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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [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: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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2
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Bedoya-Pérez LP, Aguilar-Vera A, Sánchez-Pérez M, Utrilla J, Sohlenkamp C. Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation. Appl Microbiol Biotechnol 2024; 108:288. [PMID: 38587638 PMCID: PMC11001654 DOI: 10.1007/s00253-024-13130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Escherichia coli is a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, such as variations in pH or solvent concentrations. Bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in bacteria. We wondered if this stress resistance could be transferred to bacteria not encoding the capacity to form OLs in their genome, such as E. coli. In this study, we engineered different E. coli strains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operon olsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress- and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness in OL-producing strains. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and also at low pH. Overall, this study demonstrates the potential of engineering the E. coli membrane composition for constructing robust hosts with an increased abiotic stress resistance for biotechnology and synthetic biology applications. KEY POINTS: • Ornithine lipid production in E. coli increases biomass yield under phosphate limitation. • Engineered strains show an enhanced production phenotype under low pH stress. • Transcriptome analysis and CCCP experiments revealed reduced proton leakage.
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Affiliation(s)
- Leidy Patricia Bedoya-Pérez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - Alejandro Aguilar-Vera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - Mishael Sánchez-Pérez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - José Utrilla
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México.
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México.
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de la Cruz M, Kunert F, Taymaz-Nikerel H, Sigala JC, Gosset G, Büchs J, Lara AR. Increasing the Pentose Phosphate Pathway Flux to Improve Plasmid DNA Production in Engineered E. coli. Microorganisms 2024; 12:150. [PMID: 38257977 PMCID: PMC10820320 DOI: 10.3390/microorganisms12010150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The demand of plasmid DNA (pDNA) as a key element for gene therapy products, as well as mRNA and DNA vaccines, is increasing together with the need for more efficient production processes. An engineered E. coli strain lacking the phosphotransferase system and the pyruvate kinase A gene has been shown to produce more pDNA than its parental strain. With the aim of improving pDNA production in the engineered strain, several strategies to increase the flux to the pentose phosphate pathway (PPP) were evaluated. The simultaneous consumption of glucose and glycerol was a simple way to increase the growth rate, pDNA production rate, and supercoiled fraction (SCF). The overexpression of key genes from the PPP also improved pDNA production in glucose, but not in mixtures of glucose and glycerol. Particularly, the gene coding for the glucose 6-phosphate dehydrogenase (G6PDH) strongly improved the SCF, growth rate, and pDNA production rate. A linear relationship between the G6PDH activity and pDNA yield was found. A higher flux through the PPP was confirmed by flux balance analysis, which also estimates relevant differences in fluxes of the tricarboxylic acid cycle. These results are useful for developing further cell engineering strategies to increase pDNA production and quality.
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Affiliation(s)
- Mitzi de la Cruz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
| | - Flavio Kunert
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Istanbul, Turkey
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
| | - Guillermo Gosset
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Alvaro R. Lara
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus, Denmark
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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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Cordell WT, Avolio G, Takors R, Pfleger BF. Milligrams to kilograms: making microbes work at scale. Trends Biotechnol 2023; 41:1442-1457. [PMID: 37271589 DOI: 10.1016/j.tibtech.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
If biomanufacturing can become a sustainable route for producing chemicals, it will provide a critical step in reducing greenhouse gas emissions to fight climate change. However, efforts to industrialize microbial synthesis of chemicals have met with varied success, due, in part, to challenges in translating laboratory successes to industrial scale. With a particular focus on Escherichia coli, this review examines the lessons learned when studying microbial physiology and metabolism under conditions that simulate large-scale bioreactors and methods to minimize cellular waste through reduction of maintenance energy, optimizing the stress response and minimizing culture heterogeneity. With general strategies to overcome these challenges, biomanufacturing process scale-up could be de-risked and the time and cost of bringing promising syntheses to market could be reduced.
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Affiliation(s)
- William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gennaro Avolio
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Center Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Marquez-Zavala E, Utrilla J. Engineering resource allocation in artificially minimized cells: Is genome reduction the best strategy? Microb Biotechnol 2023; 16:990-999. [PMID: 36808834 PMCID: PMC10128133 DOI: 10.1111/1751-7915.14233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/26/2023] [Indexed: 02/20/2023] Open
Abstract
The elimination of the expression of cellular functions that are not needed in a certain well-defined artificial environment, such as those used in industrial production facilities, has been the goal of many cellular minimization projects. The generation of a minimal cell with reduced burden and less host-function interactions has been pursued as a tool to improve microbial production strains. In this work, we analysed two cellular complexity reduction strategies: genome and proteome reduction. With the aid of an absolute proteomics data set and a genome-scale model of metabolism and protein expression (ME-model), we quantitatively assessed the difference of reducing genome to the correspondence of reducing proteome. We compare the approaches in terms of energy consumption, defined in ATP equivalents. We aim to show what is the best strategy for improving resource allocation in minimized cells. Our results show that genome reduction by length is not proportional to reducing resource use. When we normalize calculated energy savings, we show that strains with the larger calculated proteome reduction show the largest resource use reduction. Furthermore, we propose that reducing highly expressed proteins should be the target as the translation of a gene uses most of the energy. The strategies proposed here should guide cell design when the aim of a project is to reduce the maximum amount or cellular resources.
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Affiliation(s)
- Elisa Marquez-Zavala
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.,Synthetic Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jose Utrilla
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Ventura C, Eusébio D, Gonçalves AM, Barroca-Ferreira J, Costa D, Cui Z, Passarinha LA, Sousa Â. Maximization of the Minicircle DNA Vaccine Production Expressing SARS-CoV-2 RBD. Biomedicines 2022; 10:biomedicines10050990. [PMID: 35625727 PMCID: PMC9139101 DOI: 10.3390/biomedicines10050990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleic acid vaccines have been proven to be a revolutionary technology to induce an efficient, safe and rapid response against pandemics, like the coronavirus disease (COVID-19). Minicircle DNA (mcDNA) is an innovative vector more stable than messenger RNA and more efficient in cell transfection and transgene expression than conventional plasmid DNA. This work describes the construction of a parental plasmid (PP) vector encoding the receptor-binding domain (RBD) of the S protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the use of the Design of Experiments (DoE) to optimize PP recombination into mcDNA vector in an orbital shaker. First, the results revealed that host cells should be grown at 42 °C and the Terrific Broth (TB) medium should be replaced by Luria Broth (LB) medium containing 0.01% L-arabinose for the induction step. The antibiotic concentration, the induction time, and the induction temperature were used as DoE inputs to maximize the % of recombined mcDNA. The quadratic model was statistically significant (p-value < 0.05) and presented a non-significant lack of fit (p-value > 0.05) with a suitable coefficient of determination. The optimal point was validated using 1 h of induction, at 30 °C, without the presence of antibiotics, obtaining 93.87% of recombined mcDNA. Based on these conditions, the production of mcDNA was then maximized in a mini-bioreactor platform. The most favorable condition obtained in the bioreactor was obtained by applying 60% pO2 in the fermentation step during 5 h and 30% pO2 in the induction step, with 0.01% L-arabinose throughout 5 h. The yield of mcDNA-RBD was increased to a concentration of 1.15 g/L, when compared to the orbital shaker studies (16.48 mg/L). These data revealed that the bioreactor application strongly incremented the host biomass yield and simultaneously improved the recombination levels of PP into mcDNA. Altogether, these results contributed to improving mcDNA-RBD biosynthesis to make the scale-up of mcDNA manufacture simpler, cost-effective, and attractive for the biotechnology industry.
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Affiliation(s)
- Cathy Ventura
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
| | - Dalinda Eusébio
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
| | - Ana M. Gonçalves
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jorge Barroca-Ferreira
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Diana Costa
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Luís A. Passarinha
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia-UBIMedical, Universidade da Beira Interior, 6200-284 Covilha, Portugal
- Correspondence: (L.A.P.); (Â.S.); Tel.: +35-12-7532-9069 (L.A.P.); +35-12-7532-9052 (Â.S.)
| | - Ângela Sousa
- CICS-UBI-Health Science Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilha, Portugal; (C.V.); (D.E.); (A.M.G.); (J.B.-F.); (D.C.)
- Correspondence: (L.A.P.); (Â.S.); Tel.: +35-12-7532-9069 (L.A.P.); +35-12-7532-9052 (Â.S.)
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Taymaz-Nikerel H, Lara AR. Vitreoscilla Haemoglobin: A Tool to Reduce Overflow Metabolism. Microorganisms 2021; 10:microorganisms10010043. [PMID: 35056491 PMCID: PMC8779101 DOI: 10.3390/microorganisms10010043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022] Open
Abstract
Overflow metabolism is a phenomenon extended in nature, ranging from microbial to cancer cells. Accumulation of overflow metabolites pose a challenge for large-scale bioprocesses. Yet, the causes of overflow metabolism are not fully clarified. In this work, the underlying mechanisms, reasons and consequences of overflow metabolism in different organisms have been summarized. The reported effect of aerobic expression of Vitreoscilla haemoglobin (VHb) in different organisms are revised. The use of VHb to reduce overflow metabolism is proposed and studied through flux balance analysis in E. coli at a fixed maximum substrate and oxygen uptake rates. Simulations showed that the presence of VHb increases the growth rate, while decreasing acetate production, in line with the experimental measurements. Therefore, aerobic VHb expression is considered a potential tool to reduce overflow metabolism in cells.
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Affiliation(s)
- Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, İstanbul 34060, Turkey;
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
- Correspondence:
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