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Gotsmy M, Strobl F, Weiß F, Gruber P, Kraus B, Mairhofer J, Zanghellini J. Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes. Microb Cell Fact 2023; 22:242. [PMID: 38017439 PMCID: PMC10685491 DOI: 10.1186/s12934-023-02248-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/11/2023] [Indexed: 11/30/2023] Open
Abstract
Plasmid DNA (pDNA) is a key biotechnological product whose importance became apparent in the last years due to its role as a raw material in the messenger ribonucleic acid (mRNA) vaccine manufacturing process. In pharmaceutical production processes, cells need to grow in the defined medium in order to guarantee the highest standards of quality and repeatability. However, often these requirements result in low product titer, productivity, and yield. In this study, we used constraint-based metabolic modeling to optimize the average volumetric productivity of pDNA production in a fed-batch process. We identified a set of 13 nutrients in the growth medium that are essential for cell growth but not for pDNA replication. When these nutrients are depleted in the medium, cell growth is stalled and pDNA production is increased, raising the specific and volumetric yield and productivity. To exploit this effect we designed a three-stage process (1. batch, 2. fed-batch with cell growth, 3. fed-batch without cell growth). The transition between stage 2 and 3 is induced by sulfate starvation. Its onset can be easily controlled via the initial concentration of sulfate in the medium. We validated the decoupling behavior of sulfate and assessed pDNA quality attributes (supercoiled pDNA content) in E. coli with lab-scale bioreactor cultivations. The results showed an increase in supercoiled pDNA to biomass yield by 33% and an increase of supercoiled pDNA volumetric productivity by 13 % upon limitation of sulfate. In conclusion, even for routinely manufactured biotechnological products such as pDNA, simple changes in the growth medium can significantly improve the yield and quality.
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Affiliation(s)
- Mathias Gotsmy
- Department of Analytical Chemistry, University of Vienna, Vienna, 1090, Austria
- Doctorate School of Chemistry, University of Vienna, Vienna, 1090, Austria
| | | | | | - Petra Gruber
- Baxalta Innovations GmbH, A Part of Takeda Companies, Orth an der Donau, 2304, Austria
| | - Barbara Kraus
- Baxalta Innovations GmbH, A Part of Takeda Companies, Orth an der Donau, 2304, Austria
| | | | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, Vienna, 1090, Austria.
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2
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Islas F, Sabido A, Sigala J, Lara AR. Design of microaerobically inducible miniR1 plasmids. MLIFE 2023; 2:101-104. [PMID: 38818336 PMCID: PMC10989972 DOI: 10.1002/mlf2.12058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 06/01/2024]
Abstract
Plasmid DNA manufacture is an essential step to produce gene therapy agents and next-generation vaccines. However, little attention has been paid toward developing alternative replicons that can be coupled with large-scale production conditions. Our results demonstrate that the miniR1 replicon can be efficiently induced by oxygen limitation when a copy of the regulatory protein RepA under control of a microaerobic promoter is used. The results are potentially attractive for industrial applications.
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Affiliation(s)
- Fabiola Islas
- Departamento de Procesos y TecnologíaUniversidad Autónoma MetropolitanaCiudad de MexicoMéxico
| | - Andrea Sabido
- Departamento de Procesos y TecnologíaUniversidad Autónoma MetropolitanaCiudad de MexicoMéxico
| | - Juan‐Carlos Sigala
- Departamento de Procesos y TecnologíaUniversidad Autónoma MetropolitanaCiudad de MexicoMéxico
| | - Alvaro R. Lara
- Departamento de Procesos y TecnologíaUniversidad Autónoma MetropolitanaCiudad de MexicoMéxico
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Grijalva-Hernández F, Vega-Estrada J, Escobar-Rosales M, Ortega-López J, Aguilar-López R, Lara AR, Montes-Horcasitas MDC. High Kanamycin Concentration as Another Stress Factor Additional to Temperature to Increase pDNA Production in E. coli DH5α Batch and Fed-Batch Cultures. Microorganisms 2019; 7:E711. [PMID: 31861108 PMCID: PMC6955755 DOI: 10.3390/microorganisms7120711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/02/2019] [Accepted: 12/13/2019] [Indexed: 02/03/2023] Open
Abstract
Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We evaluated the effect of kanamycin concentration and temperature on pDNA production, overflow metabolism (organic acids) and metabolic burden (neomycin phosphotransferase II) in batch and fed-batch cultures of Escherichia coli DH5α-pVAX1-NH36. Results indicated that high kanamycin concentration increases the volumetric productivity, volumetric and specific yields of pDNA when batch cultures were carried out at 42 °C, and overflow metabolism reduced but metabolic burden increased. Micrographs taken with a scanning electron microscope (SEM) were analyzed, showing important morphological changes. The high kanamycin concentration (300 mg/L) was evaluated in high cell density culture (50 gDCW/L), which was reached using a fed-batch culture with temperature increase by controlling heating and growth rates. The pDNA volumetric yield and productivity were 759 mg/L and 31.19 mg/L/h, respectively, two-fold greater than the control with a kanamycin concentration of 50 mg/L. A stress-based process simultaneously caused by temperature and high kanamycin concentration can be successfully applied to increase pDNA production.
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Affiliation(s)
- Fernando Grijalva-Hernández
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
| | - Jesús Vega-Estrada
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
| | - Montserrat Escobar-Rosales
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
| | - Jaime Ortega-López
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
| | - Ricardo Aguilar-López
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa. Av. Vasco de Quiroga 4871, Santa Fe, México City 05348, Mexico;
| | - Ma. del Carmen Montes-Horcasitas
- Departamento de Biotecnología y Bioingeniería. Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN) Av. Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, México City 07360, Mexico; (F.G.-H.); (J.V.-E.); (M.E.-R.); (J.O.-L.); (R.A.-L.)
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Jaén KE, Velázquez D, Sigala JC, Lara AR. Design of a microaerobically inducible replicon for high-yield plasmid DNA production. Biotechnol Bioeng 2019; 116:2514-2525. [PMID: 31232477 DOI: 10.1002/bit.27091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/11/2023]
Abstract
A pUC-derived replicon inducible by oxygen limitation was designed and tested in fed-batch cultures of Escherichia coli. It included the addition of a second inducible copy of rnaII, the positive replication control element. The rnaII gene was expressed from Ptrc and cloned into pUC18 to test the hypothesis that the ratio of the positive control molecule RNAII to the negative control element, RNAI, was the determinant of plasmid copy number per chromosome (PCN). The construct was evaluated in several E. coli strains. Evaluations of the RNAII/RNAI ratio, PCN and plasmid yield normalized to biomass (YpDNA/X ) were performed and the initial hypothesis was probed. Furthermore, in high cell-density cultures in shake flasks, an outstanding amount of 126 mg/L of plasmid was produced. The microaerobically inducible plasmid was obtained by cloning the rnaII gene under the control of the oxygen-responsive Vitreoscilla stercoraria hemoglobin promoter. For this plasmid, but not for pUC18, the RNAII/RNAI ratio, PCN and YpDNA/X efficiently increased after the shift to the microaerobic regime in fed-batch cultures in a 1 L bioreactor. The YpDNA/X of the inducible plasmid reached 12 mg/g at the end of the fed-batch but the original pUC18 only reached ca. 6 mg/g. The proposed plasmid is a valuable alternative for the operation and scale-up of plasmid DNA production processes in which mass transfer limitations will not represent an issue.
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Affiliation(s)
- Karim E Jaén
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Daniela Velázquez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
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Design of a synthetic miniR1 plasmid and its production by engineered Escherichia coli. Bioprocess Biosyst Eng 2019; 42:1391-1397. [PMID: 31006041 DOI: 10.1007/s00449-019-02129-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
A synthetic plasmid consisting of the minimal elements for replication control of the R1 replicon and kanamycin resistance marker, which was named pminiR1, was developed. pminiR1 production was tested at 30 °C under aerobic and microaerobic conditions in Escherichia coli W3110 recA- (W1). The plasmid DNA yields from biomass (YpDNA/X) were only 0.06 ± 0.02 and 0.22 ± 0.11 mg/g under aerobic and microaerobic conditions, respectively. As an option to increase YpDNA/X values, pminiR1 was introduced in an engineered E. coli strain expressing the Vitreoscilla hemoglobin inserted in chromosome (W12). The YpDNA/X values using strain W12 increased to 0.85 ± 0.05 and 1.53 ± 0.14 mg/g under aerobic and microaerobic conditions, respectively. pminiR1 production in both strains was compared with that of pUC57Kan at 37 °C under aerobic and microaerobic conditions. The YpDNA/X values for pminiR1 using strain W12 were 6.25 ± 0.16 and 9.27 ± 0.95 mg/g under aerobic and microaerobic conditions, respectively. Such yields were similar to those obtained for plasmid pUC57Kan using strain W12 (6.9 ± 0.64 and 10.85 ± 1.06 mg/g for aerobic and microaerobic cultures, respectively). Therefore, the synthetic minimal plasmid based on the R1 replicon is a valuable alternative to pUC plasmids for biotechnological applications.
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Long J, Zhao X, Liang F, Liu N, Sun Y, Xi Y. Optimization of fermentation conditions for an Escherichia coli strain engineered using the response surface method to produce a novel therapeutic DNA vaccine for rheumatoid arthritis. J Biol Eng 2018; 12:22. [PMID: 30337953 PMCID: PMC6180442 DOI: 10.1186/s13036-018-0110-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/06/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Fermentation condition optimization and nutrients screening are of equal importance for efficient production of plasmid DNA vaccines. This directly affects the downstream purification and final quality and yield of plasmid DNA vaccines. The present study aimed to optimize the fermentation conditions for high-throughput production of therapeutic DNA vaccine pcDNA-CCOL2A1 by engineered Escherichia coli DH5α, using the response surface method (RSM). RESULTS We hypothesized that optimized fermentation conditions significantly increase the yield of pcDNA-CCOL2A1 therapeutic DNA vaccine, a novel DNA vaccine for treating rheumatoid arthritis (RA). Single-factor analysis was performed to evaluate the optimal basal culture medium from LB, 2 × YT, TB, M9 (Glycerol) and M9 (Glucose), respectively. Thereafter, the Plackett-Burman design (PBD) was used to ascertain the three most significant factors affecting the vaccine yields, followed by the paths of steepest ascent to move to the nearest region of maximum response. Initial screening through the PBD revealed that the most key factors were peptone, mannitol, and inoculum concentration. Subsequent use of RSM was further optimized for the production of therapeutic DNA vaccine pcDNA-CCOL2A1 through Box-Behnken design (BBD). The final optimized fermentation conditions were as follows: peptone, 25.86 g/L; mannitol, 8.08 g/L; inoculum concentration, OD = 0.36. Using this statistical experimental design, the yield of therapeutic DNA vaccine pcDNA-CCOL2A1 markedly increased from 223.37 mg/L to339.32 mg/L under optimal conditions, and a 51.9% increase was observed compared with the original medium. CONCLUSIONS The present results provide a basis for further production of high-quality and high-yield therapeutic DNA vaccine pcDNA-CCOL2A1 in pilot-scale and even industrial-scale.
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Affiliation(s)
- Juan Long
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
| | - Xiao Zhao
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
| | - Fei Liang
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
| | - Nan Liu
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
| | - Yuying Sun
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
| | - Yongzhi Xi
- Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People’s Republic of China
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Developing strategies to increase plasmid DNA production in Escherichia coli DH5α using batch culture. J Biotechnol 2016; 233:66-73. [DOI: 10.1016/j.jbiotec.2016.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 01/25/2023]
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Galindo J, Barrón BL, Lara AR. Improved production of large plasmid DNA by enzyme-controlled glucose release. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1218-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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10
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Enhanced plasmid DNA production by enzyme-controlled glucose release and an engineered Escherichia coli. Biotechnol Lett 2015; 38:651-7. [DOI: 10.1007/s10529-015-2017-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/07/2015] [Indexed: 12/17/2022]
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Cortés JT, Flores N, Bolívar F, Lara AR, Ramírez OT. Physiological effects of pH gradients onEscherichia coliduring plasmid DNA production. Biotechnol Bioeng 2015; 113:598-611. [DOI: 10.1002/bit.25817] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/02/2015] [Accepted: 08/18/2015] [Indexed: 12/29/2022]
Affiliation(s)
- José T. Cortés
- Departamento de Medicina Molecular y Bioprocesos; Instituto de Biotecnología; Universidad Nacional Autónoma de México; México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biotecnología; Instituto de Biotecnología; Universidad Nacional Autónoma de México; Av. Universidad 2001, Col. Chamilpa CP 62210 Cuernavaca Morelos México
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biotecnología; Instituto de Biotecnología; Universidad Nacional Autónoma de México; Av. Universidad 2001, Col. Chamilpa CP 62210 Cuernavaca Morelos México
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología; Universidad Autónoma Metropolitana-Cuajimalpa; Av. Vasco de Quiroga 4871, Col. Santa Fe, Del. Cuajimalpa, México, D.F. CP 05348 México
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos; Instituto de Biotecnología; Universidad Nacional Autónoma de México; México
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Pablos TE, Sigala JC, Le Borgne S, Lara AR. Aerobic expression ofVitreoscillahemoglobin efficiently reduces overflow metabolism inEscherichia coli. Biotechnol J 2014; 9:791-9. [DOI: 10.1002/biot.201300388] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/25/2014] [Accepted: 02/17/2014] [Indexed: 12/17/2022]
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Abstract
Recent developments in DNA vaccine research provide a new momentum for this rather young and potentially disruptive technology. Gene-based vaccines are capable of eliciting protective immunity in humans to persistent intracellular pathogens, such as HIV, malaria, and tuberculosis, for which the conventional vaccine technologies have failed so far. The recent identification and characterization of genes coding for tumor antigens has stimulated the development of DNA-based antigen-specific cancer vaccines. Although most academic researchers consider the production of reasonable amounts of plasmid DNA (pDNA) for immunological studies relatively easy to solve, problems often arise during this first phase of production. In this chapter we review the current state of the art of pDNA production at small (shake flasks) and mid-scales (lab-scale bioreactor fermentations) and address new trends in vector design and strain engineering. We will guide the reader through the different stages of process design starting from choosing the most appropriate plasmid backbone, choosing the right Escherichia coli (E. coli) strain for production, and cultivation media and scale-up issues. In addition, we will address some points concerning the safety and potency of the produced plasmids, with special focus on producing antibiotic resistance-free plasmids. The main goal of this chapter is to make immunologists aware of the fact that production of the pDNA vaccine has to be performed with as much as attention and care as the rest of their research.
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