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Ribosome-binding Sequences (RBS) Engineering of Key Genes in Escherichia coli for High Production of Fatty Alcohols. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-021-0354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Liu Y, Chen J, Khusnutdinova AN, Correia K, Diep P, Batyrova KA, Nemr K, Flick R, Stogios P, Yakunin AF, Mahadevan R. A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:114. [PMID: 32612677 PMCID: PMC7325246 DOI: 10.1186/s13068-020-01753-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/16/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Aldehyde decarbonylases (ADs), which convert acyl aldehydes into alkanes, supply promising solution for producing alkanes from renewable feedstock. However the instability of ADs impedes their further application. Therefore, the current study aimed to investigate the degradation mechanism of ADs and engineer it towards high stability. RESULTS Here, we describe the discovery of a degradation tag (degron) in the AD from marine cyanobacterium Prochlorococcus marinus using error-prone PCR-based directed evolution system. Bioinformatic analysis revealed that this C-terminal degron is common in bacterial ADs and identified a conserved C-terminal motif, RMSAYGLAAA, representing the AD degron (ADcon). Furthermore, we demonstrated that the ATP-dependent proteases ClpAP and Lon are involved in the degradation of AD-tagged proteins in E. coli, thereby limiting alkane production. Deletion or modification of the degron motif increased alkane production in vivo. CONCLUSION This work revealed the presence of a novel degron in bacterial ADs responsible for its instability. The in vivo experiments proved eliminating or modifying the degron could stabilize AD, thereby producing higher titers of alkanes.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Khorcheska A. Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
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Olajuyin AM, Yang M, Thygesen A, Tian J, Mu T, Xing J. Effective production of succinic acid from coconut water ( Cocos nucifera) by metabolically engineered Escherichia coli with overexpression of Bacillus subtilis pyruvate carboxylase. ACTA ACUST UNITED AC 2019; 24:e00378. [PMID: 31641622 PMCID: PMC6796535 DOI: 10.1016/j.btre.2019.e00378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/08/2019] [Accepted: 09/02/2019] [Indexed: 10/30/2022]
Abstract
Succinic acid is an important acid which is used in medicine and pharmaceutical companies. Metabolically engineered Escherichia coli strain was used for the effective production of succinic acid using Cocos nucifera water, which contained 5.00 ± 0.02 g/L glucose, 6.10 ± 0.01 g /L fructose and 6.70 ± 0.02 g /L sucrose. Fermentation of C. nucifera water with E. coli M6PM produced a final concentration of 11.78 ± 0.02 g/L succinic acid and yield of 1.23 ± 0.01 mol/mol, 0.66 ± 0.01 g/g total sugars after 72 h dual-phase fermentation in M9 medium while modeled sugar was 0.38 ± 0.02 mol/mol total sugars. It resulted in 72% of the maximum theoretical yield of succinic acid. Here we show that novel substrate of C. nucifera water resulted in effective production of succinic acid. These investigations unveil the importance of C. nucifera water as a substrate for the production of biochemicals.
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Key Words
- Bacillus subtilis
- Cocos nucifera water
- Escherichia coli
- Fermentation
- HPLC, High performance liquid chromatography
- IPTG, L isopropyl-β-D-thiogalactopyranoside
- O.D, optical density
- Succinic acid
- gnd, 6-phosphogluconate dehydrogenase
- ldhA, lactate dehydrogenase A
- mreC, murein cluster C
- pflB, pyruvate formate lyase B
- pgi, phosphoglucose isomerase
- pgl, 6-phosphogluconolactonase
- poxB, pyruvate oxidase B
- ppc, phosphoenol pyruvate carboxylase
- pta-ackA, phosphotranacetylase acetate kinase A
- pyc, pyruvate carboxylase
- rpm, revolution per minutes
- tal, transaldolase
- tkt, transketolase
- zwf, glucose 6-phosphate dehydrogenase
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Affiliation(s)
- Ayobami Matthew Olajuyin
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China.,Henan Provincial People Hospital Zhengzhou Henan China
| | - Maohua Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Anders Thygesen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark.,Sino-Danish Center for Education and Research, Niels Jensensvej 2, DK-8000, Aarhus C, Denmark
| | - Jiangnan Tian
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tingzhen Mu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jianmin Xing
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
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Efficient One-Step Fusion PCR Based on Dual-Asymmetric Primers and Two-Step Annealing. Mol Biotechnol 2018; 60:92-99. [PMID: 29230626 DOI: 10.1007/s12033-017-0050-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Gene splicing by fusion PCR is a versatile and widely used methodology, especially in synthetic biology. We here describe a rapid method for splicing two fragments by one-round fusion PCR with a dual-asymmetric primers and two-step annealing (ODT) method. During the process, the asymmetric intermediate fragments were generated in the early stage. Thereafter, they were hybridized in the subsequent cycles to serve as template for the target full-length product. The process parameters such as primer ratio, elongation temperature and cycle numbers were optimized. In addition, the fusion products produced with this method were successfully applied in seamless genome editing. The fusion of two fragments by this method takes less than 0.5 day. The method is expected to facilitate various kinds of complex genetic engineering projects with enhanced efficiency.
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Enhanced production of succinic acid from methanol-organosolv pretreated Strophanthus preussii by recombinant Escherichia coli. Bioprocess Biosyst Eng 2018; 41:1497-1508. [PMID: 30006798 DOI: 10.1007/s00449-018-1977-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/29/2018] [Indexed: 01/06/2023]
Abstract
A biorefinery process for high yield production of succinic acid from biomass sugars was investigated using recombinant Escherichia coli. The major problem been addressed is utilization of waste biomass for the production of succinic acid using metabolic engineering strategy. Here, methanol extract of Strophanthus preussii was used for fermentation. The process parameters were optimized. Glucose (9 g/L), galactose (4 g/L), xylose (6 g/L) and arabinose (0.5 g/L) were the major sugars present in the methanol extract of S. preussii. E. coli K3OS with overexpression of soluble nucleotide pyridine transhydrogenase sthA and mutation of lactate dehydrogenase A (ldhA), phosphotransacetylase acetate kinase A (pta-ackA), pyruvate formate lyase B (pflB), pyruvate oxidase B (poxB), produced a final succinic acid concentration of 14.40 g/L and yield of 1.10 mol/mol total sugars after 72 h dual-phase fermentation in M9 medium. Here, we show that the maximum theoretical yield using methanol extracts of S. preussii was 64%. Hence, methanol extract of S. preussii could be used for the production of biochemicals such as succinate, malate and pyruvate.
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Yang M, Zhang X. Construction of pyruvate producing strain with intact pyruvate dehydrogenase and genome-wide transcription analysis. World J Microbiol Biotechnol 2017; 33:59. [PMID: 28243982 DOI: 10.1007/s11274-016-2202-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022]
Abstract
To obtain strain YP211 with a high tendency for accumulating pyruvate, central metabolic pathways were modified in Escherichia coli MG1655. Specifically, seven genes (ldhA, pflB, pta-ackA, poxB, ppc, frdBC) were knocked out sequentially and full pyruvate dehydrogenase was retained. In batch fermentation with M9 medium, pyruvate yield and production rate reached 0.63 g/g glucose and 1.89 g/(1 h), respectively. Meanwhile, the production of acetate, succinate, and other carboxylates was effectively controlled. To understand the physiological observations, we further completed genome-wide transcription analysis of wild-type and YP211. As the acetic acid pathways were blocked, the pathways of convertion of pyruvate to phosphoenol pyruvate and acetyl CoA were enhanced. The transcription of pck, as an alternative gene for ppc, was increased by 2.6 times. So even if gene ppc was inactivated, the tricarboxylic acid pathway was still enhanced in YP211. In order to balance intracellular NADH/NAD+, oxidative phosphorylation and flagellar assembly system were also up-regulated significantly. Biochemical pathways involved in pyruvate accumulation in YP211 (a). Transcriptional differences of genes related to pyruvate metabolism between strain YP211 and E. coli wild-type (b).
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Affiliation(s)
- Maohua Yang
- Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.
| | - Xiang Zhang
- Institute of Agro-food Science and Technology, Shandong Academy of Agricultural Sciences, No. 202 North Industrial Road, Ji'nan, 250100, People's Republic of China
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Liu Y, Chen S, Chen J, Zhou J, Wang Y, Yang M, Qi X, Xing J, Wang Q, Ma Y. High production of fatty alcohols in Escherichia coli with fatty acid starvation. Microb Cell Fact 2016; 15:129. [PMID: 27465205 PMCID: PMC4964107 DOI: 10.1186/s12934-016-0524-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/11/2016] [Indexed: 02/08/2023] Open
Abstract
Background Microbial biofuel synthesis attracting increasing attention. Great advances have been made in producing fatty alcohols from fatty acyl-CoAs and fatty acids in Escherichia coli. However, the low titers and limited knowledge regarding the basic characteristics of fatty alcohols, such as location and toxicity, have hampered large-scale industrialization. Further research is still needed. Results In this study, we designed a novel and efficient strategy to enhance fatty alcohol production by inducing fatty acid starvation. We report the first use of deletions of acyl-ACP thioesterases to enhance fatty alcohol production. Transcriptional analysis was conducted to investigate the mechanism of the designed strategy. Then, fatty alcohol production was further enhanced by deletion of genes from competing pathways. Fatty alcohols were shown to be extracellular products with low toxicity. The final strain, E. coli MGL2, produced fatty alcohols at the remarkable level of 6.33 g/L under fed-batch fermentation, representing the highest reported titer of fatty alcohols produced by microorganisms. Conclusions Deletions of genes responsible for synthesis of fatty acids and competing products are promising strategies for fatty alcohol production. Our investigation of the location and toxicity of fatty alcohols suggest bright future for fatty alcohol production in E. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0524-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yilan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Sha Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China
| | - Jinjin Chen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiemin Zhou
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yanyan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Maohua Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xianni Qi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Jianmin Xing
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
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