1
|
Allen JR, Torres-Acosta MA, Mohan N, Lye GJ, Ward JM. Segregationally stabilised plasmids improve production of commodity chemicals in glucose-limited continuous fermentation. Microb Cell Fact 2022; 21:229. [PMID: 36329510 PMCID: PMC9632041 DOI: 10.1186/s12934-022-01958-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022] Open
Abstract
Background The production of chemicals via bio-based routes is held back by limited easy-to-use stabilisation systems. A wide range of plasmid stabilisation mechanisms can be found in the literature, however, how these mechanisms effect genetic stability and how host strains still revert to non-productive variants is poorly understood at the single-cell level. This phenomenon can generate difficulties in production-scale bioreactors as different populations of productive and non-productive cells can arise. To understand how to prevent non-productive strains from arising, it is vital to understand strain behaviour at a single-cell level. The persistence of genes located on plasmid vectors is dependent on numerous factors but can be broadly separated into structural stability and segregational stability. While structural stability refers to the capability of a cell to resist genetic mutations that bring about a loss of gene function in a production pathway, segregational stability refers to the capability of a cell to correctly distribute plasmids into daughter cells to maintain copy number. A lack of segregational stability can rapidly generate plasmid-free variants during replication, which compromises productivity. Results Citramalate synthase expression was linked in an operon to the expression of a fluorescent reporter to enable rapid screening of the retention of a model chemical synthesis pathway in a continuous fermentation of E. coli. Cells without additional plasmid stabilisation started to lose productivity immediately after entering the continuous phase. Inclusion of a multimer resolution site, cer, enabled a steady-state production period of 58 h before a drop in productivity was detected. Single-cell fluorescence measurements showed that plasmid-free variants arose rapidly without cer stabilisation and that this was likely due to unequal distribution of plasmid into daughter cells during cell division. The addition of cer increased total chemical yield by more than 50%. Conclusions This study shows the potential remains high for plasmids to be used as pathway vectors in industrial bio-based chemicals production, providing they are correctly stabilised. We demonstrate the need for accessible bacterial ‘toolkits’ to enable rapid production of known, stabilised bacterial production strains to enable continuous fermentation at scale for the chemicals industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01958-3.
Collapse
|
2
|
Wang H, Jiang K, Zhu Z, Jiang W, Yang Z, Zhu S, Qiu J, Yan X, He J, He Q, Hong Q. Optimization of fed-batch fermentation and direct spray drying in the preparation of microbial inoculant of acetochlor-degrading strain Sphingomonas sp. DC-6. 3 Biotech 2018; 8:294. [PMID: 29963354 DOI: 10.1007/s13205-018-1324-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022] Open
Abstract
Microbial inoculant preparation is a prerequisite for its application in large-scale bioremediation. In the present study, Sphingomonas sp. DC-6, an efficient acetochlor-degrading strain, was used to investigate the process of preparing the inoculant. Optimization of submerged fermentation (SmF) by response surface methodology (RSM) resulted in a first 22% increase in biomass of liquid inoculant. Then, a biomass increase of 2.18 times with 14.58% shortened incubation period was further obtained in optimized medium using a 7.5-l bioreactor. However, less than 0.4% viable cells in liquid inoculant survived after 180-days storage. Thus, optimized spray drying conditions were subsequently employed for the production of high viability powder (2.11 × 1012 cfu g- 1 powder) without additive and its survival ratio (SR) after 180-days storage was still maintained at 90.5%. Both the 180-days stored powder and the original powder showed the same degradation performance, being able to completely degrade 200 mg l- 1 acetochlor within 48 h. This study demonstrated that strain DC-6 was suitable for industrial production of bacteria powder and provided a potential approach for the preparation of pesticide-degrading microbial inoculant.
Collapse
Affiliation(s)
- Hui Wang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Kun Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Ziwei Zhu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Wankui Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Zhangong Yang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Shijun Zhu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Jiguo Qiu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Qin He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Qing Hong
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| |
Collapse
|
3
|
Hassan S, Keshavarz-Moore E, Ward J. A cell engineering strategy to enhance supercoiled plasmid DNA production for gene therapy. Biotechnol Bioeng 2016; 113:2064-71. [PMID: 26928284 PMCID: PMC4982056 DOI: 10.1002/bit.25971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/23/2015] [Accepted: 02/21/2016] [Indexed: 11/08/2022]
Abstract
With the recent revival of the promise of plasmid DNA vectors in gene therapy, a novel synthetic biology approach was used to enhance the quantity, (yield), and quality of the plasmid DNA. Quality was measured by percentage supercoiling and supercoiling density, as well as improving segregational stability in fermentation. We examined the hypothesis that adding a Strong Gyrase binding Site (SGS) would increase DNA gyrase-mediated plasmid supercoiling. SGS from three different replicons, (the Mu bacteriophage and two plasmids, pSC101 and pBR322) were inserted into the plasmid, pUC57. Different sizes of these variants were transformed into E. coli DH5α, and their supercoiling properties and segregational stability measured. A 36% increase in supercoiling density was found in pUC57-SGS, but only when SGS was derived from the Mu phage and was the larger sized version of this fragment. These results were also confirmed at fermentation scale. Total percentage supercoiled monomer was maintained to 85-90%. A twofold increase in plasmid yield was also observed for pUC57-SGS in comparison to pUC57. pUC57-SGS displayed greater segregational stability than pUC57-cer and pUC57, demonstrating a further potential advantage of the SGS site. These findings should augment the potential of plasmid DNA vectors in plasmid DNA manufacture. Biotechnol. Bioeng. 2016;113: 2064-2071. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sally Hassan
- The Advanced Center for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
| | - Eli Keshavarz-Moore
- The Advanced Center for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom.
| | - John Ward
- The Advanced Center for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, United Kingdom
| |
Collapse
|
4
|
Hailes HC, Rother D, Müller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M. Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J 2013; 280:6374-94. [DOI: 10.1111/febs.12496] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Helen C. Hailes
- Department of Chemistry; Christopher Ingold Laboratories; University College London; UK
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Germany
| | | | - John M. Ward
- Department of Biochemical Engineering; University College London; UK
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| |
Collapse
|
5
|
Silva F, Queiroz JA, Domingues FC. Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Biotechnol Adv 2012; 30:691-708. [DOI: 10.1016/j.biotechadv.2011.12.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/01/2011] [Accepted: 12/29/2011] [Indexed: 01/26/2023]
|
6
|
|
7
|
Thomas KC, Woodley JM. Process Effects of By-Product Carbon Dioxide Production from Transketolase-Catalysed Condensations. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429909015220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
8
|
Aucamp JP, Martinez-Torres RJ, Hibbert EG, Dalby PA. A microplate-based evaluation of complex denaturation pathways: Structural stability ofEscherichia coli transketolase. Biotechnol Bioeng 2008; 99:1303-10. [DOI: 10.1002/bit.21705] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
9
|
A novel assay system for the measurement of transketolase activity using xylulokinase from Saccharomyces cerevisiae. Biotechnol Lett 2007; 30:899-904. [DOI: 10.1007/s10529-007-9616-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/14/2007] [Accepted: 11/16/2007] [Indexed: 11/25/2022]
|
10
|
Costelloe SJ, Ward JM, Dalby PA. Evolutionary analysis of the TPP-dependent enzyme family. J Mol Evol 2007; 66:36-49. [PMID: 18043855 DOI: 10.1007/s00239-007-9056-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 10/24/2007] [Accepted: 11/07/2007] [Indexed: 11/26/2022]
Abstract
The evolutionary relationships of the thiamine pyrophosphate (TPP)-dependent family of enzymes was investigated by generation of a neighbor joining phylogenetic tree using sequences from the conserved pyrophosphate (PP) and pyrimidine (Pyr) binding domains of 17 TPP-dependent enzymes. This represents the most comprehensive analysis of TPP-dependent enzyme evolution to date. The phylogeny was shown to be robust by comparison with maximum likelihood trees generated for each individual enzyme and also broadly confirms the evolutionary history proposed recently from structural comparisons alone (Duggleby 2006). The phylogeny is most parsimonious with the TPP enzymes having arisen from a homotetramer which subsequently diverged into an alpha(2)beta(2) heterotetramer. The relationship between the PP- and Pyr-domains and the recruitment of additional protein domains was examined using the transketolase C-terminal (TKC)-domain as an example. This domain has been recruited by several members of the family and yet forms no part of the active site and has unknown function. Removal of the TKC-domain was found to increase activity toward beta-hydroxypyruvate and glycolaldehyde. Further truncations of the Pyr-domain yielded several variants with retained activity. This suggests that the influence of TKC-domain recruitment on the evolution of the mechanism and specificity of transketolase (TK) has been minor, and that the smallest functioning unit of TK comprises the PP- and Pyr-domains, whose evolutionary histories extend to all TPP-dependent enzymes.
Collapse
Affiliation(s)
- Seán J Costelloe
- Department of Biochemical Engineering, University College London, Torrington Place, London, UK
| | | | | |
Collapse
|
11
|
|
12
|
Hibbert EG, Senussi T, Costelloe SJ, Lei W, Smith MEB, Ward JM, Hailes HC, Dalby PA. Directed evolution of transketolase activity on non-phosphorylated substrates. J Biotechnol 2007; 131:425-32. [PMID: 17825449 DOI: 10.1016/j.jbiotec.2007.07.949] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 07/09/2007] [Accepted: 07/20/2007] [Indexed: 10/23/2022]
Abstract
We have used active-site targeted directed evolution by saturation mutagenesis to improve the activity of E. coli transketolase towards non-phosphorylated substrates. Residues were selected for each set based on either structural proximity to substrate, or on phylogenetic variation. Each library was screened towards the reaction between hydroxypyruvate (HPA) and glycolaldehyde (GA) to form L-erythrulose, and the location of improved mutants related to the natural sequence entropy at each residue. A number of mutants from the phylogenetically defined library were found to outperform the wild-type with up to 3-fold specific activity under biocatalytically relevant conditions, though interestingly with substituted residues that differed from those found in nature. Conserved residues which interact with the phosphate group in natural substrates also yielded mutants with almost 5-fold improved specific activity on the non-phosphorylated substrates. These results suggest that phylogenetically variant active-site residues are useful for modulating activity on natural or structurally-homologous substrates, and that conserved residues which no longer interact with modified target substrates are useful sites to apply saturation mutagenesis for improvement of activity.
Collapse
Affiliation(s)
- Edward G Hibbert
- Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London, UK
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Miller OJ, Hibbert EG, Ingram CU, Lye GJ, Dalby PA. Optimisation and evaluation of a generic microplate-based HPLC screen for transketolase activity. Biotechnol Lett 2007; 29:1759-70. [PMID: 17598073 DOI: 10.1007/s10529-007-9435-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Abstract
A microplate-based HPLC assay for transketolase is described for rapidly determining substrate and product concentration suitable for optimisation of biocatalytic process conditions and screening directed evolution libraries. Transketolase catalyses the enantioselective carbon-carbon bond formation of chiral keto-diol products. The assay was used to determine dissociation constants for the two cofactors required by transketolase with 5-11% error. The preparation of samples by microplate-based fermentation, cell lysis, addition of cofactor, addition of substrates was also evaluated and optimised for increased transketolase activity. The whole process enables 3-fold improved enzyme variants to be identified from a single measurement.
Collapse
Affiliation(s)
- Oliver J Miller
- Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
| | | | | | | | | |
Collapse
|
14
|
Chen BH, Baganz F, Woodley JM. Modelling and optimisation of a transketolase-mediated carbon–carbon bond formation reaction. Chem Eng Sci 2007. [DOI: 10.1016/j.ces.2007.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
LILLY MD, CHAUHAN R, FRENCH C, GYAMERAH M, HOBBS GR, HUMPHREY A, ISUPOV M, LITTLECHILD JA, MITRA RK, MORRIS KG, RUPPRECHT M, TURNER NJ, WARD JM, WILLETTS AJ, WOODLEY JM. Carbon-Carbon Bond Synthesis: The Impact of rDNA Technology on the Production and Use of E. coli Transketolase. Ann N Y Acad Sci 2006. [DOI: 10.1111/j.1749-6632.1996.tb40589.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Smith MEB, Kaulmann U, Ward JM, Hailes HC. A colorimetric assay for screening transketolase activity. Bioorg Med Chem 2006; 14:7062-5. [PMID: 16784864 DOI: 10.1016/j.bmc.2006.06.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 06/06/2006] [Indexed: 11/20/2022]
Abstract
A tetrazolium red-based colorimetric assay has been devised to screen for transketolase activity with a range of aldehyde acceptors. The colorimetric TK assay is able to detect >8% bioconversion using non-alpha-hydroxylated aldehydes as acceptor substrates and is significantly faster and more convenient to use than chromatographic procedures.
Collapse
Affiliation(s)
- Mark E B Smith
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H OAJ, UK
| | | | | | | |
Collapse
|
17
|
Abstract
The enzyme transketolase has been employed as a catalyst for asymmetric carbon-carbon bond formation in the synthesis of biologically important molecules. A number of important parameters have been addressed including substrate specificity, over-expression of the protein in suitable host systems, scale-up of the reaction and use of transketolase in multi-enzyme experiments. X-ray structural studies have been used to probe the origin of the asymmetry of the carbon-carbon bond-forming process.
Collapse
Affiliation(s)
- N J Turner
- Department of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK.
| |
Collapse
|
18
|
|
19
|
|
20
|
French C, Ward JM. Production and modification of E. coli transketolase for large-scale biocatalysis. Ann N Y Acad Sci 1996; 799:11-8. [PMID: 8958067 DOI: 10.1111/j.1749-6632.1996.tb33171.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C French
- Department of Biochemistry and Molecular Biology, University College London, United Kingdom
| | | |
Collapse
|
21
|
Chauhan RP, Woodley JM, Powell LW. In situ product removal from E. coli transketolase-catalyzed biotransformations. Ann N Y Acad Sci 1996; 799:545-54. [PMID: 8958111 DOI: 10.1111/j.1749-6632.1996.tb33254.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- R P Chauhan
- Department of Chemical and Biochemical Engineering, University College, London, United Kingdom
| | | | | |
Collapse
|
22
|
|
23
|
|
24
|
Morris K, Smith ME, Turner NJ, Lilly MD, Mitra RK, Woodley JM. Transketolase from Escherichia coli: A practical procedure for using the biocatalyst for asymmetric carbon-carbon bond synthesis. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0957-4166(96)00266-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Hobbs GR, Mitra RK, Chauhan RP, Woodley JM, Lilly MD. Enzyme-catalysed carbon-carbon bond formation: large-scale production of Escherichia coli transketolase. J Biotechnol 1996; 45:173-9. [PMID: 9147449 DOI: 10.1016/0168-1656(95)00165-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Escherichia coli strain JM107/pQR700 possesses the vector pBGS18, a high copy number plasmid carrying kanamycin resistance, into which a 4.4 kb fragment containing the transketolase gene had been cloned. The bacterium was grown at 20 and 1000 1 scale for the production of transketolase. The specific growth rate was maintained at 0.15 h-1 until the bacterial concentration reached 20 g dry wt per litre at which point the culture was harvested. The clarified cell extract obtained after disruption of the bacteria in a high-pressure homogeniser contained about 230 U ml-1 of the enzyme, which represented about 40% of the total protein released. No further purification was done at large scale as the clarified cell extract could be used satisfactorily for biotransformations.
Collapse
Affiliation(s)
- G R Hobbs
- The Advanced Centre for Biochemical Engineering, Department of Chemical and Biochemical Engineering, University College London, UK
| | | | | | | | | |
Collapse
|
26
|
|