2-hydroxyisovaleric acid in Escherichia coli and demonstrate how pathway design can be supplemented with metabolic engineering approaches to improve pathway performance from various carbon sources. Drawing inspiration from the native pathway for the synthesis of the 5-carbon amino acid l-valine, we exploit the decarboxylative condensation of two molecules of pyruvate, with subsequent reduction and dehydration reactions enabling the synthesis of 2-hydroxyisovaleric acid. Key to our approach was the utilization of an acetolactate synthase which minimized kinetic and regulatory constraints to ensure sufficient flux entering the pathway. Critical host modifications enabling maximum product synthesis from either glycerol or glucose were then examined, with the varying degree of reduction of these carbons sources playing a major role in the required host background. Through these engineering efforts, the designed pathway produced 6.2 g/L 2-hydroxyisovaleric acid from glycerol at 58% of maximum theoretical yield and 7.8 g/L 2-hydroxyisovaleric acid from glucose at 73% of maximum theoretical yield. These results demonstrate how the combination of synthetic biology and metabolic engineering approaches can facilitate bio-based chemical production.
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Acedos MG, Ramon A, de la Morena S, Santos VE, Garcia-Ochoa F. Isobutanol production by a recombinant biocatalyst Shimwellia blattae (p424IbPSO): Study of the operational conditions. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002. Int J Biol Macromol 2018; 114:188-193. [PMID: 29574001 DOI: 10.1016/j.ijbiomac.2018.03.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/22/2022]
Abstract
α-Ketoglutarate decarboxylase (α-KGD), one member of α-keto acid decarboxylases, catalyzing non-oxidative decarboxylation of α-ketoglutarate to form succinic semialdehyde, was proposed to play critical role in completing tricarboxylic acid (TCA) cycle of cyanobacteria. Although the catalytic function of α-KGD from Synechococcus sp. PCC7002 was demonstrated previously, there was no detailed biochemical characterization of α-KGD from Synechococcus sp. PCC7002 yet. In this study, the gene encoding α-KGD from Synechococcus sp. PCC7002 was amplified and soluble expression of recombinant α-KGD was achieved by coexpressing with pTf16 chaperone plasmid in E. coli BL21 (DE3). Kinetic analysis showed that the activity of α-KGD was dependent on cofactors of thiamine pyrophosphate and divalent cation. Meanwhile this α-KGD was specific for α-ketoglutarate with respect to the decarboxylation activity despite of the pretty low activity of acetolactate synthase. The catalytic efficiency of α-KGD (the values of kcat and kcat/Km for α-ketoglutarate were 1.2s-1 and 6.3×103M-1s-1, respectively) might provide evidence for its physiological role in TCA cycle of Synechococcus sp. PCC7002.
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Biofuel production with a stress-resistant and growth phase-independent promoter: mechanism revealed by in vitro transcription assays. Appl Microbiol Biotechnol 2018; 102:2929-2940. [DOI: 10.1007/s00253-018-8809-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
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32
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Wang X, Lei G, Wu X, Wang F, Lai C, Li Z. Expression, purification and characterization of sll1981 protein from cyanobacterium Synechocystis sp. PCC6803. Protein Expr Purif 2017; 139:21-28. [DOI: 10.1016/j.pep.2017.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/14/2017] [Accepted: 07/17/2017] [Indexed: 11/26/2022]
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33
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Huo Y, Zhan Y, Wang Q, Li S, Yang S, Nomura CT, Wang C, Chen S. Acetolactate synthase (AlsS) in Bacillus licheniformis WX-02: enzymatic properties and efficient functions for acetoin/butanediol and L-valine biosynthesis. Bioprocess Biosyst Eng 2017; 41:87-96. [PMID: 29026998 DOI: 10.1007/s00449-017-1847-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/23/2017] [Indexed: 11/25/2022]
Abstract
Acetolactate synthase catalyzes two molecules of pyruvates to form α-acetolactate, which is further converted to acetoin and 2,3-butanediol. In this study, by heterologous expression in Escherichia coli, the enzymatic properties of acetolactate synthase (AlsS) from Bacillus licheniformis WX-02 were characterized. Its K m and k cat for pyruvate were 3.96 mM and 514/s, respectively. It has the optimal activity at pH 6.5, 37 °C and was feedback inhibited by L-valine, L-leucine and L-isoleucine. Furthermore, the alsS-deficient strain could not produce acetoin, 2,3-butanediol, and L-valine, while the complementary strain was able to restore these capacities. The alsS overexpressing strain produced higher amounts of acetoin/2,3-butanediol (57.06 g/L) and L-valine (2.68 mM), which were 10.90 and 92.80% higher than those of the control strain, respectively. This is the first report regarding the in-depth understanding of AlsS enzymatic properties and its functions in B. licheniformis, and overexpression of AlsS can effectively improve acetoin/2,3-butanediol and L-valine production in B. licheniformis. We envision that this AlsS can also be applied in the improvement of acetoin/2,3-butanediol and L-valine production in other microbes.
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Affiliation(s)
- Yanli Huo
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yangyang Zhan
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Qin Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Shunyi Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Christopher T Nomura
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
- Department of Chemistry, The State University of New York College of Environmental Science and Forestry (SUNY ESF), Syracuse, NY, 13210, USA
| | - Changjun Wang
- Tobacco Research Institute of Hubei Province, Wuhan, 430062, People's Republic of China.
| | - Shouwen Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Isobutanol and 2-ketoisovalerate production by Klebsiella pneumoniae via a native pathway. Metab Eng 2017; 43:71-84. [DOI: 10.1016/j.ymben.2017.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 07/01/2017] [Accepted: 07/20/2017] [Indexed: 01/31/2023]
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Kim SJ, Kim JW, Lee YG, Park YC, Seo JH. Metabolic engineering of Saccharomyces cerevisiae for 2,3-butanediol production. Appl Microbiol Biotechnol 2017; 101:2241-2250. [DOI: 10.1007/s00253-017-8172-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 01/04/2023]
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Wong SS, Mi L, Liao JC. Microbial Production of Butanols. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sio Si Wong
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - Luo Mi
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
| | - James C. Liao
- University of California; Department of Chemical and Biomolecular Engineering; 420 Westwood Plaza, 5531Boelter Hall Los Angeles CA 90095 USA
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Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 2016; 9:699-717. [PMID: 27629544 PMCID: PMC5072187 DOI: 10.1111/1751-7915.12408] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 12/04/2022] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
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Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Qiang Fei
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Eram MS, Ma K. Pyruvate decarboxylase activity of the acetohydroxyacid synthase of Thermotoga maritima. Biochem Biophys Rep 2016; 7:394-399. [PMID: 28955930 PMCID: PMC5613635 DOI: 10.1016/j.bbrep.2016.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) catalyzes the production of acetolactate from pyruvate. The enzyme from the hyperthermophilic bacterium Thermotoga maritima has been purified and characterized (kcat ~100 s−1). It was found that the same enzyme also had the ability to catalyze the production of acetaldehyde and CO2 from pyruvate, an activity of pyruvate decarboxylase (PDC) at a rate approximately 10% of its AHAS activity. Compared to the catalytic subunit, reconstitution of the individually expressed and purified catalytic and regulatory subunits of the AHAS stimulated both activities of PDC and AHAS. Both activities had similar pH and temperature profiles with an optimal pH of 7.0 and temperature of 85 °C. The enzyme kinetic parameters were determined, however, it showed a non-Michaelis-Menten kinetics for pyruvate only. This is the first report on the PDC activity of an AHAS and the second bifunctional enzyme that might be involved in the production of ethanol from pyruvate in hyperthermophilic microorganisms. The acetohydroxyacid synthase of T. maritima has pyruvate decarboxylase activity The AHAS and PDC activities share the same temperature and pH optima Reconstitution of the catalytic and regulatory subunits increases both PDC and AHAS activities
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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40
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Chen CT, Liao JC. Frontiers in microbial 1-butanol and isobutanol production. FEMS Microbiol Lett 2016; 363:fnw020. [PMID: 26832641 DOI: 10.1093/femsle/fnw020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 12/14/2022] Open
Abstract
The heavy dependence on petroleum-derived fuel has raised concerns about energy sustainability and climate change, which have prompted researchers to explore fuel production from renewable sources. 1-Butanol and isobutanol are promising biofuels that have favorable properties and can also serve as solvents or chemical feedstocks. Microbial production of these alcohols provides great opportunities to access a wide spectrum of renewable resources. In recent years, research has improved the native 1-butanol production and has engineered isobutanol production in various organisms to explore metabolic diversity and a broad range of substrates. This review focuses on progress in metabolic engineering for the production of these two compounds using various resources.
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Affiliation(s)
- Chang-Ting Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - James C Liao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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Nazem-Bokaee H, Gopalakrishnan S, Ferry JG, Wood TK, Maranas CD. Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. Microb Cell Fact 2016; 15:10. [PMID: 26776497 PMCID: PMC4716644 DOI: 10.1186/s12934-015-0404-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/22/2015] [Indexed: 12/26/2022] Open
Abstract
Background Methanosarcina acetivorans is a model archaeon with renewed interest due to its unique reversible methane production pathways. However, the mechanism and relevant pathways implicated in (co)utilizing novel carbon substrates in this organism are still not fully understood. This paper provides a comprehensive inventory of thermodynamically feasible routes for anaerobic methane oxidation, co-reactant utilization, and maximum carbon yields of major biofuel candidates by M. acetivorans. Results Here, an updated genome-scale metabolic model of M. acetivorans is introduced (iMAC868 containing 868 genes, 845 reactions, and 718 metabolites) by integrating information from two previously reconstructed metabolic models (i.e., iVS941 and iMB745), modifying 17 reactions, adding 24 new reactions, and revising 64 gene-protein-reaction associations based on newly available information. The new model establishes improved predictions of growth yields on native substrates and is capable of correctly predicting the knockout outcomes for 27 out of 28 gene deletion mutants. By tracing a bifurcated electron flow mechanism, the iMAC868 model predicts thermodynamically feasible (co)utilization pathway of methane and bicarbonate using various terminal electron acceptors through the reversal of the aceticlastic pathway. Conclusions This effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0404-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hadi Nazem-Bokaee
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Saratram Gopalakrishnan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Thomas K Wood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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Kim JW, Kim J, Seo SO, Kim KH, Jin YS, Seo JH. Enhanced production of 2,3-butanediol by engineered Saccharomyces cerevisiae through fine-tuning of pyruvate decarboxylase and NADH oxidase activities. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:265. [PMID: 27990176 PMCID: PMC5148919 DOI: 10.1186/s13068-016-0677-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/01/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND 2,3-Butanediol (2,3-BD) is a promising compound for various applications in chemical, cosmetic, and agricultural industries. Pyruvate decarboxylase (Pdc)-deficient Saccharomyces cerevisiae is an attractive host strain for producing 2,3-BD because a large amount of pyruvate could be shunted to 2,3-BD production instead of ethanol synthesis. However, 2,3-BD yield, productivity, and titer by engineered yeast were inferior to native bacterial producers because of the following metabolic limitations. First, the Pdc-deficient yeast showed growth defect due to a shortage of C2-compounds. Second, redox imbalance during the 2,3-BD production led to glycerol formation that lowered the yield. RESULTS To overcome these problems, the expression levels of Pdc from a Crabtree-negative yeast were optimized in S. cerevisiae. Specifically, Candida tropicalis PDC1 (CtPDC1) was used to minimize the production of ethanol but maximize cell growth and 2,3-BD productivity. As a result, productivity of the BD5_G1CtPDC1 strain expressing an optimal level of Pdc was 2.3 folds higher than that of the control strain in flask cultivation. Through a fed-batch fermentation, 121.8 g/L 2,3-BD was produced in 80 h. NADH oxidase from Lactococcus lactis (noxE) was additionally expressed in the engineered yeast with an optimal activity of Pdc. The fed-batch fermentation with the optimized 2-stage aeration control led to production of 154.3 g/L 2,3-BD in 78 h. The overall yield of 2,3-BD was 0.404 g 2,3-BD/g glucose which corresponds to 80.7% of theoretical yield. CONCLUSIONS A massive metabolic shift in the engineered S. cerevisiae (BD5_G1CtPDC1_nox) expressing NADH oxidase was observed, suggesting that redox imbalance was a major bottleneck for efficient production of 2,3-BD by engineered yeast. Maximum 2,3-BD titer in this study was close to the highest among the reported microbial production studies. The results demonstrate that resolving both C2-compound limitation and redox imbalance is critical to increase 2,3-BD production in the Pdc-deficient S. cerevisiae. Our strategy to express fine-tuned PDC and noxE could be applicable not only to 2,3-BD production, but also other chemical production systems using Pdc-deficient S. cerevisiae.
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Affiliation(s)
- Jin-Woo Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921 Republic of Korea
| | - Jungyeon Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, 136-713 Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Human Nutrition, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Kyoung Heon Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, 136-713 Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921 Republic of Korea
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Combinatorial application of two aldehyde oxidoreductases on isobutanol production in the presence of furfural. ACTA ACUST UNITED AC 2016; 43:37-44. [DOI: 10.1007/s10295-015-1718-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/29/2015] [Indexed: 11/26/2022]
Abstract
Abstract
Furfural is a toxic by-product formulated from pretreatment processes of lignocellulosic biomass. In order to utilize the lignocellulosic biomass on isobutanol production, inhibitory effect of the furfural on isobutanol production was investigated and combinatorial application of two oxidoreductases, FucO and YqhD, was suggested as an alternative strategy. Furfural decreased cell growth and isobutanol production when only YqhD or FucO was employed as an isobutyraldehyde oxidoreductase. However, combinatorial overexpression of FucO and YqhD could overcome the inhibitory effect of furfural giving higher isobutanol production by 110 % compared with overexpression of YqhD. The combinatorial oxidoreductases increased furfural detoxification rate 2.1-fold and also accelerated glucose consumption 1.4-fold. When it compares to another known system increasing furfural tolerance, membrane-bound transhydrogenase (pntAB), the combinatorial aldehyde oxidoreductases were better on cell growth and production. Thus, to control oxidoreductases is important to produce isobutanol using furfural-containing biomass and the combinatorial overexpression of FucO and YqhD can be an alternative strategy.
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Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL. Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 2015; 6:978. [PMID: 26441909 PMCID: PMC4585186 DOI: 10.3389/fmicb.2015.00978] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Andrea Firrincieli
- Department for Innovation Biological, Agro-Food and Forest System, University of Tuscia Tuscia, Italy
| | - Robert Otillar
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA ; HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Zareen Khan
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | | | - Neil D Fleck
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
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Kim JW, Seo SO, Zhang GC, Jin YS, Seo JH. Expression of Lactococcus lactis NADH oxidase increases 2,3-butanediol production in Pdc-deficient Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2015; 191:512-9. [PMID: 25769689 DOI: 10.1016/j.biortech.2015.02.077] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 05/04/2023]
Abstract
To minimize glycerol production during 2,3-BD fermentation by the engineered Saccharomyces cerevisiae, the Lactococcus lactis water-forming NADH oxidase gene (noxE) was expressed at five different levels. The expression of NADH oxidase substantially decreased the intracellular NADH/NAD(+) ratio. The S. cerevisiae BD5_T2nox strain expressing noxE produced 2,3-BD with yield of 0.359 g 2,3-BD/gglucose and glycerol with 0.069gglycerol/gglucose, which are 23.8% higher and 65.3% lower than those of the isogenic strain without noxE. These results demonstrate that the carbon flux could be redirected from glycerol to 2,3-BD through alteration of the NADH/NAD(+) ratio by the expression of NADH oxidase.
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Affiliation(s)
- Jin-Woo Kim
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Human Nutrition, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Republic of Korea.
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Yang T, Rao Z, Zhang X, Xu M, Xu Z, Yang ST. Enhanced 2,3-butanediol production from biodiesel-derived glycerol by engineering of cofactor regeneration and manipulating carbon flux in Bacillus amyloliquefaciens. Microb Cell Fact 2015; 14:122. [PMID: 26296537 PMCID: PMC4546283 DOI: 10.1186/s12934-015-0317-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Bacillus amyloliquefaciens B10-127 exhibited an excellent ability for industrial-scale microbial fermentation of 2,3-butanediol (2,3-BD) from biodiesel-derived glycerol. However, the accumulation of by-products (acetoin, acetoin, lactate and succinate) and the 2,3-BD yield remains prohibitively low for commercial production. RESULTS Several strategies were developed to manipulate the carbon flux to 2,3-BD branch in a designed B. amyloliquefaciens. Firstly, extra copies of NADH/NAD(+) regeneration system were introduced into B. amyloliquefaciens by co-overproduction of glycerol dehydrogenase and acetoin reductase, which resulting in improvement of 2,3-BD production and suppression of by-products accumulation. Subsequently, the transcriptional regulator ALsR under the control of a moderate promoter PbdhA was introduced into B. amyloliquefaciens, which increased carbon flux to 2,3-BD branch. Finally, a three-stage dissolved oxygen control strategy were proposed based on analysis of the characteristic of 2,3-BD fermentation, and a two-stage pH control strategy were proposed based on different pH preferences of ACR for reduction and oxidation. Following these strategies, a high titer (102.3 g/L), yield (0.44 g/g), and productivity (1.16 g/L/h) of 2,3-BD were achieved. CONCLUSIONS To our knowledge, this is the highest reported 2,3-BD production using biodiesel-derived glycerol as substrate, and this designed B. amyloliquefaciens should be an excellent candidate for producing 2,3-BD on an industrial scale.
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Affiliation(s)
- Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China.
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China.
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China.
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, 214122, China.
| | - Zhenghong Xu
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu Province, 214122, China.
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA.
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Tashiro Y, Desai SH, Atsumi S. Two-dimensional isobutyl acetate production pathways to improve carbon yield. Nat Commun 2015; 6:7488. [PMID: 26108471 PMCID: PMC4491173 DOI: 10.1038/ncomms8488] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/13/2015] [Indexed: 11/21/2022] Open
Abstract
For an economically competitive biological process, achieving high carbon yield of a target chemical is crucial. In biochemical production, pyruvate and acetyl-CoA are primary building blocks. When sugar is used as the sole biosynthetic substrate, acetyl-CoA is commonly generated by pyruvate decarboxylation. However, pyruvate decarboxylation during acetyl-CoA formation limits the theoretical maximum carbon yield (TMCY) by releasing carbon, and in some cases also leads to redox imbalance. To avoid these problems, we describe here the construction of a metabolic pathway that simultaneously utilizes glucose and acetate. Acetate is utilized to produce acetyl-CoA without carbon loss or redox imbalance. We demonstrate the utility of this approach for isobutyl acetate (IBA) production, wherein IBA production with glucose and acetate achieves a higher carbon yield than with either sole carbon source. These results highlight the potential for this multiple carbon source approach to improve the TMCY and balance redox in biosynthetic pathways. Achieving high carbon yields is crucial for biotechnological production of metabolites in engineered microorganisms. Here, Tashiro et al. generate E. coli strains that produce acetyl-CoA and a derived metabolite (isobutyl acetate) in the absence of pyruvate decarboxylation, leading to increased carbon yields.
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Affiliation(s)
- Yohei Tashiro
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Shuchi H Desai
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA.,Microbiology Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA.,Microbiology Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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Spakowicz DJ, Strobel SA. Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential. Appl Microbiol Biotechnol 2015; 99:4943-51. [PMID: 25957494 DOI: 10.1007/s00253-015-6641-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/22/2015] [Accepted: 04/29/2015] [Indexed: 01/05/2023]
Abstract
Recent advances in the biological production of fuels have relied on the optimization of pathways involving genes from diverse organisms. Several recent articles have highlighted the potential to expand the pool of useful genes by looking to filamentous fungi. This review highlights the enzymes and organisms used for the production of a variety of fuel types and commodity chemicals with a focus on the usefulness and promise of those from filamentous fungi.
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Affiliation(s)
- Daniel J Spakowicz
- Department of Molecular Biophysics and Biochemistry, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT, 06520-8114, USA
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Li S, Liu L, Chen J. Compartmentalizing metabolic pathway in Candida glabrata for acetoin production. Metab Eng 2015; 28:1-7. [DOI: 10.1016/j.ymben.2014.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 01/28/2023]
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Sinha M, Sørensen A, Ahamed A, Ahring BK. Production of hydrocarbons by Aspergillus carbonarius ITEM 5010. Fungal Biol 2015; 119:274-82. [PMID: 25813514 DOI: 10.1016/j.funbio.2015.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/09/2014] [Accepted: 01/08/2015] [Indexed: 11/17/2022]
Abstract
The filamentous fungus, Asperigillus carbonarius, is able to produce a series of hydrocarbons in liquid culture using lignocellulosic biomasses, such as corn stover and switch grass as carbon source. The hydrocarbons produced by the fungus show similarity to jet fuel composition and might have industrial application. The production of hydrocarbons was found to be dependent on type of media used. Therefore, ten different carbon sources (oat meal, wheat bran, glucose, carboxymethyl cellulose, avicel, xylan, corn stover, switch grass, pretreated corn stover, and pretreated switch grass) were tested to identify the maximum number and quantity of hydrocarbons produced. Several hydrocarbons were produced include undecane, dodecane, tetradecane, hexadecane 2,4-dimethylhexane, 4-methylheptane, 3-methyl-1-butanol, ethyl benzene, o-xylene. Oatmeal was found to be the carbon source resulting in the largest amounts of hydrocarbon products. The production of fungal hydrocarbons, especially from lignocellulosic biomasses, holds a great potential for future biofuel production whenever our knowledge on regulators and pathways increases.
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Affiliation(s)
- Malavika Sinha
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
| | - Annette Sørensen
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA; Section for Sustainable Biotechnology, Aalborg University Copenhagen, AC Meyers Vaenge 15, DK-2450 Copenhagen SV, Denmark
| | - Aftab Ahamed
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
| | - Birgitte Kiær Ahring
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA.
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