1
|
Ito Y, Yoshidome D, Hidaka M, Araki Y, Ito K, Kosono S, Nishiyama M. Improvement of the nitrogenase activity in Escherichia coli that expresses the nitrogen fixation-related genes from Azotobacter vinelandii. Biochem Biophys Res Commun 2024; 728:150345. [PMID: 38971001 DOI: 10.1016/j.bbrc.2024.150345] [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: 04/09/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The transfer of nitrogen fixation (nif) genes from diazotrophs to non-diazotrophic hosts is of increasing interest for engineering biological nitrogen fixation. A recombinant Escherichia coli strain expressing Azotobacter vinelandii 18 nif genes (nifHDKBUSVQENXYWZMF, nifiscA, and nafU) were previously constructed and showed nitrogenase activity. In the present study, we constructed several E. coli strain derivatives in which all or some of the 18 nif genes were additionally integrated into the fliK locus of the chromosome in various combinations. E. coli derivatives with the chromosomal integration of nifiscA, nifU, and nifS, which are involved in the biosynthesis of the [4Fe-4S] cluster of dinitrogenase reductase, exhibited enhanced nitrogenase activity. We also revealed that overexpression of E. coli fldA and ydbK, which encode flavodoxin and flavodoxin-reducing enzyme, respectively, enhanced nitrogenase activity, likely by facilitating electron transfer to dinitrogenase reductase. The additional expression of nifM, putatively involved in maturation of dinitrogenase reductase, further enhanced nitrogenase activity and the amount of soluble NifH. By combining these factors, we successfully improved nitrogenase activity 10-fold.
Collapse
Affiliation(s)
- Yusuke Ito
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Daisuke Yoshidome
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Makoto Hidaka
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yasuko Araki
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research & Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Saori Kosono
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nishiyama
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
2
|
Liu C, Lv X, Li J, Liu L, Du G, Liu Y. Metabolic Engineering of Escherichia coli for Increased Bioproduction of N-Acetylneuraminic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15859-15868. [PMID: 36475707 DOI: 10.1021/acs.jafc.2c05994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-Acetylneuraminic acid (NeuAc) is widely used in the food and pharmaceutical industries. Therefore, it is important to develop an efficient and eco-friendly method for NeuAc production. Here, we achieved de novo biosynthesis of NeuAc in an engineered plasmid-free Escherichia coli strain, which efficiently synthesizes NeuAc using glycerol as the sole carbon source, via clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9-based genome editing. NeuAc key precursor, N-acetylmannosamine (ManNAc; 0.40 g/L), was produced by expressing UDP-N-acetylglucosamine-2-epimerase and glucosamine-6-phosphate synthase (GlmS) mutants and blocking the NeuAc catabolic pathway in E. coli BL21 (DE3). The expression levels of GlmM and GlmU-GlmSA metabolic modules were optimized, significantly increasing the ManNAc titer to 8.95 g/L. Next, the expression levels of NeuAc synthase from different microorganisms were optimized, leading to the production of 6.27 g/L of NeuAc. Blocking the competing pathway of NeuAc biosynthesis increased the NeuAc titer to 9.65 g/L. In fed-batch culture in a 3 L fermenter, NeuAc titer reached 23.46 g/L with productivity of 0.69 g/L/h, which is the highest level achieved by microbial synthesis using glycerol as the sole carbon source in E. coli. The strategies used in our study can aid in the efficient bioproduction of NeuAc and its derivatives.
Collapse
Affiliation(s)
- Chang Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| |
Collapse
|
3
|
Semi-rational design of L-amino acid deaminase for production of pyruvate and D-alanine by Escherichia coli whole-cell biocatalyst. Amino Acids 2021; 53:1361-1371. [PMID: 34417892 DOI: 10.1007/s00726-021-03067-8] [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: 05/29/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
In our previous study, one-step pyruvate and D-alanine production from D,L-alanine by a whole-cell biocatalyst Escherichia coli expressing L-amino acid deaminase (Pm1) derived from Proteus mirabilis was investigated. However, due to the low catalytic efficiency of Pm1, the pyruvate titer was relatively low. Here, semi-rational design based on site-directed saturation mutagenesis was carried out to improve the catalytic efficiency of Pm1. A novel high-throughput screening (HTS) method for pyruvate based on 2,4-dinitrophenylhydrazine indicator was then established. The catalytic efficiency (kcat/Km) of the mutant V437I screened out by this method was 1.88 times higher than wild type. Next, to improve the growth of the engineered strain BLK07, the genes encoding for Xpk and Fbp were integrated into its genome to construct non-oxidative glycolysis (NOG) pathway. Finally, the CRISPR/Cas9 system was used to integrate the N6-pm1-V437I gene into the genome of BLK07. Pyruvic acid titer of the plasmid-free strain reached 42.20 g/L with an L-alanine conversion rate of 77.62% and a D-alanine resolution of 82.4%. This work would accelerate the industrial production of pyruvate and D-alanine by biocatalysis, and the HTS method established here could be used to screen other Pm1 mutants with high pyruvate titers.
Collapse
|
4
|
High-yield and plasmid-free biocatalytic production of 5-methylpyrazine-2-carboxylic acid by combinatorial genetic elements engineering and genome engineering of Escherichia coli. Enzyme Microb Technol 2020; 134:109488. [DOI: 10.1016/j.enzmictec.2019.109488] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/17/2019] [Accepted: 12/08/2019] [Indexed: 02/06/2023]
|
5
|
Hausjell J, Kutscha R, Gesson JD, Reinisch D, Spadiut O. The Effects of Lactose Induction on a Plasmid-Free E. coli T7 Expression System. Bioengineering (Basel) 2020; 7:E8. [PMID: 31935883 PMCID: PMC7175309 DOI: 10.3390/bioengineering7010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
Recombinant production of pharmaceutical proteins like antigen binding fragments (Fabs) in the commonly-used production host Escherichia coli presents several challenges. The predominantly-used plasmid-based expression systems exhibit the drawback of either excessive plasmid amplification or plasmid loss over prolonged cultivations. To improve production, efforts are made to establish plasmid-free expression, ensuring more stable process conditions. Another strategy to stabilize production processes is lactose induction, leading to increased soluble product formation and cell fitness, as shown in several studies performed with plasmid-based expression systems. Within this study we wanted to investigate lactose induction for a strain with a genome-integrated gene of interest for the first time. We found unusually high specific lactose uptake rates, which we could attribute to the low levels of lac-repressor protein that is usually encoded not only on the genome but additionally on pET plasmids. We further show that these unusually high lactose uptake rates are toxic to the cells, leading to increased cell leakiness and lysis. Finally, we demonstrate that in contrast to plasmid-based T7 expression systems, IPTG induction is beneficial for genome-integrated T7 expression systems concerning cell fitness and productivity.
Collapse
Affiliation(s)
- Johanna Hausjell
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
| | - Regina Kutscha
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
| | - Jeannine D. Gesson
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria; (J.D.G.); (D.R.)
| | - Daniela Reinisch
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria; (J.D.G.); (D.R.)
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
| |
Collapse
|
6
|
Driller R, Garbe D, Mehlmer N, Fuchs M, Raz K, Major DT, Brück T, Loll B. Current understanding and biotechnological application of the bacterial diterpene synthase CotB2. Beilstein J Org Chem 2019; 15:2355-2368. [PMID: 31666870 PMCID: PMC6808215 DOI: 10.3762/bjoc.15.228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
CotB2 catalyzes the first committed step in cyclooctatin biosynthesis of the soil bacterium Streptomyces melanosporofaciens. To date, CotB2 represents the best studied bacterial diterpene synthase. Its reaction mechanism has been addressed by isoptope labeling, targeted mutagenesis and theoretical computations in the gas phase, as well as full enzyme molecular dynamic simulations. By X-ray crystallography different snapshots of CotB2 from the open, inactive, to the closed, active conformation have been obtained in great detail, allowing us to draw detailed conclusions regarding the catalytic mechanism at the molecular level. Moreover, numerous alternative geranylgeranyl diphosphate cyclization products obtained by CotB2 mutagenesis have exciting applications for the sustainable production of high value bioactive substances.
Collapse
Affiliation(s)
- Ronja Driller
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
- present address: Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
- present address: Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus C, Denmark
| | - Daniel Garbe
- Werner Siemens Chair of Synthetic Biotechnology, Dept. of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens Chair of Synthetic Biotechnology, Dept. of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Monika Fuchs
- Werner Siemens Chair of Synthetic Biotechnology, Dept. of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Keren Raz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Dept. of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| |
Collapse
|
7
|
Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin. Appl Microbiol Biotechnol 2019; 103:1667-1680. [PMID: 30637495 DOI: 10.1007/s00253-018-09611-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
Collapse
Affiliation(s)
- Chee-Hoo Yip
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Orr Yarkoni
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - James Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| |
Collapse
|
8
|
Ou B, Garcia C, Wang Y, Zhang W, Zhu G. Techniques for chromosomal integration and expression optimization in Escherichia coli. Biotechnol Bioeng 2018; 115:2467-2478. [PMID: 29981268 DOI: 10.1002/bit.26790] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 12/31/2022]
Abstract
Due to the inherent expression stability and low metabolic burden to the host cell, the expression of heterologous proteins in the bacterial chromosome in a precise and efficient manner is highly desirable for metabolic engineering and live bacterial applications. However, obtaining suitable chromosome expression levels is particularly challenging. In this minireview, we briefly present the technologies available for the integration of heterologous genes into Escherichia coli chromosomes and strategies to optimize the expression levels of heterologous proteins.
Collapse
Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Carolina Garcia
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Weiping Zhang
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
9
|
Juhas M, Ajioka JW. T7 RNA polymerase-driven inducible cell lysis for DNA transfer from Escherichia coli to Bacillus subtilis. Microb Biotechnol 2017; 10:1797-1808. [PMID: 28815907 PMCID: PMC5658589 DOI: 10.1111/1751-7915.12843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/15/2017] [Accepted: 07/28/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. Reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis are therefore of the highest importance. Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, we integrated genetic circuits pT7L123, Repr‐ts‐1 and pLT7pol encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E. coli chromosome. In this system, T7 RNA polymerase regulated by the thermosensitive repressor drives the expression of the phage lysis genes. We showed that T7 RNA polymerase significantly increases efficiency of cell lysis and transfer of the plasmid and bacterial artificial chromosome‐encoded DNA from the lysed E. coli into B. subtilis. The T7 RNA polymerase‐driven inducible cell lysis system is suitable for the efficient cell lysis and transfer of the DNA engineered in E. coli to other naturally competent hosts, such as B. subtilis.
Collapse
Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, UK
| | - James W Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, UK
| |
Collapse
|
10
|
Juhas M, Wong C, Ajioka JW. Combining Genes from Multiple Phages for Improved Cell Lysis and DNA Transfer from Escherichia coli to Bacillus subtilis. PLoS One 2016; 11:e0165778. [PMID: 27798678 PMCID: PMC5087902 DOI: 10.1371/journal.pone.0165778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 01/02/2023] Open
Abstract
The ability to efficiently and reliably transfer genetic circuits between the key synthetic biology chassis, such as Escherichia coli and Bacillus subtilis, constitutes one of the major hurdles of the rational genome engineering. Using lambda Red recombineering we integrated the thermosensitive lambda repressor and the lysis genes of several bacteriophages into the E. coli chromosome. The lysis of the engineered autolytic cells is inducible by a simple temperature shift. We improved the lysis efficiency by introducing different combinations of lysis genes from bacteriophages lambda, ΦX174 and MS2 under the control of the thermosensitive lambda repressor into the E. coli chromosome. We tested the engineered autolytic cells by transferring plasmid and bacterial artificial chromosome (BAC)-borne genetic circuits from E. coli to B. subtilis. Our engineered system combines benefits of the two main synthetic biology chassis, E. coli and B. subtilis, and allows reliable and efficient transfer of DNA edited in E. coli into B. subtilis.
Collapse
Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MJ); (JWA)
| | - Christine Wong
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - James W. Ajioka
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MJ); (JWA)
| |
Collapse
|
11
|
Juhas M, Ajioka JW. Lambda Red recombinase-mediated integration of the high molecular weight DNA into the Escherichia coli chromosome. Microb Cell Fact 2016; 15:172. [PMID: 27716307 PMCID: PMC5050610 DOI: 10.1186/s12934-016-0571-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/28/2016] [Indexed: 01/15/2023] Open
Abstract
Background Escherichia coli K-12 is a frequently used host for a number of synthetic biology and biotechnology applications and chassis for the development of the minimal cell factories. Novel approaches for integrating high molecular weight DNA into the E. coli chromosome would therefore greatly facilitate engineering efforts in this bacterium. Results We developed a reliable and flexible lambda Red recombinase-based system, which utilizes overlapping DNA fragments for integration of the high molecular weight DNA into the E. coli chromosome. Our chromosomal integration strategy can be used to integrate high molecular weight DNA of variable length into any non-essential locus in the E. coli chromosome. Using this approach we integrated 15 kb DNA encoding sucrose catabolism and lactose metabolism and transport operons into the fliK locus of the flagellar region 3b in the E. coli K12 MG1655 chromosome. Furthermore, with this system we integrated 50 kb of Bacillus subtilis 168 DNA into two target sites in the E. coli K12 MG1655 chromosome. The chromosomal integrations into the fliK locus occurred with high efficiency, inhibited motility, and did not have a negative effect on the growth of E. coli. Conclusions In addition to the rational design of synthetic biology devices, our high molecular weight DNA chromosomal integration system will facilitate metabolic and genome-scale engineering of E. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0571-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| | - James W Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| |
Collapse
|
12
|
Deb SS, Reshamwala SMS, Lali AM. A series of template plasmids for Escherichia coli genome engineering. J Microbiol Methods 2016; 125:49-57. [PMID: 27071533 DOI: 10.1016/j.mimet.2016.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 12/16/2022]
Abstract
Metabolic engineering strategies often employ multi-copy episomal vectors to overexpress genes. However, chromosome-based overexpression is preferred as it avoids the use of selective pressure and reduces metabolic burden on the cell. We have constructed a series of template plasmids for λ Red-mediated Escherichia coli genome engineering. The template plasmids allow construction of genome integrating cassettes that can be used to integrate single copies of DNA sequences at predetermined sites or replace promoter regions. The constructed cassettes provide flexibility in terms of expression levels achieved and antibiotics used for selection, as well as allowing construction of marker-free strains. The modular design of the template plasmids allows replacement of genetic parts to construct new templates. Gene integration and promoter replacement using the template plasmids are illustrated.
Collapse
Affiliation(s)
- Shalini S Deb
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Shamlan M S Reshamwala
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India.
| | - Arvind M Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India; Department of Chemical Engineering, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| |
Collapse
|
13
|
Juhas M, Ajioka JW. Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome. J Microbiol Methods 2016; 125:1-7. [PMID: 27033694 DOI: 10.1016/j.mimet.2016.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/23/2016] [Accepted: 03/23/2016] [Indexed: 10/22/2022]
Abstract
Bacillus subtilis is a well-characterized model bacterium frequently used for a number of biotechnology and synthetic biology applications. Novel strategies combining the advantages of B. subtilis with the DNA assembly and editing tools of Escherichia coli are crucial for B. subtilis engineering efforts. We combined Gibson Assembly and λ red recombineering in E. coli with RecA-mediated homologous recombination in B. subtilis for bacterial artificial chromosome-mediated DNA integration into the well-characterized amyE target locus of the B. subtilis chromosome. The engineered integrative bacterial artificial chromosome iBAC(cav) can accept any DNA fragment for integration into B. subtilis chromosome and allows rapid selection of transformants by B. subtilis-specific antibiotic resistance and the yellow fluorescent protein (mVenus) expression. We used the developed iBAC(cav)-mediated system to integrate 10kb DNA fragment from E. coli K12 MG1655 into B. subtilis chromosome. iBAC(cav)-mediated chromosomal integration approach will facilitate rational design of synthetic biology applications in B. subtilis.
Collapse
Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, UK.
| | - James W Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, UK
| |
Collapse
|
14
|
Juhas M, Ajioka JW. High molecular weight DNA assembly in vivo for synthetic biology applications. Crit Rev Biotechnol 2016; 37:277-286. [PMID: 26863154 DOI: 10.3109/07388551.2016.1141394] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.
Collapse
Affiliation(s)
- Mario Juhas
- a Department of Pathology , University of Cambridge , Tennis Court Road , Cambridge , UK
| | - James W Ajioka
- a Department of Pathology , University of Cambridge , Tennis Court Road , Cambridge , UK
| |
Collapse
|