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Ríos-Alvarado J, Avitia-Rodríguez ON, Urtiz-Estrada N, Zazueta-Álvarez DE, López-Miranda J, Vázquez-Ortega PG, Rojas-Contreras JA. Expression and characterization of a novel β-1,4-endoglucanase from Bacillus subtilis strain isolated from a pulp and paper mill wastewater. Protein Expr Purif 2024; 220:106490. [PMID: 38697589 DOI: 10.1016/j.pep.2024.106490] [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: 01/28/2024] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The production of fermentable sugars from lignocellulosic biomass is achieved by the synergistic action of a group of enzymes called cellulases. Cellulose is a long chain of chemically linked glucoses by β-1,4 bonds. The enzyme β-1,4-endoglucanase is the first cellulase involved in the degradation, breaking the bond of the amorphous regions. A β-1,4-endoglucanase enzyme with high activity was obtained from a Bacillus subtilis strain isolated from wastewater of a pulp and paper mill. Sequencing and bioinformatic analysis showed that the gene amplified by PCR consisting of 1407 nucleotides and coding for a β-1,4-endoglucanase enzyme of approximately 55 kDa. The open reading frame (ORF) encoding the mature endoglucanase (eglS) was successfully inserted in a modified cloning plasmid (pITD03) and into the pYD1 plasmid used for its expression in yeast. Carboxymethylcellulose (CMC) plate assay, SDS-PAGE, and zymogram confirmed the production and secretion by the transformed E. coli BL21-SI strain of a 39 kDa β-1,4-endoglucanase consistent with the catalytic domain without the cellulose-binding module (CBM). The results showed that the truncated β-1,4-endoglucanase had higher activity and stability.
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Affiliation(s)
- Joel Ríos-Alvarado
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Olga Noelia Avitia-Rodríguez
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Norma Urtiz-Estrada
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinaria S/N, Col. Valle del Sur, 34120, Durango, Dgo., Mexico
| | - David Enrique Zazueta-Álvarez
- Universidad Politécnica de Durango, Departamento de Ingeniería en Tecnología Ambiental, Carretera Durango-México Km 9.5. Col, Los Encinos, C.P. 34300, Durango, Dgo, Mexico
| | - Javier López-Miranda
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Perla Guadalupe Vázquez-Ortega
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico.
| | - Juan Antonio Rojas-Contreras
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico.
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Chen J, Guo L, Zhang Y, Zhao M, Li M, Zhao Z, Qi Q, Xian M, Liu M, Zhao G. Metabolic Engineering of Escherichia coli for Bioproduction of ( R)-3-Hydroxybutyric Acid through a Three-Pronged Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39024463 DOI: 10.1021/acs.jafc.4c04123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
(R)-3-Hydroxybutyric acid (R-3HB) is an important chiral chemical with extensive applications in the agricultural, food, and chemical industries. The synthesis of R-3HB by microbial fermentation is of interest due to its remarkable stereoselectivity and economy. However, the low production of R-3HB failed to meet the needs of large-scale industrial production. In this study, an engineered strain for the efficient biosynthesis of R-3HB was constructed through a three-pronged approach encompassing biosynthetic pathway optimization, engineering of NADPH regenerators, and central metabolism regulation. The engineered strain Q5081 produced 75.7 g/L R-3HB, with a productivity of 1.26 g/L/h and a yield of 0.34 g/g glucose in fed-batch fermentation, showing the highest reported titer and productivity of R-3HB to date. We also performed transcriptome sequencing and annotation to illustrate the mechanism underlying the enhanced R-3HB production. The systematic metabolic engineering by a three-pronged approach demonstrated the feasibility of improving the biosynthesis, and the engineered strain Q5081 has the potential for widespread applications in the industrial production of R-3HB.
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Affiliation(s)
- Jinhong Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mohan Zhao
- Qingdao No. 2 Middle School, Qingdao 266061, China
| | - Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhe Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Beganovic S, Wittmann C. Medical properties, market potential, and microbial production of golden polyketide curcumin for food, biomedical, and cosmetic applications. Curr Opin Biotechnol 2024; 87:103112. [PMID: 38518404 DOI: 10.1016/j.copbio.2024.103112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Curcumin, a potent plant polyketide in turmeric, has gained recognition for its outstanding health benefits, including anti-inflammatory, antioxidant, and anticancer effects. Classical turmeric farming, which is widely used to produce curcumin, is linked to deforestation, soil degradation, excessive water use, and reduced biodiversity. In recent years, the microbial synthesis of curcumin has been achieved and optimized through novel strategies, offering increased safety, improved sustainability, and the potential to revolutionize production. Here, we discuss recent breakthroughs in microbial engineering and fermentation techniques, as well as their capacity to increase the yield, purity, and cost-effectiveness of curcumin production. The utilization of microbial systems not only addresses supply chain limitations but also helps meet the growing demand for curcumin in various industries, including pharmaceuticals, foods, and cosmetics.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Germany
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Huh E, Choi JG, Lee MY, Kim JH, Choi Y, Ju IG, Eo H, Park MG, Kim DH, Park HJ, Lee CH, Oh MS. Peripheral metabolic alterations associated with pathological manifestations of Parkinson's disease in gut-brain axis-based mouse model. Front Mol Neurosci 2023; 16:1201073. [PMID: 37635904 PMCID: PMC10447900 DOI: 10.3389/fnmol.2023.1201073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Parkinson's disease (PD) is a representative neurodegenerative disease, and its diagnosis relies on the evaluation of clinical manifestations or brain neuroimaging in the absence of a crucial noninvasive biomarker. Here, we used non-targeted metabolomics profiling to identify metabolic alterations in the colon and plasma samples of Proteus mirabilis (P. mirabilis)-treated mice, which is a possible animal model for investigating the microbiota-gut-brain axis. Methods We performed gas chromatography-mass spectrometry to analyze the samples and detected metabolites that could reflect P. mirabilis-induced disease progression and pathology. Results and discussion Pattern, correlation and pathway enrichment analyses showed significant alterations in sugar metabolism such as galactose metabolism and fructose and mannose metabolism, which are closely associated with energy metabolism and lipid metabolism. This study indicates possible metabolic factors for P. mirabilis-induced pathological progression and provides evidence of metabolic alterations associated with P. mirabilis-mediated pathology of brain neurodegeneration.
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Affiliation(s)
- Eugene Huh
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | - Jin Gyu Choi
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | - Mee Youn Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Jin Hee Kim
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Yujin Choi
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - In Gyoung Ju
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | - Hyeyoon Eo
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Myoung Gyu Park
- MetaCen Therapeutics Inc. R&D Center, Suwon, Republic of Korea
| | - Dong-Hyun Kim
- Neurobiota Research Center, College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | - Hi-Joon Park
- Acupuncture and Meridian Science Research Center (AMSRC), College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Myung Sook Oh
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
- Department of Integrated Drug Development and Natural Products, Graduate School, Kyung Hee University, Seoul, Republic of Korea
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Li J, Li P, Liu Q, Li J, Qi H. Translation initiation consistency between in vivo and in vitro bacterial protein expression systems. Front Bioeng Biotechnol 2023; 11:1201580. [PMID: 37304134 PMCID: PMC10248181 DOI: 10.3389/fbioe.2023.1201580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023] Open
Abstract
Strict on-demand control of protein synthesis is a crucial aspect of synthetic biology. The 5'-terminal untranslated region (5'-UTR) is an essential bacterial genetic element that can be designed for the regulation of translation initiation. However, there is insufficient systematical data on the consistency of 5'-UTR function among various bacterial cells and in vitro protein synthesis systems, which is crucial for the standardization and modularization of genetic elements in synthetic biology. Here, more than 400 expression cassettes comprising the GFP gene under the regulation of various 5'-UTRs were systematically characterized to evaluate the protein translation consistency in the two popular Escherichia coli strains of JM109 and BL21, as well as an in vitro protein expression system based on cell lysate. In contrast to the very strong correlation between the two cellular systems, the consistency between in vivo and in vitro protein translation was lost, whereby both in vivo and in vitro translation evidently deviated from the estimation of the standard statistical thermodynamic model. Finally, we found that the absence of nucleotide C and complex secondary structure in the 5'-UTR significantly improve the efficiency of protein translation, both in vitro and in vivo.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
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Li F, Wang MM, Liu QH, Ma ZW, Wang JJ, Wang ZY, Tang JW, Lyu JW, Zhu ZB, Wang L. Molecular mechanisms of glycogen particle assembly in Escherichia coli. Carbohydr Polym 2023; 299:120200. [PMID: 36876811 DOI: 10.1016/j.carbpol.2022.120200] [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: 09/14/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
It has been reported that glycogen in Escherichia coli has two structural states, that is, fragility and stability, which alters dynamically. However, molecular mechanisms behind the structural alterations are not fully understood. In this study, we focused on the potential roles of two important glycogen degradation enzymes, glycogen phosphorylase (glgP) and glycogen debranching enzyme (glgX), in glycogen structural alterations. The fine molecular structure of glycogen particles in Escherichia coli and three mutants (ΔglgP, ΔglgX and ΔglgP/ΔglgX) were examined, which showed that glycogen in E. coli ΔglgP and E. coli ΔglgP/ΔglgX were consistently fragile while being consistently stable in E. coli ΔglgX, indicating the dominant role of GP in glycogen structural stability control. In sum, our study concludes that glycogen phosphorylase is essential in glycogen structural stability, leading to molecular insights into structural assembly of glycogen particles in E. coli.
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Affiliation(s)
- Fen Li
- Laboratory Medicine, The Fifth People's Hospital of Huai'an, Huai'an, Jiangsu Province, China
| | - Meng-Meng Wang
- Department of Pharmacy, Qingdao Eighth People's Hospital, Qingdao, Shandong Province, China; Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Qing-Hua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zhang-Wen Ma
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jun-Jiao Wang
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Zi-Yi Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jia-Wei Tang
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jing-Wen Lyu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Zuo-Bin Zhu
- Department of Genetics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu Province, China.
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China.
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Zheng LJ, Guo Q, Zhang YX, Liu CY, Fan LH, Zheng HD. Engineering of Escherichia coli for D-allose fermentative synthesis from D-glucose through izumoring cascade epimerization. Front Bioeng Biotechnol 2022; 10:1050808. [PMID: 36338116 PMCID: PMC9633178 DOI: 10.3389/fbioe.2022.1050808] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/11/2022] [Indexed: 10/13/2023] Open
Abstract
D-Allose is a potential alternative to sucrose in the food industries and a useful additive for the healthcare products in the future. At present, the methods for large-scale production of D-allose are still under investigation, most of which are based on in vitro enzyme-catalyzed Izumoring epimerization. In contrast, fermentative synthesis of D-allose has never been reported, probably due to the absence of available natural microorganisms. In this work, we co-expressed D-galactose: H+ symporter (GalP), D-glucose isomerase (DGI), D-allulose 3-epimerase (DAE), and ribose-5-phosphate isomerase (RPI) in Escherichia coli, thereby constructing an in vivo Izumoring pathway for yielding D-allose from D-glucose. The carbon fluxes and carbon catabolite repression (CCR) were rationally regulated by knockout of FruA, PtsG, Glk, Mak, PfkA, and PfkB involved in the pathways capable of phosphorylating D-fructose, D-glucose, and fructose-6-phosphate. Moreover, the native D-allose transporter was damaged by inactivation of AlsB, thus driving the reversible Izumoring reactions towards the target product. Fermentation was performed in the M9 medium supplemented with glycerol as a carbon source and D-glucose as a substrate. The results show that the engineered E. coli cell factory was able to produce approximately 127.35 mg/L of D-allose after 84 h. Our achievements in the fermentative production of D-allose in this work may further promote the green manufacturing of rare sugars.
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Affiliation(s)
- Ling-Jie Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Qiang Guo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Ya-Xing Zhang
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Chen-Yang Liu
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
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Mayer F, Cserjan-Puschmann M, Haslinger B, Shpylovyi A, Dalik T, Sam C, Hahn R, Striedner G. Strain specific properties of Escherichia coli can prevent non-canonical amino acid misincorporation caused by scale-related process heterogeneities. Microb Cell Fact 2022; 21:170. [PMID: 35999607 PMCID: PMC9396823 DOI: 10.1186/s12934-022-01895-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is one of the most important hosts for production of recombinant proteins in biopharmaceutical industry. However, when selecting a suitable production strain, it is often not considered that a lot of different sub-species exist, which can differ in their genotypes and phenotypes. Another important development step is the scale-up of bioprocesses with the particular challenge that heterogeneities and gradients occur at production scale. These in turn can affect the production organism and can have negative impact on the process and the product quality. Therefore, researchers developed scale-down reactors, which are used to mimic manufacturing conditions in laboratory scale. The main objectives of this study were to determine the extent to which scale-related process inhomogeneities affect the misincorporation of non-canonical amino acids into the recombinant target protein, which is an important quality attribute, and whether strain specific properties may have an impact. Results We investigated two industrially relevant E. coli strains, BL21(DE3) and HMS174(DE3), which produced an antigen binding fragment (Fab). The cells were cultivated in high cell density fed-batch mode at laboratory scale and under scale-down conditions. We demonstrated that the two host strains differ significantly with respect to norleucine misincorporation into the target protein, especially under heterogeneous cultivation conditions in the scale-down reactor. No norleucine misincorporation was observed in E. coli BL21(DE3) for either cultivation condition. In contrast, norleucine incorporation into HMS174(DE3) was already detectable in the reference process and increased dramatically in scale-down experiments. Norleucine incorporation was not random and certain positions were preferred over others, even though only a single codon exists. Differences in biomass and Fab production between the strains during scale-down cultivations could be observed as well. Conclusions This study has shown that E. coli BL21(DE3) is much more robust to scale-up effects in terms of norleucine misincorporation than the K12 strain tested. In this respect, BL21(DE3) enables better transferability of results at different scales, simplifies process implementation at production scale, and helps to meet regulatory quality guidelines defined for biopharmaceutical manufacturing. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01895-1.
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Affiliation(s)
- Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Benedikt Haslinger
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Anton Shpylovyi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Thomas Dalik
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christian Sam
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Sun Y, Chen Z, Wang G, Lv H, Mao Y, Ma K, Wang Y. De novo production of versatile oxidized kaurene diterpenes in Escherichia coli. Metab Eng 2022; 73:201-213. [DOI: 10.1016/j.ymben.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
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Liu S, Xu JZ, Zhang WG. Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. World J Microbiol Biotechnol 2022; 38:22. [PMID: 34989926 DOI: 10.1007/s11274-021-03212-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.
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Affiliation(s)
- Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
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Sibley M, Ward JM. A cell engineering approach to enzyme-based fed-batch fermentation. Microb Cell Fact 2021; 20:146. [PMID: 34303374 PMCID: PMC8310608 DOI: 10.1186/s12934-021-01634-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/16/2021] [Indexed: 11/21/2022] Open
Abstract
Background A fundamental problem associated with E. coli fermentations is the difficulty in achieving high cell densities in batch cultures, attributed in large part to the production and accumulation of acetate through a phenomenon known as overflow metabolism when supplying enough glucose for the cell density desired. Although a fed-batch configuration is the standard method for reducing such issues, traditional fed-batch systems require components which become problematic when applying them at smaller scale. One alternative has been the development of a system whereby the enzymatic degradation of starch is used to release glucose at a controlled rate. However, to date, amylolytic enzymes have only been applied to the culture exogenously, whereas our goal is to design and construct a self-secreting amylolytic chassis capable of self-regulated enzyme-based fed-batch fermentation. Results A putative glucoamylase from C. violaceum has been cloned and expressed in E. coli BL21(DE3) and W3110, which exhibits significant glucose releasing amylolytic activity. Extracellular amylolytic activity was enhanced following a replacement of the enzymes native signal peptide with the DsbA signal sequence, contributing to a glucoamylase secreting strain capable of utilising starch as a sole carbon source in defined media. Introduction of PcstA, a glucose sensitive K12 compatible promoter, and the incorporation of this alongside C. violaceum glucoamylase in E. coli W3110, gave rise to increased cell densities in cultures grown on starch (OD600 ∼ 30) compared to those grown on an equivalent amount of glucose (OD600 ∼ 15). Lastly, a novel self-secreting enzyme-based fed-batch fermentation system was demonstrated via the simultaneous expression of the C. violaceum glucoamylase and a recombinant protein of interest (eGFP), resulting in a fourfold increase in yield when grown in media containing starch compared with the glucose equivalent. Conclusions This study has developed, through the secretion of a previously uncharacterised bacterial glucoamylase, a novel amylolytic E. coli strain capable of direct starch to glucose conversion. The ability of this strain to achieve increased cell densities as well as an associated increase in recombinant protein yield when grown on starch compared with an equivalent amount of glucose, demonstrates for the first time a cell engineering approach to enzyme-based fed-batch fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01634-y.
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Affiliation(s)
- Michael Sibley
- Department of Biochemical Engineering, UCL, Gower Street, London, WC1E 6BT, UK
| | - John M Ward
- Department of Biochemical Engineering, UCL, Gower Street, London, WC1E 6BT, UK.
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12
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El-Mansi M, Phue JN, Shiloach J. Expression of the ace operon in Escherichia coli is triggered in response to growth rate-dependent flux-signal of ATP. FEMS Microbiol Lett 2021; 368:6070649. [PMID: 33417680 DOI: 10.1093/femsle/fnaa221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023] Open
Abstract
The signal that triggers the expression of the ace operon and, in turn, the transition of central metabolism's architecture from acetogenic to gluconeogenic in Escherichia coli remains elusive despite extensive research both in vivo and in vitro. Here, with the aid of flux analysis together with measurements of the enzymic activity of isocitrate lyase (ICL) and its aceA-messenger ribonucleuc acid (mRNA) transcripts, we provide credible evidence suggesting that the expression of the ace operon in E. coli is triggered in response to growth rate-dependent threshold flux-signal of adenosine triphosphate (ATP). Flux analysis revealed that the shortfall in ATP supply observed as the growth rate ($\mu $) diminishes from µmax to ≤ 0.43h-1 ($ \pm 0.02;n4)\ $is partially redressed by up-regulating flux through succinyl CoA synthetase. Unlike glycerol and glucose, pyruvate cannot feed directly into the two glycolytic ATP-generating reactions catalyzed by phosphoglycerokinase and pyruvate kinase. On the other hand, glycerol, which upon its conversion to D-glyceraldehyde, feeds into the phosphorylation and dephosphorylation parts of glycolysis including the substrate-level phosphorylation-ATP generating reactions, thus preventing ATP flux from dropping to the critical threshold signal required to trigger the acetate-diauxic switch until glycerol is fully consumed. The mRNA transcriptional patterns of key gluconeogenic enzymes, namely, ackA, acetate kinase; pta, phosphotransacetylase; acs, acetyl CoA synthetase and aceA, ICL, suggest that the pyruvate phenotype is better equipped than the glycerol phenotype for the switch from acetogenic to gluconeogenic metabolism.
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Affiliation(s)
- Mansi El-Mansi
- Bio-Ed, Scotland UK, 17/7 Watson Crescent, Edinburgh EGH11 1HA, Scotland, UK.,University of Africa, Toru-Orua, Department of Biotechnology, Faculty of Science, Sagbama L.G.A. Bayelsa State, Nigeria
| | - Je-Nie Phue
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
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13
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Gao Q, Chen H, Wang G, Yang W, Zhong X, Liu J, Huo X, Liu W, Huang J, Tao Y, Lin B. Highly Efficient Production of Menaquinone-7 from Glucose by Metabolically Engineered Escherichia coli. ACS Synth Biol 2021; 10:756-765. [PMID: 33755417 DOI: 10.1021/acssynbio.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Menaquinone-7 (MK-7) possesses wide health and medical value, and the market demand for MK-7 has increased. Metabolic engineering for MK-7 production in Escherichia coli still remains challenging due to the characteristics of the competing quinone synthesis, and cells mainly synthesized menaquinones under anaerobic conditions. To increase the production of MK-7 in engineered E. coli strains under aerobic conditions, we divided the whole MK-7 biosynthetic pathway into three modules (MVA pathway, DHNA pathway, and MK-7 pathway) and systematically optimized each of them. First, by screening and enhancing Idi expression, the amounts of MK-7/DMK-7 increased significantly. Then, in the MK-7 pathway, by combinatorial overexpression of endogenous MenA and exogenous UbiE, and fine-tuning the expression of HepPPS, MenA, and UbiE, 70 μM MK-7 was achieved. Third, the DHNA synthetic pathway was enhanced, and 157 μM MK-7 was achieved. By the combinational metabolic engineering strategies and membrane engineering, an efficient metabolic engineered E. coli strain for MK-7 synthesis was developed, and 200 μM (129 mg/L) MK-7 was obtained in shake flask experiment, representing a 306-fold increase compared to the starting strain. In the scale-up fermentation, 2074 μM (1350 mg/L) MK-7 was achieved after 52 h fermentation with a productivity of 26 mg/L/h. This is the highest titer of MK-7 ever reported. This study offers an alternative method for MK-7 production from biorenewable feedstock (glucose) by engineered E. coli. The high titer of our process should make it a promising cost-effective resource for MK-7.
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Affiliation(s)
- Quanxiu Gao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Hao Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoyan Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaotong Zhong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiezheng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - XiaoJing Huo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianzhong Huang
- National Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Lara AR, Galindo J, Jaén KE, Juárez M, Sigala JC. Physiological Response of Escherichia coli W3110 and BL21 to the Aerobic Expression of Vitreoscilla Hemoglobin. J Microbiol Biotechnol 2020; 30:1592-1596. [PMID: 32699196 PMCID: PMC9728183 DOI: 10.4014/jmb.2004.04030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
The aerobic growth and metabolic performance of Escherichia coli strains BL21 and W3110 were studied when the Vitreoscilla hemoglobin (VHb) was constitutively expressed in the chromosome. When VHb was expressed, acetate production decreased in both strains and was nearly eliminated in BL21. Transcriptional levels of the glyoxylate shunt genes decreased in both strains when VHb was expressed. However, higher transcription of the α-ketoglutarate dehydrogenase genes were observed for W3110, while for BL21 transcription levels decreased. VHb expression reduced the transcription of the cytochrome bo3 genes only in BL21. These results are useful for better selecting a production host.
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Affiliation(s)
- Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico,Corresponding author Phone: +52-55-58146500 Fax: +52-55-58146500 E-mail:
| | - Janet Galindo
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Karim E. Jaén
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Mariana Juárez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Santa Fe, CP 05348, Mexico City, Mexico
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15
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Liu M, Fu Y, Gao W, Xian M, Zhao G. Highly Efficient Biosynthesis of Hypoxanthine in Escherichia coli and Transcriptome-Based Analysis of the Purine Metabolism. ACS Synth Biol 2020; 9:525-535. [PMID: 32049513 DOI: 10.1021/acssynbio.9b00396] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleosides and purine analogues have multiple functions in cell physiology, food additives, and pharmaceuticals, and some are produced on a large scale using different microorganisms. However, biosynthesis of purines is still lacking. In the present study, we engineered the de novo purine biosynthesis pathway, branched pathways, and a global regulator to ensure highly efficient hypoxanthine production by Escherichia coli. The engineered strain Q2973 produced 1243 mg/L hypoxanthine in fed-batch fermentation, accompanied by an extremely low accumulation of byproducts such as acetate and xanthine. We also performed global gene expression analysis to illustrate the mechanism for improving hypoxanthine production. This study demonstrated the feasibility of large-scale hypoxanthine production byan engineered E. coli strain, and provides a reference for subsequent studies on purine analogues and nucleosides.
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Affiliation(s)
- Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Yingxin Fu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Wenjie Gao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Siences, Qingdao, 266101, China
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16
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Liu W, Zhang R, Wei M, Cao Y, Xian M. Increasing the pyruvate pool by overexpressing phosphoenolpyruvate carboxykinase or triosephosphate isomerase enhances phloroglucinol production in Escherichia coli. Biotechnol Lett 2020; 42:633-640. [PMID: 31965395 DOI: 10.1007/s10529-020-02812-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Acetyl-CoA is a precursor for phloroglucinol (PG), and pyruvate is one of the sources of intracellular acetyl-CoA. Therefore, enhancing intracellular pyruvate levels may help to improve the anabolic pathway of PG. RESULTS In this study, the effects of phosphoenolpyruvate carboxykinase (PckA, encoded by pckA) or triosephosphate isomerase (TpiA, encoded by tpiA) overexpression on the production of PG were studied. Overexpression of pckA or tpiA could enhance the pyruvate anabolic pathway in shake-flask culture compared to the control strain, and the concentration of PG also increased by 44% and 92%, respectively. In addition, the acetate levels were all down regulated by the overexpression of the two genes to some extent and lower acetate level resulted in lower ATP pool and higher survival rate. CONCLUSIONS These results indicate that overexpression of pckA or tpiA can enhance the pyruvate "pool" and PG production in Escherichia coli, which provides a new reference for further increasing the production of PG.
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Affiliation(s)
- Wen Liu
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Manman Wei
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Yujin Cao
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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17
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Choi YH, Park BS, Seo JH, Kim BG. Biosynthesis of the human milk oligosaccharide 3-fucosyllactose in metabolically engineered Escherichia coli via the salvage pathway through increasing GTP synthesis and β-galactosidase modification. Biotechnol Bioeng 2019; 116:3324-3332. [PMID: 31478191 DOI: 10.1002/bit.27160] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/27/2019] [Accepted: 08/25/2019] [Indexed: 12/13/2022]
Abstract
3-Fucosyllactose (3-FL) is one of the major fucosylated oligosaccharides in human milk. Along with 2'-fucosyllactose (2'-FL), it is known for its prebiotic, immunomodulator, neonatal brain development, and antimicrobial function. Whereas the biological production of 2'-FL has been widely studied and made significant progress over the years, the biological production of 3-FL has been hampered by the low activity and insoluble expression of α-1,3-fucosyltransferase (FutA), relatively low abundance in human milk oligosaccharides compared with 2'-FL, and lower digestibility of 3-FL than 2'-FL by bifidobacteria. In this study, we report the gram-scale production of 3-FL using E. coli BL21(DE3). We previously generated the FutA quadruple mutant (mFutA) with four site mutations at S46F, A128N, H129E, Y132I, and its specific activity was increased by nearly 15 times compared with that of wild-type FutA owing to the increase in kcat and the decrease in Km . We overexpressed mFutA in its maximum expression level, which was achieved by the optimization of yeast extract concentration in culture media. We also overexpressed L-fucokinase/GDP- L-fucose pyrophosphorylase to increase the supply of GDP-fucose in the cytoplasm. To increase the mass of recombinant whole-cell catalysts, the host E. coli BW25113 was switched to E. coli BL21(DE3) because of the lower acetate accumulation of E. coli BL21(DE3) than that of E. coli BW25113. Finally, the lactose operon was modified by partially deleting the sequence of LacZ (lacZΔm15) for better utilization of D-lactose. Production using the lacZΔm15 mutant yielded 3-FL concentration of 4.6 g/L with the productivity of 0.076 g·L-1 ·hr-1 and the specific 3-FL yield of 0.5 g/g dry cell weight.
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Affiliation(s)
- Yun Hee Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Bum Seok Park
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,School of Chemical and Biological Engineering, Institute of Engineering Research, Seoul National University, Seoul, Republic of Korea
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul, Republic of Korea
| | - Byung-Gee Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,School of Chemical and Biological Engineering, Institute of Engineering Research, Seoul National University, Seoul, Republic of Korea
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18
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Han Q, Eiteman MA. Acetate formation during recombinant protein production in Escherichia coli K-12 with an elevated NAD(H) pool. Eng Life Sci 2019; 19:770-780. [PMID: 32624970 DOI: 10.1002/elsc.201900045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Acetate formation is a disadvantage in the use of Escherichia coli for recombinant protein production, and many studies have focused on optimizing fermentation processes or altering metabolism to eliminate acetate accumulation. In this study, E. coli MEC697 (MG1655 nadR nudC mazG) maintained a larger pool of NAD(H) compared to the wild-type control, and also accumulated lower concentrations of acetate when grown in batch culture on glucose. In steady-state cultures, the elevated total NAD(H) found in MEC697 delayed the threshold dilution rate for acetate formation to a growth rate of 0.27 h-1. Batch and fed-batch processes using MEC697 were examined for the production of β-galactosidase as a model recombinant protein. Fed-batch culture of MEC697/pTrc99A-lacZ compared to MG1655/pTrc99A-lacZ at a growth rate of 0.22 h-1 showed only a modest increase of protein formation. However, 1 L batch growth of MEC697/pTrc99A-lacZ resulted in 50% lower acetate formation compared to MG1655/pTrc99A-lacZ and a two-fold increase in recombinant protein production.
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Affiliation(s)
- Qi Han
- School of Chemical Materials and Biomedical Engineering University of Georgia Athens GA USA
| | - Mark A Eiteman
- School of Chemical Materials and Biomedical Engineering University of Georgia Athens GA USA
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19
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Cánovas Díaz M, de Diego Puente T. Engineering protein production by rationally choosing a carbon and nitrogen source using E. coli BL21 acetate metabolism knockout strains. Microb Cell Fact 2019; 18:151. [PMID: 31484572 PMCID: PMC6724240 DOI: 10.1186/s12934-019-1202-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a bacteria that is widely employed in many industries for the production of high interest bio-products such as recombinant proteins. Nevertheless, the use of E. coli for recombinant protein production may entail some disadvantages such as acetate overflow. Acetate is accumulated under some culture conditions, involves a decrease in biomass and recombinant protein production, and its metabolism is related to protein lysine acetylation. Thereby, the carbon and nitrogen sources employed are relevant factors in cell host metabolism, and the study of the central metabolism of E. coli and its regulation is essential for optimizing the production of biomass and recombinant proteins. In this study, our aim was to find the most favourable conditions for carrying out recombinant protein production in E. coli BL21 using two different approaches, namely, manipulation of the culture media composition and the deletion of genes involved in acetate metabolism and Nε-lysine acetylation. RESULTS We evaluated protein overexpression in E. coli BL21 wt and five mutant strains involved in acetate metabolism (Δacs, ΔackA and Δpta) and lysine acetylation (ΔpatZ and ΔcobB) grown in minimal medium M9 (inorganic ammonium nitrogen source) and in complex TB7 medium (peptide-based nitrogen source) supplemented with glucose (PTS carbon source) or glycerol (non-PTS carbon source). We observed a dependence of recombinant protein production on acetate metabolism and the carbon and nitrogen source employed. The use of complex medium supplemented with glycerol as a carbon source entails an increase in protein production and an efficient use of resources, since is a sub-product of biodiesel synthesis. Furthermore, the deletion of the ackA gene results in a fivefold increase in protein production with respect to the wt strain and a reduction in acetate accumulation. CONCLUSION The results showed that the use of diverse carbon and nitrogen sources and acetate metabolism knockout strains can redirect E. coli carbon fluxes to different pathways and affect the final yield of the recombinant protein bioprocess. Thereby, we obtained a fivefold increase in protein production and an efficient use of the resources employing the most suitable strain and culture conditions.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain.
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain.
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20
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Perez-Zabaleta M, Guevara-Martínez M, Gustavsson M, Quillaguamán J, Larsson G, van Maris AJA. Comparison of engineered Escherichia coli AF1000 and BL21 strains for (R)-3-hydroxybutyrate production in fed-batch cultivation. Appl Microbiol Biotechnol 2019; 103:5627-5639. [PMID: 31104101 PMCID: PMC6597613 DOI: 10.1007/s00253-019-09876-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
Accumulation of acetate is a limiting factor in recombinant production of (R)-3-hydroxybutyrate (3HB) by Escherichia coli in high-cell-density processes. To alleviate this limitation, this study investigated two approaches: (i) deletion of phosphotransacetylase (pta), pyruvate oxidase (poxB), and/or the isocitrate lyase regulator (iclR), known to decrease acetate formation, on bioreactor cultivations designed to achieve high 3HB concentrations. (ii) Screening of different E. coli strain backgrounds (B, BL21, W, BW25113, MG1655, W3110, and AF1000) for their potential as low acetate-forming, 3HB-producing platforms. Deletion of pta and pta-poxB in the AF1000 strain background was to some extent successful in decreasing acetate formation, but also dramatically increased excretion of pyruvate and did not result in increased 3HB production in high-cell-density fed-batch cultivations. Screening of the different E. coli strains confirmed BL21 as a low acetate-forming background. Despite low 3HB titers in low-cell-density screening, 3HB-producing BL21 produced five times less acetic acid per mole of 3HB, which translated into a 2.3-fold increase in the final 3HB titer and a 3-fold higher volumetric 3HB productivity over 3HB-producing AF1000 strains in nitrogen-limited fed-batch cultivations. Consequently, the BL21 strain achieved the hitherto highest described volumetric productivity of 3HB (1.52 g L−1 h−1) and the highest 3HB concentration (16.3 g L−1) achieved by recombinant E. coli. Screening solely for 3HB titers in low-cell-density batch cultivations would not have identified the potential of this strain, reaffirming the importance of screening with the final production conditions in mind.
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Affiliation(s)
- Mariel Perez-Zabaleta
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Mónica Guevara-Martínez
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Martin Gustavsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Jorge Quillaguamán
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Gen Larsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Antonius J. A. van Maris
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
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21
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Correia DM, Sargo CR, Silva AJ, Santos ST, Giordano RC, Ferreira EC, Zangirolami TC, Ribeiro MPA, Rocha I. Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis. Metab Eng 2019; 52:303-314. [PMID: 30529284 DOI: 10.1016/j.ymben.2018.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022]
Abstract
In the last years, Salmonella has been extensively studied not only due to its importance as a pathogen, but also as a host to produce pharmaceutical compounds. However, the full exploitation of Salmonella as a platform for bioproduct delivery has been hampered by the lack of information about its metabolism. Genome-scale metabolic models can be valuable tools to delineate metabolic engineering strategies as long as they closely represent the actual metabolism of the target organism. In the present study, a 13C-MFA approach was applied to map the fluxes at the central carbon pathways of S. typhimurium LT2 growing at glucose-limited chemostat cultures. The experiments were carried out in a 2L bioreactor, using defined medium enriched with 20% 13C-labeled glucose. Metabolic flux distributions in central carbon pathways of S. typhimurium LT2 were estimated using OpenFLUX2 based on the labeling pattern of biomass protein hydrolysates together with biomass composition. The results suggested that pentose phosphate is used to catabolize glucose, with minor fluxes through glycolysis. In silico simulations, using Optflux and pFBA as simulation method, allowed to study the performance of the genome-scale metabolic model. In general, the accuracy of in silico simulations was improved by the superimposition of estimated intracellular fluxes to the existing genome-scale metabolic model, showing a better fitting to the experimental extracellular fluxes, whereas the intracellular fluxes of pentose phosphate and anaplerotic reactions were poorly described.
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Affiliation(s)
- Daniela M Correia
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Cintia R Sargo
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Adilson J Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Sophia T Santos
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal
| | - Roberto C Giordano
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Eugénio C Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal
| | - Teresa C Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Marcelo P A Ribeiro
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus De Gualtar, Braga 4710-057, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
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22
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Moon BJ, Lee KH, Kim DM. Effects of ATP regeneration systems on the yields and solubilities of cell-free synthesized proteins. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2018.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Oeggl R, Neumann T, Gätgens J, Romano D, Noack S, Rother D. Citrate as Cost-Efficient NADPH Regenerating Agent. Front Bioeng Biotechnol 2018; 6:196. [PMID: 30631764 PMCID: PMC6315136 DOI: 10.3389/fbioe.2018.00196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 11/28/2018] [Indexed: 11/15/2022] Open
Abstract
The economically efficient utilization of NAD(P)H-dependent enzymes requires the regeneration of consumed reduction equivalents. Classically, this is done by substrate supplementation, and if necessary by addition of one or more enzymes. The simplest method thereof is whole cell NADPH regeneration. In this context we now present an easy-to-apply whole cell cofactor regeneration approach, which can especially be used in screening applications. Simply by applying citrate to a buffer or directly using citrate/-phosphate buffer NADPH can be regenerated by native enzymes of the TCA cycle, practically present in all aerobic living organisms. Apart from viable-culturable cells, this regeneration approach can also be applied with lyophilized cells and even crude cell extracts. This is exemplarily shown for the synthesis of 1-phenylethanol from acetophenone with several oxidoreductases. The mechanism of NADPH regeneration by TCA cycle enzymes was further investigated by a transient isotopic labeling experiment feeding [1,5-13C]citrate. This revealed that the regeneration mechanism can further be optimized by genetic modification of two competing internal citrate metabolism pathways, the glyoxylate shunt, and the glutamate dehydrogenase.
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Affiliation(s)
- Reinhard Oeggl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Timo Neumann
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Jochem Gätgens
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Stephan Noack
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Dörte Rother
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
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24
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Effect of amino acids on transcription and translation of key genes in E. coli K and B grown at a steady state in minimal medium. N Biotechnol 2018; 49:120-128. [PMID: 30385399 DOI: 10.1016/j.nbt.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 02/01/2023]
Abstract
Growing E. coli to high densities is a common strategy for biologicals production. The process is implemented by using complex or minimal media with different feeding strategies. To understand the effect of amino acids, E. coli B and K were grown at a steady state of 0.35 h-1 in glucose minimal medium with and without amino acids, while their metabolism, protein abundance and gene expression were compared. The results showed that amino acids promoted higher acetate excretion, higher fatty acid biosynthesis (K strain), repressed glucose uptake rate, and decreased expression of proteins associated with the TCA cycle, glyoxylate shunt and amino acid biosynthesis. In presence of amino acids, E. coli K upregulated fatty acid biosynthesis and repressed more genes and proteins involved in amino acid biosynthesis than E. coli B. These findings are correlated with higher yield on glucose (Yx/s) and high specific biomass production rate (qx) in K strain in the presence of amino acids. In contrast, pre-formed precursor molecules such as amino acids did not affect fatty acid biosynthesis in E. coli B or Yx/s and qx, which were higher than those of E. coli K, suggesting that constitutive synthesis of energetically demanding precursors and higher fatty acid β-oxidation activity is key for high biomass-performer E. coli B. Both strains turned off unnecessary pathways and directed their metabolism to proteome efficient overflow metabolism likely to generate energy and provide protein to functions supporting higher growth rate.
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25
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Kim H, Kim S, Yoon SH. Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PLoS One 2018; 13:e0204375. [PMID: 30240424 PMCID: PMC6150544 DOI: 10.1371/journal.pone.0204375] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins. However, despite its important role in scientific research and biotechnological applications, a high-quality metabolic network model for metabolic engineering is yet to be developed. Here, we present the comprehensive metabolic network model of E. coli BL21(DE3), named iHK1487, based on the latest genome reannotation and phenome analysis. The metabolic model consists of 1,164 unique metabolites, 2,701 metabolic reactions, and 1,487 genes. The model was validated and improved by comparing the simulation results with phenome data from phenotype microarray tests. Previous transcriptome profile data was incorporated during model reconstruction, and flux prediction was simulated using the model. iHK1487 was simulated to explore the metabolic features of BL21(DE3) such as broad spectrum amino acid utilization and enhanced flux through the upper glycolytic pathway and TCA cycle. iHK1487 will contribute to systematic understanding of cellular physiology and metabolism of E. coli BL21(DE3) and highlight its biotechnological applications.
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Affiliation(s)
- Hanseol Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sinyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
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26
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27
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Pandey R, Kumar N, Monteiro GA, Veeranki VD, Prazeres DMF. Re-engineering of an Escherichia coli K-12 strain for the efficient production of recombinant human Interferon Gamma. Enzyme Microb Technol 2018; 117:23-31. [PMID: 30037548 DOI: 10.1016/j.enzmictec.2018.06.001] [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: 02/06/2018] [Revised: 05/23/2018] [Accepted: 06/03/2018] [Indexed: 01/17/2023]
Abstract
The Escherichia coli phosphoglucose isomerase (pgi) mutant strain GALG20 was developed previously from wild-type K12 strain MG1655 for increased plasmid yield. To investigate the potential effects of the pgi deletion/higher plasmid levels on recombinant human Interferon Gamma (IFN-γ) production, a detailed network of the central metabolic pathway (100 metabolites, 114 reactions) of GALG20 and MG1655 was constructed. Elementary mode analysis (EMA) was then performed to compare the phenotypic spaces of both the strains and to check the effect of the pgi deletion on flux efficiency of each metabolic reaction. The results suggested that pgi deletion increases amino acid biosynthesis and flux efficiency towards IFN-γ synthesis by 11%. To further confirm the qualitative prediction that the pgi mutation favours recombinant human IFN-γ expression, GALG20 and MG1655 were lysogenised, transformed with a plasmid coding for IFN-γ and tested alongside with BL21(DE3) for their expression capabilities in shake flask experiments using complex media. IFN-γ gene expression was analysed by quantifying plasmid and mRNA copy number per cell and IFN-γ protein production level. Specific IFN-γ yields confirmed the in silico metabolic network predictions, with GALG20(DE3) producing 3.0-fold and 1.5-fold more IFN-γ as compared to MG1655(DE3) and BL21(DE3), respectively. Most of the total IFN-γ was expressed as inclusion bodies across the three strains: 95% in GALG20(DE3), 97% in BL21(DE3) and 72% in MG1655(DE3). The copy number of mRNA coding for IFN-γ was found to be higher in GALG20(DE3) as compared to the other two strains. Overall, these findings show that GALG20(DE3) has the potential to become an excellent protein expression strain.
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Affiliation(s)
- Rajat Pandey
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal; Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, India.
| | - Nitin Kumar
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal; Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Gabriel A Monteiro
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal
| | - Venkata Dasu Veeranki
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - D M F Prazeres
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal
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28
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Negrete A, Shiloach J. Improving E. coli growth performance by manipulating small RNA expression. Microb Cell Fact 2017; 16:198. [PMID: 29137641 PMCID: PMC5686845 DOI: 10.1186/s12934-017-0810-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/02/2017] [Indexed: 12/17/2022] Open
Abstract
Efficient growth of E. coli, especially for production of recombinant proteins, has been a challenge for the biotechnological industry since the early 1970s. By employing multiple approaches, such as different media composition, various growth strategies and specific genetic manipulations, it is now possible to grow bacteria to concentrations exceeding 100 g/L and to achieve high concentrations of recombinant proteins. Although the growth conditions are carefully monitored and maintained, it is likely that during the growth process cells are exposed to periodic stress conditions, created by fluctuations in pH, dissolved oxygen, temperature, glucose, and salt concentration. These stress circumstances which can occur especially in large volume bioreactors, may affect the growth and production process. In the last several years, it has been recognized that small non-coding RNAs can act as regulators of bacterial gene expression. These molecules are found to be specifically involved in E. coli response to different environmental stress conditions; but so far, have not been used for improving production strains. The review provides summary of small RNAs identified on petri dish or in shake flask culture that can potentially affect growth characteristics of E. coli grown in bioreactor. Among them MicC and MicF that are involved in response to temperature changes, RyhB that responds to iron concentration, Gady which is associated with lower pH, Sgrs that is coupled with glucose transport and OxyS that responds to oxygen concentration. The manipulation of some of these small RNAs for improving growth of E. coli in Bioreactor is described in the last part of the review. Overexpression of SgrS was associated with improved growth and reduced acetate expression, over expression of GadY improved cell growth at acidic conditions and over expression of OxyS reduced the effect of oxidative stress. One of the possible advantages of manipulating sRNAs for improving cell growth is that the modifications occur at a post-translational level. Therefore, the use of sRNAs may exert minimal effect on the overall bacterial metabolism. The elucidation of the physiological role of newly discovered sRNAs will open new possibilities for creating strains with improved growth and production capabilities.
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Affiliation(s)
- Alejandro Negrete
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, 20892, USA.,MilliporeSigma, Carlsbad, CA, 92009, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, 20892, USA.
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29
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Kim S, Jeong H, Kim EY, Kim JF, Lee SY, Yoon SH. Genomic and transcriptomic landscape of Escherichia coli BL21(DE3). Nucleic Acids Res 2017; 45:5285-5293. [PMID: 28379538 PMCID: PMC5435950 DOI: 10.1093/nar/gkx228] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/26/2017] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli BL21(DE3) has long served as a model organism for scientific research, as well as a workhorse for biotechnology. Here we present the most current genome annotation of E. coli BL21(DE3) based on the transcriptome structure of the strain that was determined for the first time. The genome was annotated using multiple automated pipelines and compared to the current genome annotation of the closely related strain, E. coli K-12. High-resolution tiling array data of E. coli BL21(DE3) from several different stages of cell growth in rich and minimal media were analyzed to characterize the transcriptome structure and to provide supporting evidence for open reading frames. This new integrated analysis of the genomic and transcriptomic structure of E. coli BL21(DE3) has led to the correction of translation initiation sites for 88 coding DNA sequences and provided updated information for most genes. Additionally, 37 putative genes and 66 putative non-coding RNAs were also identified. The panoramic landscape of the genome and transcriptome of E. coli BL21(DE3) revealed here will allow us to better understand the fundamental biology of the strain and also advance biotechnological applications in industry.
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Affiliation(s)
- Sinyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eun-Youn Kim
- School of Basic Sciences, Hanbat National University, Daejeon 34158, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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30
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Umenhoffer K, Draskovits G, Nyerges Á, Karcagi I, Bogos B, Tímár E, Csörgő B, Herczeg R, Nagy I, Fehér T, Pál C, Pósfai G. Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis. ACS Synth Biol 2017; 6:1471-1483. [PMID: 28426191 DOI: 10.1021/acssynbio.6b00378] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, nonessential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization. Here, we sought to establish a rapid methodology to improve the stability of microbial hosts. The novel workflow involves genome shuffling between a mobile genetic element-free strain and the target cell, and subsequent rounds of CRISPR/Cas-assisted MAGE on multiplex targets. The power and speed of the procedure was demonstrated on E. coli BL21(DE3), a host routinely used for plasmid-based heterologous protein expression. All 9 prophages and 50 insertion elements were efficiently deleted or inactivated. Together with additional targeted manipulations (e.g., inactivation of error-prone DNA-polymerases), the changes resulted in an improved bacterial host with a hybrid (harboring segments of K-12 DNA), 9%-downsized and clean genome. The combined capacity of phage-mediated generalized transduction and CRISPR/Cas-selected MAGE offers a way for rapid, large scale editing of bacterial genomes.
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Affiliation(s)
- Kinga Umenhoffer
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Gábor Draskovits
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ákos Nyerges
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ildikó Karcagi
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Balázs Bogos
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Edit Tímár
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Bálint Csörgő
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd, 6782 Mórahalom, Hungary
- Institute
of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Tamás Fehér
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Csaba Pál
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - György Pósfai
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
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31
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Panichkin VB, Livshits VA, Biryukova IV, Mashko SV. Metabolic engineering of Escherichia coli for L-tryptophan production. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683816090052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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32
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Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Comput Biol 2017; 13:e1005396. [PMID: 28187134 PMCID: PMC5328398 DOI: 10.1371/journal.pcbi.1005396] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/27/2017] [Accepted: 02/03/2017] [Indexed: 11/23/2022] Open
Abstract
The metabolism of microorganisms is regulated through two main mechanisms: changes of enzyme capacities as a consequence of gene expression modulation (“hierarchical control”) and changes of enzyme activities through metabolite-enzyme interactions. An increasing body of evidence indicates that hierarchical control is insufficient to explain metabolic behaviors, but the system-wide impact of metabolic regulation remains largely uncharacterized. To clarify its role, we developed and validated a detailed kinetic model of Escherichia coli central metabolism that links growth to environment. Metabolic control analyses confirm that the control is widely distributed across the network and highlight strong interconnections between all the pathways. Exploration of the model solution space reveals that several robust properties emerge from metabolic regulation, from the molecular level (e.g. homeostasis of total metabolite pool) to the overall cellular physiology (e.g. coordination of carbon uptake, catabolism, energy and redox production, and growth), while allowing a large degree of flexibility at most individual metabolic steps. These properties have important physiological implications for E. coli and significantly expand the self-regulating capacities of its metabolism. Metabolism is a fundamental biochemical process that enables cells to operate and grow by converting nutrients into ‘building blocks’ and energy. Metabolism happens through the work of enzymes, which are encoded by genes. Thus, genes and their regulation are often thought of controlling metabolism, somewhat at the top of a hierarchical control system. However, an increasing body of evidence indicates that metabolism plays an active role in the control of its own operation via a dense network of metabolite-enzyme interactions. The system-wide role of metabolic regulation is hard to dissect and so far remains largely uncharacterized. To better understand its role, we constructed a detailed kinetic model of the carbon and energy metabolism of the bacterium Escherichia coli, a model organism in Systems and Synthetic biology. Model simulations indicate that kinetic considerations of metabolism alone can explain data from hundreds of experiments, without needing to invoke regulation of gene expression. In particular, metabolic regulation is sufficient to coordinate carbon utilization, redox and energy production, and growth, while maintaining local flexibility at individual metabolic steps. These findings indicate that the self-regulating capacities of E. coli metabolism are far more significant than previously expected, and improve our understanding on how cells work.
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33
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Liu M, Ding Y, Chen H, Zhao Z, Liu H, Xian M, Zhao G. Improving the production of acetyl-CoA-derived chemicals in Escherichia coli BL21(DE3) through iclR and arcA deletion. BMC Microbiol 2017; 17:10. [PMID: 28061812 PMCID: PMC5219675 DOI: 10.1186/s12866-016-0913-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/13/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Acetyl-CoA-derived chemicals are suitable for multiple applications in many industries. The bio-production of these chemicals has become imperative owing to the economic and environmental problems. However, acetate overflow is the major drawback for acetyl-CoA-derived chemicals production. Approaches for overcoming acetate overflow may be beneficial for the production of acetyl-CoA-derived chemicals. RESULTS In this study, a transcriptional regulator iclR was knocked out in E.coli BL21(DE3) to overcome acetate overflow and improve the chemicals production. Two important acetyl-CoA-derived chemicals, phloroglucinol (PG) and 3-hydroxypropionate (3HP) were used to evaluate it. It is revealed that knockout of iclR significantly increased expressions of aceBAK operon. The cell yields and glucose utilization efficiencies were higher than those of control strains. The acetate concentrations were decreased by more than 50% and the productions of PG and 3HP were increased more than twice in iclR mutants. The effects of iclR knockout on cell physiology, cell metabolism and production of acetyl-CoA-derived chemicals were similar to those of arcA knockout in our previous study. However, the arcA-iclR double mutants couldn't gain higher productions of PG and 3HP. The mechanisms are unclear and needed to be resolved in future. CONCLUSIONS Knockout of iclR significantly increased gene expression of aceBAK operon and concomitantly activated glyoxylate pathway. This genetic modification may be a good way to overcome acetate overflow, and improve the production of a wide range of acetyl-CoA-derived chemicals.
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Affiliation(s)
- Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hailin Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huizhou Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. .,Randian Technology Company Limited, Tianjin, 300457, China.
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34
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Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst 2016; 3:238-251.e12. [PMID: 27667363 DOI: 10.1016/j.cels.2016.08.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/25/2016] [Accepted: 08/19/2016] [Indexed: 11/16/2022]
Abstract
Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.
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Affiliation(s)
- Jonathan M Monk
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Miguel A Campodonico
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA; Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Daniel Machado
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Jose Miguel Seoane
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Adam M Feist
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
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35
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Bernal V, Castaño-Cerezo S, Cánovas M. Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond. Appl Microbiol Biotechnol 2016; 100:8985-9001. [DOI: 10.1007/s00253-016-7832-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022]
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36
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Han MJ. Exploring the proteomic characteristics of the Escherichia coli B and K-12 strains in different cellular compartments. J Biosci Bioeng 2016; 122:1-9. [DOI: 10.1016/j.jbiosc.2015.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/24/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
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37
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Liu M, Feng X, Ding Y, Zhao G, Liu H, Xian M. Metabolic engineering of Escherichia coli to improve recombinant protein production. Appl Microbiol Biotechnol 2015; 99:10367-77. [DOI: 10.1007/s00253-015-6955-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/18/2015] [Accepted: 08/22/2015] [Indexed: 01/13/2023]
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38
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Leone S, Sannino F, Tutino ML, Parrilli E, Picone D. Acetate: friend or foe? Efficient production of a sweet protein in Escherichia coli BL21 using acetate as a carbon source. Microb Cell Fact 2015. [PMID: 26208726 PMCID: PMC4514960 DOI: 10.1186/s12934-015-0299-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Escherichia coli is, to date, the most used microorganism for the production of recombinant proteins and biotechnologically relevant metabolites. High density cell cultures allow efficient biomass and protein yields. However, their main limitation is the accumulation of acetate as a by-product of unbalanced carbon metabolism. Increased concentrations of acetate can inhibit cellular growth and recombinant protein production, and many efforts have been made to overcome this problem. On the other hand, it is known that E. coli is able to grow on acetate as the sole carbon source, although this mechanism has never been employed for the production of recombinant proteins. RESULTS By optimization of the fermentation parameters, we have been able to develop a new acetate containing medium for the production of a recombinant protein in E. coli BL21(DE3). The medium is based on a buffering phosphate system supplemented with 0.5% yeast extract for essential nutrients and sodium acetate as additional carbon source, and it is compatible with lactose induction. We tested these culture conditions for the production of MNEI, a single chain derivative of the sweet plant protein monellin, with potential for food and beverage industries. We noticed that careful oxygenation and pH control were needed for efficient protein production. The expression method was also coupled to a faster and more efficient purification technique, which allowed us to obtain MNEI with a purity higher than 99%. CONCLUSIONS The method introduced represents a new strategy for the production of MNEI in E. coli BL21(DE3) with a simple and convenient process, and offers a new perspective on the capabilities of this microorganism as a biotechnological tool. The conditions employed are potentially scalable to industrial processes and require only low-priced reagents, thus dramatically lowering production costs on both laboratory and industrial scale. The yield of recombinant MNEI in these conditions was the highest to date from E. coli cultures, reaching on average ~180 mg/L of culture, versus typical LB/IPTG yields of about 30 mg/L.
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Affiliation(s)
- Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Naples, Italy.
| | - Filomena Sannino
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Naples, Italy.
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Naples, Italy.
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126, Naples, Italy.
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39
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Wang X, Wang Q, Qi Q. Identification of riboflavin: revealing different metabolic characteristics between Escherichia coli BL21(DE3) and MG1655. FEMS Microbiol Lett 2015; 362:fnv071. [PMID: 25926527 DOI: 10.1093/femsle/fnv071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2015] [Indexed: 01/07/2023] Open
Abstract
There are many physiological differences between Escherichia coli B and K-12 strains, owing to their different origins. Deeper insight into the metabolic and regulative mechanisms of these strains will inform improved usage of these industrial workhorses. In the present study, we observed that BL21 fermentation broth gradually turned yellow during cultivation. By spectral analysis and liquid chromatography-mass spectrometry identification, we confirmed for the first time that the yellow substance accumulated in the fermentation broth is riboflavin. Comparing the enzyme sequences involved in riboflavin metabolism between BL21 and MG1655, we identified a site mutation on the 115 residue of bifunctional riboflavin kinase/FMN adenylyltransferase (RibF) in BL21. This His115Leu mutation was found to reduce enzyme activity to 55% of that of MG1655, which is probably one reason for riboflavin accumulation in BL21. Quantitative PCR analysis showed that genes of the entire branch of the riboflavin and FAD biosynthesis pathways in BL21 were up-regulated. Several physiological and metabolic characteristics of BL21 and MG1655 were found to be different, and may also be related to the riboflavin accumulation.
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Affiliation(s)
- Xinran Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
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Castaño-Cerezo S, Bernal V, Röhrig T, Termeer S, Cánovas M. Regulation of acetate metabolism in Escherichia coli BL21 by protein Nε-lysine acetylation. Appl Microbiol Biotechnol 2014; 99:3533-45. [DOI: 10.1007/s00253-014-6280-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/16/2014] [Accepted: 11/29/2014] [Indexed: 11/29/2022]
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41
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Morshedi D, Aliakbari F, Nouri HR, Lotfinia M, Fallahi J. Using small molecules as a new challenge to redirect metabolic pathway. 3 Biotech 2014; 4:513-522. [PMID: 28324386 PMCID: PMC4162896 DOI: 10.1007/s13205-013-0185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/09/2013] [Indexed: 11/26/2022] Open
Abstract
The presence of acetate in the bacterial medium leads to a reduction in the growth rate of cells and recombinant protein production. In this study, three compounds including propionic acid, lithium chloride and butyric acid were added to the medium which decreased acetate levels and enhanced recombinant protein production (alpha-synuclein). In fact, propionic acid and lithium chloride are both known as acetate kinase inhibitors. The results obtained in the case of butyric acid were similar to those of the two other compounds indicating that butyric acid may act through a mechanism similar to propionic acid and lithium chloride. Consequently, it was shown that the presence of each of these supplements (5–200 μM) increased recombinant alpha-synuclein production and cell density by approximately 10–15 %. HPLC analysis showed that the levels of acetate in the media containing the supplements were considerably less than those of the control. Furthermore, pH values remained almost constant in the supplemented cultures. Growing the bacteria at lower temperatures (25 °C) indicated that the positive effects of these supplements were not as effective as at higher temperatures (37 °C), presumably due to the adequate balance between oxygen and carbon consumption. This study can confirm the viewpoint regarding the harmful effects of acetate on the recombinant protein production and cell density. Besides, such methods represent easy and complementary ways to increase target recombinant protein production without negatively affecting host cell density, and requiring complex genetic manipulation.
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Affiliation(s)
- Dina Morshedi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran.
| | - Farhang Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
- Department of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamid Reza Nouri
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| | - Majid Lotfinia
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Jafar Fallahi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
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42
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Lopes MB, Martins G, Calado CR. Kinetic modeling of plasmid bioproduction in Escherichia coli DH5α cultures over different carbon-source compositions. J Biotechnol 2014; 186:38-48. [DOI: 10.1016/j.jbiotec.2014.06.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/18/2014] [Accepted: 06/23/2014] [Indexed: 11/29/2022]
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Bakhtiari N, Mirshahi M, Babaeipour V, Maghsoudi N, Tahzibi A. Down Regulation of ackA-pta Pathway in Escherichia coli BL21 (DE3): A Step Toward Optimized Recombinant Protein Expression System. Jundishapur J Microbiol 2014; 7:e8990. [PMID: 25147677 PMCID: PMC4138692 DOI: 10.5812/jjm.8990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/01/2012] [Accepted: 02/19/2013] [Indexed: 01/27/2023] Open
Abstract
Background: One of the most important problems in production of recombinant protein is to attain over-expression of the target gene and high cell density. In such conditions, the secondary metabolites of bacteria become toxic for the medium and cause cells to die. One of these aforementioned metabolites is acetate, which enormously accumulated in the medium, so that both cell and protein yields are affected. Objectives: To overcome this problem, several strategies applied. In this research we used antisense RNA strategy, where the transcription of phosphotransacetylase (PTA) and acetate kinase (ACK), two acetate pathway key enzymes, could be controlled, which led to reduced acetate production. Materials and Methods: In order to achieve this, recombinant plasmid harboring antisense sequences targeting both of pta and ackA was assembled, after transfecting to the cells, its effects on the cell growth and acetate accumulation in the minimal media was assessed and compared with the control, the plasmid without antisense cassette, in presence and absence of IPTG in Escherichia coli BL21 (DE3). Results: It was observed that the mentioned strategy partially affect the growth and amount of excreted acetate in comparison with the control. In addition it was found that high down-regulation of the acetate production pathway reduces the growth rate of E. coli BL21 (DE3). Conclusions: The study principally proved the importance of this strategy in acetate excretion control.
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Affiliation(s)
- Nahid Bakhtiari
- Biochemistry Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Manouchehr Mirshahi
- Biochemistry Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Valiollah Babaeipour
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, IR Iran
- Corresponding author: Valiollah Babaeipour, Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, IR Iran. Tel: +98-2122974614; Fax: +98-2122974614, E-mail:
| | - Nader Maghsoudi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Abbas Tahzibi
- Food and Drug Organization, Ministry of Health of Iran, Tehran, IR Iran
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44
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Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Appl Environ Microbiol 2014; 80:6223-42. [PMID: 25085490 DOI: 10.1128/aem.01542-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-cell-density fermentation for industrial production of chemicals can impose numerous stresses on cells due to high substrate, product, and by-product concentrations; high osmolarity; reactive oxygen species; and elevated temperatures. There is a need to develop platform strains of industrial microorganisms that are more tolerant toward these typical processing conditions. In this study, the growth of six industrially relevant strains of Escherichia coli was characterized under eight stress conditions representative of fed-batch fermentation, and strains W and BL21(DE3) were selected as platforms for transposon (Tn) mutagenesis due to favorable resistance characteristics. Selection experiments, followed by either targeted or genome-wide next-generation-sequencing-based Tn insertion site determination, were performed to identify mutants with improved growth properties under a subset of three stress conditions and two combinations of individual stresses. A subset of the identified loss-of-function mutants were selected for a combinatorial approach, where strains with combinations of two and three gene deletions were systematically constructed and tested for single and multistress resistance. These approaches allowed identification of (i) strain-background-specific stress resistance phenotypes, (ii) novel gene deletion mutants in E. coli that confer single and multistress resistance in a strain-background-dependent manner, and (iii) synergistic effects of multiple gene deletions that confer improved resistance over single deletions. The results of this study underscore the suboptimality and strain-specific variability of the genetic network regulating growth under stressful conditions and suggest that further exploration of the combinatorial gene deletion space in multiple strain backgrounds is needed for optimizing strains for microbial bioprocessing applications.
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45
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Collins T, Barroca M, Branca F, Padrão J, Machado R, Casal M. High Level Biosynthesis of a Silk-Elastin-like Protein in E. coli. Biomacromolecules 2014; 15:2701-8. [DOI: 10.1021/bm5005564] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tony Collins
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Mário Barroca
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Fernando Branca
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jorge Padrão
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Raul Machado
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Margarida Casal
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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46
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Overton TW. Recombinant protein production in bacterial hosts. Drug Discov Today 2014; 19:590-601. [DOI: 10.1016/j.drudis.2013.11.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/03/2013] [Accepted: 11/08/2013] [Indexed: 10/26/2022]
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47
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Li Z, Nimtz M, Rinas U. The metabolic potential of Escherichia coli BL21 in defined and rich medium. Microb Cell Fact 2014; 13:45. [PMID: 24656150 PMCID: PMC4021462 DOI: 10.1186/1475-2859-13-45] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis. RESULTS The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery. CONCLUSIONS The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.
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Affiliation(s)
| | | | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany.
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48
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Improvement on the yield of polyhydroxyalkanotes production from cheese whey by a recombinant Escherichia coli strain using the proton suicide methodology. Enzyme Microb Technol 2014; 55:151-8. [DOI: 10.1016/j.enzmictec.2013.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/16/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
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49
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Chong H, Yeow J, Wang I, Song H, Jiang R. Improving acetate tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS One 2013; 8:e77422. [PMID: 24124618 PMCID: PMC3790751 DOI: 10.1371/journal.pone.0077422] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The presence of acetate exceeding 5 g/L is a major concern during E. coli fermentation due to its inhibitory effect on cell growth, thereby limiting high-density cell culture and recombinant protein production. Hence, engineered E. coli strains with enhanced acetate tolerance would be valuable for these bioprocesses. In this work, the acetate tolerance of E. coli was much improved by rewiring its global regulator cAMP receptor protein (CRP), which is reported to regulate 444 genes. Error-prone PCR method was employed to modify crp and the mutagenesis libraries (~3×10(6)) were subjected to M9 minimal medium supplemented with 5-10 g/L sodium acetate for selection. Mutant A2 (D138Y) was isolated and its growth rate in 15 g/L sodium acetate was found to be 0.083 h(-1), much higher than that of the control (0.016 h(-1)). Real-time PCR analysis via OpenArray(®) system revealed that over 400 CRP-regulated genes were differentially expressed in A2 with or without acetate stress, including those involved in the TCA cycle, phosphotransferase system, etc. Eight genes were chosen for overexpression and the overexpression of uxaB was found to lead to E. coli acetate sensitivity.
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Affiliation(s)
- Huiqing Chong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Ivy Wang
- Life Technologies R&D, Singapore, Singapore
| | - Hao Song
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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50
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Caspeta L, Lara AR, Pérez NO, Flores N, Bolívar F, Ramírez OT. Enhancing thermo-induced recombinant protein production in Escherichia coli by temperature oscillations and post-induction nutrient feeding strategies. J Biotechnol 2013; 167:47-55. [DOI: 10.1016/j.jbiotec.2013.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 11/15/2022]
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