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Guessous G, Blake L, Bui A, Woo Y, Manzanarez G. Disentangling the Web: An Interdisciplinary Review on the Potential and Feasibility of Spider Silk Bioproduction. ACS Biomater Sci Eng 2024; 10:5412-5438. [PMID: 39136701 PMCID: PMC11388149 DOI: 10.1021/acsbiomaterials.4c00145] [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] [Indexed: 09/10/2024]
Abstract
The remarkable material properties of spider silk, such as its high toughness and tensile strength combined with its low density, make it a highly sought-after material with myriad applications. In addition, the biological nature of spider silk makes it a promising, potentially sustainable alternative to many toxic or petrochemical-derived materials. Therefore, interest in the heterologous production of spider silk proteins has greatly increased over the past few decades, making recombinant spider silk an important frontier in biomanufacturing. This has resulted in a diversity of potential host organisms, a large space for sequence design, and a variety of downstream processing techniques and product applications for spider silk production. Here, we highlight advances in each of these technical aspects as well as white spaces therein, still ripe for further investigation and discovery. Additionally, industry landscaping, patent analyses, and interviews with Key Opinion Leaders help define both the research and industry landscapes. In particular, we found that though textiles dominated the early products proposed by companies, the versatile nature of spider silk has opened up possibilities in other industries, such as high-performance materials in automotive applications or biomedical therapies. While continuing enthusiasm has imbued scientists and investors alike, many technical and business considerations still remain unsolved before spider silk can be democratized as a high-performance product. We provide insights and strategies for overcoming these initial hurdles, and we highlight the importance of collaboration between academia, industry, and policy makers. Linking technical considerations to business and market entry strategies highlights the importance of a holistic approach for the effective scale-up and commercial viability of spider silk bioproduction.
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Affiliation(s)
- Ghita Guessous
- Department of Physics, University of California at San Diego, La Jolla, California 92092, United States
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
| | - Lauren Blake
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
- Tufts University Center for Cellular Agriculture (TUCCA), Tufts University, Medford, Massachusetts 02155, United States
| | - Anthony Bui
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850, United States
| | - Yelim Woo
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Questrom School of Business, Boston University, Boston, Massachusetts 02215, United States
| | - Gabriel Manzanarez
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92092, United States
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Trindade Mazala T, Costa Viana M, Carneiro G, Lee Nelson D, de Freitas-Marques MB, De Martinis BS, Florêncio J, Mazzé FM, da Silva SGD, Barbosa SL. Purification and use of crude green glycerol from the transesterification of triglycerides in the formulation of an alcohol gel hand sanitizer. Sci Rep 2024; 14:5510. [PMID: 38448502 PMCID: PMC10917745 DOI: 10.1038/s41598-023-49422-5] [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: 11/07/2023] [Accepted: 12/07/2023] [Indexed: 03/08/2024] Open
Abstract
The aim of this study was to produce an alcohol gel hand sanitizer containing green glycerol. Crude glycerol was purified using chemical and physical treatments. The sanitizer was prepared using 71.100 g of 99.3° GL ethanol, 28.0 g H2O, 0.5 g of Carboxypolymethylene [Carbopol 940® or Carbomer], 5 drops of triethanolamine (pH 5-7), and glycerol (1.5% w/w). The thermal behavior of the ethanol, carbopol, triethanolamine, glycerol, and alcohol gels were evaluated using Thermogravimetry and Differential Thermal Analysis. The apparent viscosity was obtained using a rotary viscometer. The determination of in vitro spreadability was achieved by an adaptation of the Knorst method. The ethanol content was measured by headspace gas chromatography using a flame ionization detector. The thermal behavior of the gels was influenced by the presence of glycerol, which confirms the possible network interactions formed. The relative densities of the samples were between 0.887 and 0.890 g/cm3. No alteration of the pH of the formulation resulted from the incorporation of glycerol. The apparent viscosities of the alcohol gels were greater than 20,000 cP. No alteration in the in vitro spreadability of the gel alcohol (530.6 mm2) resulted from the addition of glycerol. Hand sanitizer was produced using glycerol from a transesterification reaction. It represents an alternative use for the glycerol being produced in biodiesel processes. The product satisfied the requirements of WHO that preconize a formulation containing 1.45% glycerol as an humectant to protect skin against dryness and dermatitis.
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Affiliation(s)
- Tassio Trindade Mazala
- Department of Pharmacy, Universidade Federal dos Vales do Jequitinhonha e Mucuri-UFVJM, Campus JK, Rodovia MGT 367 - Km 583, n° 5.000, Alto da Jacuba, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Mateus Costa Viana
- Department of Pharmacy, Universidade Federal dos Vales do Jequitinhonha e Mucuri-UFVJM, Campus JK, Rodovia MGT 367 - Km 583, n° 5.000, Alto da Jacuba, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Guilherme Carneiro
- Department of Pharmacy, Universidade Federal dos Vales do Jequitinhonha e Mucuri-UFVJM, Campus JK, Rodovia MGT 367 - Km 583, n° 5.000, Alto da Jacuba, Diamantina, Minas Gerais, 39100-000, Brazil
| | - David Lee Nelson
- Department of Pharmacy, Universidade Federal dos Vales do Jequitinhonha e Mucuri-UFVJM, Campus JK, Rodovia MGT 367 - Km 583, n° 5.000, Alto da Jacuba, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Maria B de Freitas-Marques
- Department of Chemistry, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Curso de Farmácia. Faculdade de Minas, Faminas-BH, Av. Cristiano Machado, 12001, Vila Clóris, Belo Horizonte, Minas Gerais, 31744-007, Brazil
| | - Bruno Spinosa De Martinis
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900, Ribeirão Prêto, SP, 14040-900, Brazil
| | - Jacques Florêncio
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900, Ribeirão Prêto, SP, 14040-900, Brazil
| | - Fernanda Marur Mazzé
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN, 59078-900, Brazil
| | | | - Sandro L Barbosa
- Department of Pharmacy, Universidade Federal dos Vales do Jequitinhonha e Mucuri-UFVJM, Campus JK, Rodovia MGT 367 - Km 583, n° 5.000, Alto da Jacuba, Diamantina, Minas Gerais, 39100-000, Brazil.
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3
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Balázs M, Bartos H, Lányi S, Bodor Z, Miklóssy I. Substrate type and CO 2 addition significantly influence succinic acid production of Basfia succiniciproducens. Biotechnol Lett 2023; 45:1133-1145. [PMID: 37395870 PMCID: PMC10432361 DOI: 10.1007/s10529-023-03406-7] [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: 11/18/2022] [Revised: 05/28/2023] [Accepted: 06/10/2023] [Indexed: 07/04/2023]
Abstract
Metabolic engineering has shown that optimizing metabolic pathways' fluxes for industrial purposes requires a methodical approach. Accordingly, in this study, in silico metabolic modeling was utilized to characterize the lesser-known strain Basfia succiniciproducens under different environmental conditions, followed by the use of industrially relevant substrates for succinic acid synthesis. Based on RT-qPCR carried out in flask experiments, we discovered a relatively large difference in the expression levels of ldhA gene compared to glucose in both xylose and glycerol cultures. In bioreactor-scale fermentations, the impact of different gas phases (CO2, CO2/AIR) on biomass yield, substrate consumption, and metabolite profiles was also investigated. In the case of glycerol, the addition of CO2 increased biomass as well as target product formation, while using CO2/AIR gas phase resulted in higher target product yield (0.184 mM⋅mM-1). In case of xylose, using CO2 alone would result in higher succinic acid production (0.277 mM⋅mM-1). The promising rumen bacteria, B. succiniciproducens, has shown to be suitable for succinic acid production from both xylose and glycerol. As a result, our findings present new opportunities for broadening the range of raw materials used in this significant biochemical process. Our study also sheds light on fermentation parameter optimization for this strain, namely that, CO2/AIR supply has a positive effect on target product formation.
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Affiliation(s)
- Márta Balázs
- Faculty of Science, University of Pécs, Ifjúság 6, 7624, Pécs, Hungary
| | - Hunor Bartos
- Faculty of Science, University of Pécs, Ifjúság 6, 7624, Pécs, Hungary
| | - Szabolcs Lányi
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania
| | - Zsolt Bodor
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania.
- Institute for Research and Development of Hunting and Mountain Resources, St. Progresului 35B, 530240, Miercurea Ciuc, Romania.
| | - Ildikó Miklóssy
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania
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Liu H, Liu D, Chen Y. FDH/Hases-S-chain mediated electron redistributing in Citrobacter freundii JH@FeS during degradation of sulfamethoxazole and nitrate. WATER RESEARCH 2023; 243:120431. [PMID: 37572458 DOI: 10.1016/j.watres.2023.120431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Considering the negligent degradation of sulfamethoxazole (SMX) by Citrobacter freundii JH, the incorporation of bio-FeS could initiate the SMX biodegradation to 0.0444 (S-FeS), and further to 0.0564 mg L-1 mg-1 protein d-1 (SN-FeS) when coexisted with nitrate. Electrochemical (LSV, I-t, DPV, EIS and EDC) and respiratory inhibition experiments clarified that the bio-FeS could greatly switch/redistribute electron transmembrane-transfer from intracellular to extracellular mainly via FDH/Hases-S-chain, as revealed by the significant increase of ipa-FDH/Hases/ipa-FC-Cyts and ipc-FDH/Hases/ipc-FC-Cyts (from 1.09 and 1.07 (SN-native) to 1.50 and 3.58 (SN-FeS)), while nitrate (linear fitting with NADH (R2 = 0.9903)) mainly intensified CoQ-L-chain related INET from Complex I to CoQ to compensate for the electronic competition with SMX. SN-FeS system detoxified the SMX on microbial metabolism (such as membrane rupture and oxidative stress induction) with high SOD activity (737.93 U gFW-1). Structural equation modeling indicated that bio-FeS up-regulated PMF-mediated ATP synthesis (PPMF-ATPs from 0.12 (SN-native) to 0.74 (SN-FeS)) and PMF-mediated NADH (PPMF-NADH from -0.72 (SN-native) to 0.63 (SN-FeS)), and the nitrate addition intensified this positive feedback. Overall, this study provides a new perspective for bionanoparticles via electron transfer/redistribution to detoxify and launch the antibiotics biodegradation in ecological environment.
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Affiliation(s)
- Huimin Liu
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou, Guangdong 510006, PR China
| | - Dejin Liu
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou, Guangdong 510006, PR China
| | - Yuancai Chen
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou, Guangdong 510006, PR China.
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Phakatkar AH, Gonçalves JM, Zhou J, Ritter TG, Tamadoni Saray M, Sorokina LV, Amiri A, Angnes L, Shokuhfar T, Shahbazian-Yassar R. Enhanced Bacterial Growth by Polyelemental Glycerolate Particles. ACS APPLIED BIO MATERIALS 2023; 6:1515-1524. [PMID: 36933270 DOI: 10.1021/acsabm.2c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
While polyelemental alloys are shown to be promising for healthcare applications, their effectiveness in promoting bacterial growth remains unexplored. In the present work, we evaluated the interaction of polyelemental glycerolate particles (PGPs) with Escherichia coli (E. coli) bacteria. PGPs were synthesized using the solvothermal route, and nanoscale random distribution of metal cations in the glycerol matrix of PGPs was confirmed. We observed 7-fold growth of E. coli bacteria upon 4 h of interaction with quinary glycerolate (NiZnMnMgSr-Gly) particles in comparison to control E. coli bacteria. Nanoscale microscopic studies on bacteria interactions with PGPs showed the release of metal cations in the bacterium cytoplasm from PGPs. The electron microscopy imaging and chemical mapping indicated bacterial biofilm formation on PGPs without causing significant cell membrane damage. The data showed that the presence of glycerol in PGPs is effective in controlling the release of metal cations, thus preventing bacterial toxicity. The presence of multiple metal cations is expected to provide synergistic effects of nutrients needed for bacterial growth. The present work provides key microscopic insights of mechanisms by which PGPs enhance biofilm growth. This study opens the door for future applications of PGPs in areas where bacterial growth is essential including healthcare, clean energy, and the food industry.
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Affiliation(s)
- Abhijit H Phakatkar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Josué M Gonçalves
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Fundamental Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-060, Brazil
| | - Jianshu Zhou
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Timothy G Ritter
- Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Mahmoud Tamadoni Saray
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lioudmila V Sorokina
- Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Azadeh Amiri
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lucio Angnes
- Department of Fundamental Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-060, Brazil
| | - Tolou Shokuhfar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Reza Shahbazian-Yassar
- Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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de Divitiis M, Ami D, Pessina A, Palmioli A, Sciandrone B, Airoldi C, Regonesi ME, Brambilla L, Lotti M, Natalello A, Brocca S, Mangiagalli M. Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:30. [PMID: 36823649 PMCID: PMC9948444 DOI: 10.1186/s13068-023-02281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose. RESULTS The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness. CONCLUSIONS CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
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Affiliation(s)
- Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. Metabolic pathways and ΔpH regulation in Escherichia coli during the fermentation of glucose and glycerol in the presence of formate at pH 6.5: the role of FhlA transcriptional activator. FEMS Microbiol Lett 2022; 369:6825452. [PMID: 36370455 DOI: 10.1093/femsle/fnac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli is able to ferment mixed carbon sources and produce various fermentation end-products. In this study, the function of FhlA protein in the specific growth rate (µ), metabolism, regulation of ΔpH and proton ATPase activity was investigated. Reduced µ in fhlA mutant of ∼25% was shown, suggesting the role of FhlA in the growth process. The utilization rate of glycerol is decreased in fhlA ∼ 2 fold, depending on the oxidation-reduction potential values. Bacteria regulate the activity of hydrogenase enzymes during growth depending on the external pH, which manifests as a lack of hydrogen gas generation during glycerol utilization at pH values below 5.9. It is suggested that cells maintain ΔpH during the fermentative growth via formate-lactate-succinate exchange. The decrement of the value of pHin, but not of pHex in mutant cells, is regulating ΔpH and consequently proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Anait Vassilian
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
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Glycerol Utilization as a Sole Carbon Source Disrupts the Membrane Architecture and Solventogenesis in Clostridium beijerinckii NCIMB 8052. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8070339] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Efficient bioconversion of abundant waste glycerol to value-added chemicals calls for a wider range of fermentative workhorses that can catabolize glycerol. In this study, we used quantitative gene expression and solvent profiling, qualitative metabolite analysis, and enzyme activity assays to investigate the factors that limit glycerol utilization as a sole carbon source by Clostridium beijerinckii NCIMB 8052. C. beijerinckii NCIMB 8052 did not produce acetate, acetone and butanol on glycerol. Congruently, the genes encoding the coenzyme A transferase subunits (ctfAB) and bifunctional acetaldehyde-CoA/alcohol dehydrogenase (adhE) were down-regulated up to 135- and 21-fold, respectively, at 12 h in glycerol-grown cells compared to glucose-grown cells. Conversely, NADH-dependent butanol dehydrogenase A (bdhA) was upregulated 2-fold. Glycerol dehydrogenase (gldA) and dihydroxyacetone kinase (subunit dhaK) were upregulated up to 5- and 881-fold, respectively. Glyceraldehyde-3-phosphate dehydrogenase (gapdh) showed mostly similar expression profiles at 12 h on glucose and glycerol. At 24 h, gapdh was downregulated 1.5-fold, while NADP+-dependent gapdh was upregulated up to 1.9-fold. Glycerol-grown cells showed higher or similar activity profiles for all solventogenic enzymes studied, compared to glucose-grown cells. Butyraldehyde (3 g/L) supplementation led to the production of ~0.1 g/L butanol, whilst butyrate (3.5 g/L) supplementation produced 0.7 and 0.5 g/L acetone and butanol, respectively, with glycerol. Further, the long chain saturated fatty acids cyclopentaneundecanoic acid, methyl ester and hexadecanoic acid, butyl ester were detected in glucose- but not in glycerol-grown cells. Collectively, growth on glycerol appears to disrupt synthesis of saturated long chain fatty acids, as well as solventogenesis in C. beijerinckii NCIMB 8052.
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Eghtesadi N, Olaifa K, Perna FM, Capriati V, Trotta M, Ajunwa O, Marsili E. Electroactivity of weak electricigen Bacillus subtilis biofilms in solution containing deep eutectic solvent components. Bioelectrochemistry 2022; 147:108207. [PMID: 35839687 DOI: 10.1016/j.bioelechem.2022.108207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022]
Abstract
Bacillus subtilis is a Gram-positive, spore-forming bacterium with a versatile and adaptable metabolism, which makes it a viable cell factory for microbial production. Electroactivity has recently been identified as a cellular characteristic linked with the metabolic activity of B. subtilis. The enhancement of B. subtilis electroactivity can positively enhance bioproduction of high-added value metabolites under electrofermentative conditions. Here, we explored the use of deep eutectic solvents (DESs) and DES components as biocompatible nutrient additives for enhancing electroactivity of B. subtilis. The strongest electroactivity was obtained in an aqueous choline chloride: glycerol (1:2 mol mol-1) eutectic mixture. At low concentration (50-500 mM), this mixture induced a pseudo-diauxic increase in planktonic growth and increased biofilm formation, likely due to a nutritional and osmoprotectant effect. Similarities in electroactivity enhancements of choline chloride-based eutectic mixtures and quinone redox metabolism in B. subtilis were detected using high performance liquid chromatography and differential pulse voltammetry. Results show that choline chloride-based aqueous eutectic mixtures can enhance biomass and productivity in biofilm-based electrofermentation. However, the specific mechanism needs to be fully elucidated.
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Affiliation(s)
- Neda Eghtesadi
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan
| | - Kayode Olaifa
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan
| | - Filippo Maria Perna
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro," via E. Orabona 4, I-70125 Bari, Italy
| | - Vito Capriati
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro," via E. Orabona 4, I-70125 Bari, Italy
| | - Massimo Trotta
- Istituto per i Processi Chimico Fisici, CNR, via E. Orabona 4, I-70125 Bari, Italy
| | - Obinna Ajunwa
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan; Department of Microbiology, Modibbo Adama University, Yola, Nigeria.
| | - Enrico Marsili
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan.
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Microbial Biogas Production from Pork Gelatine. HYDROGEN 2022. [DOI: 10.3390/hydrogen3020012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This research describes the results of the anaerobic digestion of gelatine as a potential hydrogen source with heat-shocked inoculum. The concentrations of applied gelatine were of VSS (volatile suspended solids) ranging from 10 g VSS/L to 30 g VSS/L. The initial process pH was 5.5, and, depending on the concentration, reached pH values from 7.5 to 7.8 after 55 days. Although the inoculum was heat-shocked in 30 g VSS/L of collagen, the process that occurred was hydrogenotrophic anaerobic digestion. In gelatine concentrations below 30 g VSS/L, hydrogen production was dominant only during the first 5 days of the experiments. Then, there was a change from dark fermentation to hydrogenotrophic methane production. The optimal hydrogen and methane yields resulted from the concentrations of 10 g VSS/L (7.65 mL ± 0.01 mL H2/g VSS and 3.49 ± 0.01 L CH4/g VSS). Additionally, 10 g VSS/L had the lowest accumulated emission of hydrogen sulphide (10.3 ± 0.01 mL of H2S), while 30 g VSS/L (0.440 ± 0.01mL H2S/g VSS) produced the lowest yield. After a lag time, the hydrogen production and hydrogen sulphide grew with a specific ratio, depending on the concentration. The hydrogen sulphide emission and sulphur added analysis proved that hydrogen sulphide originating from biogas created by bacteria remains longer than that from a substrate.
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11
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Boecker S, Espinel-Ríos S, Bettenbrock K, Klamt S. Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metab Eng 2022; 73:50-57. [DOI: 10.1016/j.ymben.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 05/21/2022] [Indexed: 11/29/2022]
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12
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Engineering E. coli to synthesize butanol. Biochem Soc Trans 2022; 50:867-876. [PMID: 35356968 DOI: 10.1042/bst20211009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
Biobutanol is gaining much attention as a potential biofuel due to its superior properties over ethanol. Butanol has been naturally produced via acetone-butanol-ethanol (ABE) fermentation by many Clostridium species, which are not very user-friendly bacteria. Therefore, to improve butanol titers and yield, various butanol synthesis pathways have been engineered in Escherichia coli, a much more robust and convenient host than Clostridium species. This review mainly focuses on the biosynthesis of n-butanol in engineered E. coli with an emphasis on efficient enzymes for butanol production in E. coli, butanol competing pathways, and genome engineering of E. coli for butanol production. In addition, the use of alternate strategies for butanol biosynthesis/enhancement, alternate substrates for the low cost of butanol production, and genetic improvement for butanol tolerance in E. coli have also been discussed.
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13
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Heiden RW, Schober S, Mittelbach M. Solubility limitations of residual steryl glucosides, saturated monoglycerides and glycerol in commercial biodiesel fuels as determinants of filter blockages. J AM OIL CHEM SOC 2021. [DOI: 10.1002/aocs.12547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard W. Heiden
- R. W. Heiden Associates LLC, Laboratory/Greenfield Corporate Center Lancaster Pennsylvania USA
| | - Sigurd Schober
- Institute of Chemistry University of Graz—NAWI Graz Graz Austria
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Clomburg JM, Cintolesi A, Gonzalez R. In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Microb Biotechnol 2021; 15:289-304. [PMID: 34699695 PMCID: PMC8719807 DOI: 10.1111/1751-7915.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2 , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Angela Cintolesi
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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15
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An Escherichia coli FdrA Variant Derived from Syntrophic Coculture with a Methanogen Increases Succinate Production Due to Changes in Allantoin Degradation. mSphere 2021; 6:e0065421. [PMID: 34494882 PMCID: PMC8550087 DOI: 10.1128/msphere.00654-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wild-type Escherichia coli was adapted to syntrophic growth with Methanobacterium formicicum for glycerol fermentation over 44 weeks. Succinate production by E. coli started to increase in the early stages of syntrophic growth. Genetic analysis of the cultured E. coli population by pooled sequencing at eight time points suggests that (i) rapid evolution occurred through repeated emergence of mutators that introduced a large number of nucleotide variants and (ii) many mutators increased to high frequencies but remained polymorphic throughout the continuous cultivation. The evolved E. coli populations exhibited gains both in fitness and succinate production, but only for growth under glycerol fermentation with M. formicicum (the condition for this laboratory evolution) and not under other growth conditions. The mutant alleles of the 69 single nucleotide polymorphisms (SNPs) identified in the adapted E. coli populations were constructed individually in the ancestral wild-type E. coli. We analyzed the phenotypic changes caused by 84 variants, including 15 nonsense variants, and found that FdrAD296Y was the most significant variant leading to increased succinate production. Transcription of fdrA was induced under anaerobic allantoin degradation conditions, and FdrA was shown to play a crucial role in oxamate production. The FdrAD296Y variant increased glyoxylate conversion to malate by accelerating oxamate production, which promotes carbon flow through the C4 branch, leading to increased succinate production. IMPORTANCE Here, we demonstrate the ability of E. coli to perform glycerol fermentation in coculture with the methanogen M. formicicum to produce succinate. We found that the production of succinate by E. coli significantly increased during successive cocultivation. Genomic DNA sequencing, evaluation of relative fitness, and construction of SNPs were performed, from which FdrAD296Y was identified as the most significant variant to enable increased succinate production by E. coli. The function of FdrA is uncertain. In this study, experiments with gene expression assays and metabolic analysis showed for the first time that FdrA could be the “orphan enzyme” oxamate:carbamoyltransferase in anaerobic allantoin degradation. Furthermore, we demonstrate that the anaerobic allantoin degradation pathway is linked to succinate production via the glyoxylate pathway during glycerol fermentation.
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16
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Cheng J, Li J, Zheng L. Achievements and Perspectives in 1,4-Butanediol Production from Engineered Microorganisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10480-10485. [PMID: 34478293 DOI: 10.1021/acs.jafc.1c03769] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
1,4-Butanediol (1,4-BDO), a significant commodity chemical, is currently manufactured exclusively from a host of energy-intensive processes, accompanied by severe environmental issues, such as the greenhouse effect and air pollution. As a result of the ever-increasing global market demands and increasing applications of 1,4-BDO, attention has turned to the sustainable bioproduction of 1,4-BDO, and several bio-based approaches for 1,4-BDO production have been successfully established in engineered Escherichia coli, including de novo biosynthesis and biocatalysis. Recent achievements in enhancing the accumulation of 1,4-BDO have been achieved by metabolic engineering strategies, such as improving precursor supply, enhancing activities of critical enzymes, and fewer byproduct synthesis. Here, we summarize the primary advances of the biological pathway for 1,4-BDO synthesis and put forward the future development prospect of bio-based 1,4-BDO production.
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Affiliation(s)
- Jie Cheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science,Xiamen University, Xiamen, Fujian 361102, People's Republic of China
| | - Juan Li
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science,Xiamen University, Xiamen, Fujian 361102, People's Republic of China
- Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, People's Republic of China
| | - Linggang Zheng
- College of Ocean and Earth Sciences, State Key Laboratory of Marine Environmental Science,Xiamen University, Xiamen, Fujian 361102, People's Republic of China
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao 999078, People's Republic of China
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17
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Abstract
Phosphorus (P) is essential for life. As the fifth-most-abundant element in living cells, P is required for the synthesis of an array of biological molecules including (d)NTPs, nucleic acids, and membranes. Organisms typically acquire environmental P as inorganic phosphate (Pi). While essential for growth and viability, excess intracellular Pi is toxic for both bacteria and eukaryotes. Using the bacterium Salmonella enterica serovar Typhimurium as a model, we establish that Pi cytotoxicity is manifested following its assimilation into adenosine triphosphate (ATP), which acts as a chelating agent for Mg2+ and other cations. Our findings identify physiological processes disrupted by excessive Pi and how bacteria tune P assimilation to cytoplasmic Mg2+ levels. Phosphorus (P) is an essential component of core biological molecules. In bacteria, P is acquired mainly as inorganic orthophosphate (Pi) and assimilated into adenosine triphosphate (ATP) in the cytoplasm. Although P is essential, excess cytosolic Pi hinders growth. We now report that bacteria limit Pi uptake to avoid disruption of Mg2+-dependent processes that result, in part, from Mg2+ chelation by ATP. We establish that the MgtC protein inhibits uptake of the ATP precursor Pi when Salmonella enterica serovar Typhimurium experiences cytoplasmic Mg2+ starvation. This response prevents ATP accumulation and overproduction of ribosomal RNA that together ultimately hinder bacterial growth and result in loss of viability. Even when cytoplasmic Mg2+ is not limiting, excessive Pi uptake increases ATP synthesis, depletes free cytoplasmic Mg2+, inhibits protein synthesis, and hinders growth. Our results provide a framework to understand the molecular basis for Pi toxicity. Furthermore, they suggest a regulatory logic that governs P assimilation based on its intimate connection to cytoplasmic Mg2+ homeostasis.
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18
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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19
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Augustiniene E, Valanciene E, Matulis P, Syrpas M, Jonuskiene I, Malys N. Bioproduction of l- and d-lactic acids: advances and trends in microbial strain application and engineering. Crit Rev Biotechnol 2021; 42:342-360. [PMID: 34412525 DOI: 10.1080/07388551.2021.1940088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lactic acid is an important platform chemical used in the food, agriculture, cosmetic, pharmaceutical, and chemical industries. It serves as a building block for the production of polylactic acid (PLA), a biodegradable polymer, which can replace traditional petroleum-based plastics and help to reduce environmental pollution. Cost-effective production of optically pure l- and d-lactic acids is necessary to achieve a quality and thermostable PLA product. This paper evaluates research advances in the bioproduction of l- and d-lactic acids using microbial fermentation. Special emphasis is given to the development of metabolically engineered microbial strains and processes tailored to alternative and flexible feedstock concepts such as: lignocellulose, glycerol, C1-gases, and agricultural-food industry byproducts. Alternative fermentation concepts that can improve lactic acid production are discussed. The potential use of inducible gene expression systems for the development of biosensors to facilitate the screening and engineering of lactic acid-producing microorganisms is discussed.
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Affiliation(s)
- Ernesta Augustiniene
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
| | - Egle Valanciene
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
| | - Paulius Matulis
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
| | - Michail Syrpas
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
| | - Ilona Jonuskiene
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
| | - Naglis Malys
- Faculty of Chemical Technology, Bioprocess Research Centre, Kaunas University of Technology, Kaunas, Lithuania
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20
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Kumar J, Chauhan AS, Gupta JA, Rathore AS. Supplementation of critical amino acids improves glycerol and lactose uptake and enhances recombinant protein production in Escherichia coli. Biotechnol J 2021; 16:e2100143. [PMID: 34047499 DOI: 10.1002/biot.202100143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Lactose-based induction strategy in E. coli cultivation has several advantages over IPTG as it is cheap, does not impart metabolic stress to cells, and is non-toxic to cells. However, complexity of lactose as an inducer limits its application in fed-batch cultivation. A mixed glycerol-lactose based induction strategy is generally opted during fed-batch cultivation of E. coli. However, slow growth of E. coli in glycerol and lactose results in slower induction of heterologous protein. MAIN METHODS AND MAJOR RESULTS In this study, initially we have demonstrated supplementation of critical amino acids (AAs) improves uptake rate of glycerol and lactose in wildtype E. coli BL21(DE3) in defined medium. A feeding strategy of mixed glycerol-lactose feed along with supplement of critical AAs enhances recombinant production of pramlintide multimer (rPramlintide). High cell density cultivation of E. coli using mixed glycerol-lactose feed and critical AAs supplement resulted in final cell density of 52.2 ± 0.90 g L-1 and rPramlintide titer of 7.8 g L-1 . RT-qPCR analysis of genes involved in glycerol and lactose metabolism of recombinant culture showed upregulation with AAs supplementation. CONCLUSIONS AND IMPLICATIONS We hypothesize that supplementation of critical AAs serves dual purpose: (i) faster assimilation of carbon sources, and (ii) combating metabolic stress arises due to AAs starvation. The substrate uptake and gene expression profiles demonstrate that AAs addition enhances glycerol and lactose assimilation due to overall improvement in their metabolism governed by global regulators of carbon metabolism.
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Affiliation(s)
- Jashwant Kumar
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Ashish S Chauhan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Jaya A Gupta
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
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21
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Abstract
By evolving strains of E. coli that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Mutations in rcsC, lpp, igaA, or the yjbEFGH operon were sufficient to stimulate sedimentation resistance, while mutations altering the cps promoter, cdgI, or yjbF provided phenotypic enhancements. The sedimentation resistances changed in response to temperature, growth phase, and carbon source and each mutant exhibited significantly reduced biofilm formation. We discovered that the degree of colony mucoidy exhibited by these mutants was not related to the degree of Rcs pathways activation or to the amount of CAP that was produced; rather, it was related to the fraction of CAP that was shed as a true exopolysaccharide. Therefore, these and other mutations that activate this phenotype are likely to be absent from genetic screens that relied on centrifugation to harvest bacteria. We also found that this anchored CAP form is not linked to LPS cores and may not be attached to the outer membrane.IMPORTANCEBacteria can partition in aqueous environments between surface-dwelling, planktonic, sedimentary, and biofilm forms. Residence in each location provides an advantage depending on nutritional and environmental stresses and a community of a single species is often observed to be distributed throughout two or more of these niches. Another adaptive strategy is to produce an extracellular capsule, which provides an environmental shield for the microbe and can allow escape from predators and immune systems. We discovered that bacteria can either shed or stably anchor capsules to dramatically alter their propensity to sediment. The degree to which the bacteria anchor their capsule is controlled by a stress sensing system, suggesting that anchoring may be used as an adaptive response to severe environmental challenges.
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22
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. The role of Escherichia coli FhlA transcriptional activator in generation of proton motive force and F O F 1 -ATPase activity at pH 7.5. IUBMB Life 2021; 73:883-892. [PMID: 33773019 DOI: 10.1002/iub.2470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/29/2022]
Abstract
Escherichia coli is able to utilize the mixture of carbon sources and produce molecular hydrogen (H2 ) via formate hydrogen lyase (FHL) complexes. In current work role of transcriptional activator of formate regulon FhlA in generation of fermentation end products and proton motive force, N'N'-dicyclohexylcarbodiimide (DCCD)-sensitive ATPase activity at 20 and 72 hr growth during utilization of mixture of glucose, glycerol, and formate were investigated. It was shown that in fhlA mutant specific growth rate was ~1.5 fold lower compared to wt, while addition of DCCD abolished the growth in fhlA but not in wt. Formate was not utilized in fhlA mutant but wt cells simultaneously utilized formate with glucose. Glycerol utilization started earlier (from 2 hr) in fhlA than in wt. The DCCD-sensitive ATPase activity in wt cells membrane vesicles increased ~2 fold at 72 hr and was decreased 70% in fhlA. Addition of formate in the assays increased proton ATPase activity in wt and mutant strain. FhlA absence mainly affected the ΔpH but not ΔΨ component of Δp in the cells grown at 72 hr but not in 24 hr. The Δp in wt cells decreased from 24 to 72 hr of growth ~40 mV while in fhlA mutant it was stable. Taken together, it is suggested that FhlA regulates the concentration of fermentation end products and via influencing FO F1 -ATPase activity contributes to the proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia.,Laboratory of Neuroscience, Yerevan State Medical University, Yerevan, Armenia
| | - Anait Vassilian
- Department of Ecology and Nature Protection, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
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Tafur Rangel AE, Ríos W, Mejía D, Ojeda C, Carlson R, Gómez Ramírez JM, González Barrios AF. In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. Front Genet 2021; 12:633073. [PMID: 33868371 PMCID: PMC8044919 DOI: 10.3389/fgene.2021.633073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, it is important to use tools that allow predicting gene deletions. An in silico experiment was performed to model and understand the metabolic engineering effects on the cell factory considering a second complexity level by transcriptomics data integration. In this study, a systems-based metabolic engineering target prediction was used to increase glycerol bioconversion to succinic acid based on Escherichia coli. Transcriptomics analysis suggests insights on how to increase cell glycerol utilization to further design efficient cell factories. Three E. coli models were used: a core model, a second model based on the integration of transcriptomics data obtained from growth in an optimized culture media, and a third one obtained after integration of transcriptomics data from adaptive laboratory evolution (ALE) experiments. A total of 2,402 strains were obtained with fumarase and pyruvate dehydrogenase being frequently predicted for all the models, suggesting these reactions as essential to increase succinic acid production. Finally, based on using flux balance analysis (FBA) results for all the mutants predicted, a machine learning method was developed to predict new mutants as well as to propose optimal metabolic engineering targets and mutants based on the measurement of the importance of each knockout's (feature's) contribution. Glycerol has become an interesting carbon source for industrial processes due to biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. The combination of transcriptome, systems metabolic modeling, and machine learning analyses revealed the versatility of computational models to predict key metabolic engineering targets in a less cost-, time-, and laborious-intensive process. These data provide a platform to improve the prediction of metabolic engineering targets to design efficient cell factories. Our results may also work as a guide and platform for the selection/engineering of microorganisms for the production of interesting chemical compounds.
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Affiliation(s)
- Albert Enrique Tafur Rangel
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
- Grupo de Investigación CINBIOS, Department of Microbiology, Universidad Popular del Cesar, Valledupar, Colombia
| | - Wendy Ríos
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Daisy Mejía
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Carmen Ojeda
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Ross Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Jorge Mario Gómez Ramírez
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
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24
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Novel Mode Engineering for β-Alanine Production in Escherichia coli with the Guide of Adaptive Laboratory Evolution. Microorganisms 2021; 9:microorganisms9030600. [PMID: 33803992 PMCID: PMC8000549 DOI: 10.3390/microorganisms9030600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
The strategy of anaerobic biosynthesis of β-alanine by Escherichia coli (E. coli) has been reported. However, the low energy production under anaerobic condition limited cell growth and then affected the production efficiency of β-alanine. Here, the adaptive laboratory evolution was carried out to improve energy production of E. coli lacking phosphoenolpyruvate carboxylase under anaerobic condition. Five mutants were isolated and analyzed. Sequence analysis showed that most of the consistent genetic mutations among the mutants were related with pyruvate accumulation, indicating that pyruvate accumulation enabled the growth of the lethal parent. It is possible that the accumulated pyruvate provides sufficient precursors for energy generation and CO2 fixing reaction catalyzed by phosphoenolpyruvate carboxykinase. B0016-100BB (B0016-090BB, recE::FRT, mhpF::FRT, ykgF::FRT, mhpB:: mhpB *, mhpD:: mhpD *, rcsA:: rcsA *) was engineered based on the analysis of the genetic mutations among the mutants for the biosynthesis of β-alanine. Along with the recruitment of glycerol as the sole carbon source, 1.07 g/L β-alanine was generated by B0016-200BB (B0016-100BB, aspA::FRT) harboring pET24a-panD-AspDH, which was used for overexpression of two key enzymes in β-alanine fermentation process. Compared with the starting strain, which can hardly generate β-alanine under anaerobic condition, the production efficiency of β-alanine of the engineered cell factory was significantly improved.
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Pedebos C, Smith IPS, Boags A, Khalid S. The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli. Structure 2021; 29:444-456.e2. [PMID: 33577754 DOI: 10.1016/j.str.2021.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/11/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022]
Abstract
The periplasm of Gram-negative bacteria is a complex, highly crowded molecular environment. Little is known about how antibiotics move across the periplasm and the interactions they experience. Here, atomistic molecular dynamics simulations are used to study the antibiotic polymyxin B1 within models of the periplasm, which are crowded to different extents. We show that PMB1 is likely to be able to "hitchhike" within the periplasm by binding to lipoprotein carriers-a previously unreported passive transport route. The simulations reveal that PMB1 forms both transient and long-lived interactions with proteins, osmolytes, lipids of the outer membrane, and the cell wall, and is rarely uncomplexed when in the periplasm. Furthermore, it can interfere in the conformational dynamics of native proteins. These are important considerations for interpreting its mechanism of action and are likely to also hold for other antibiotics that rely on diffusion to cross the periplasm.
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Affiliation(s)
- Conrado Pedebos
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Iain Peter Shand Smith
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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Grigaitis P, Olivier BG, Fiedler T, Teusink B, Kummer U, Veith N. Protein cost allocation explains metabolic strategies in Escherichia coli. J Biotechnol 2020; 327:54-63. [PMID: 33309962 DOI: 10.1016/j.jbiotec.2020.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/15/2020] [Accepted: 11/01/2020] [Indexed: 12/14/2022]
Abstract
In-depth understanding of microbial growth is crucial for the development of new advances in biotechnology and for combating microbial pathogens. Condition-specific proteome expression is central to microbial physiology and growth. A multitude of processes are dependent on the protein expression, thus, whole-cell analysis of microbial metabolism using genome-scale metabolic models is an attractive toolset to investigate the behaviour of microorganisms and their communities. However, genome-scale models that incorporate macromolecular expression are still inhibitory complex: the conceptual and computational complexity of these models severely limits their potential applications. In the need for alternatives, here we revisit some of the previous attempts to create genome-scale models of metabolism and macromolecular expression to develop a novel framework for integrating protein abundance and turnover costs to conventional genome-scale models. We show that such a model of Escherichia coli successfully reproduces experimentally determined adaptations of metabolism in a growth condition-dependent manner. Moreover, the model can be used as means of investigating underutilization of the protein machinery among different growth settings. Notably, we obtained strongly improved predictions of flux distributions, considering the costs of protein translation explicitly. This finding in turn suggests protein translation being the main regulation hub for cellular growth.
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Affiliation(s)
- Pranas Grigaitis
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany; Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Brett G Olivier
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany; Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Center, Schillingallee 70, D-18055 Rostock, Germany
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU Amsterdam, De Boelelaan 1085, NL-1081HZ Amsterdam, The Netherlands
| | - Ursula Kummer
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany
| | - Nadine Veith
- Modeling of Biological Processes, BioQuant/Center for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany.
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Increasement of O-acetylhomoserine production in Escherichia coli by modification of glycerol-oxidative pathway coupled with optimization of fermentation. Biotechnol Lett 2020; 43:105-117. [PMID: 33083859 DOI: 10.1007/s10529-020-03031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE O-acetylhomoserine (OAH) is an important platform chemical to produce high-valuable chemicals. To improve the production of O-acetylhomoserine from glycerol, the glycerol-oxidative pathway was investigated and the optimization of fermentation with crude glycerol was carried out. RESULTS The glycerol-uptake system and glycerol-oxidative pathway were modified and O-acetyltransferase from Corynebacterium glutamicum was introduced into the engineered strain to produce O-acetylhomoserine. It was found that overexpression of glycerol 3-phosphate dehydrogenase improved the OAH production to 6.79 and 4.21 g/L from pure and crude glycerol, respectively. And the higher OAH production depending on higher level of transcription of glpD. Two-step statistical approach was employed to optimize the fermentation conditions. The significant effects of glycerol, ammonium chloride and yeast extract were screened applying Plackett-Burman design and were optimized further by employing the Response Surface Methodology. Under optimized conditions, the OAH production was up to 9.42 and 7.01 g/L when pure and crude glycerol were used in shake flask cultivations, respectively. CONCLUSIONS The enzymatic step catalyzing the oxidation of glycerol through GlpD was the key step for OAH production, which served the foundation for realization of a consistent OAH production from crude glycerol in the future.
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Abedi E, Hashemi SMB. Lactic acid production - producing microorganisms and substrates sources-state of art. Heliyon 2020; 6:e04974. [PMID: 33088933 PMCID: PMC7566098 DOI: 10.1016/j.heliyon.2020.e04974] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/08/2020] [Accepted: 09/16/2020] [Indexed: 01/18/2023] Open
Abstract
Lactic acid is an organic compound produced via fermentation by different microorganisms that are able to use different carbohydrate sources. Lactic acid bacteria are the main bacteria used to produce lactic acid and among these, Lactobacillus spp. have been showing interesting fermentation capacities. The use of Bacillus spp. revealed good possibilities to reduce the fermentative costs. Interestingly, lactic acid high productivity was achieved by Corynebacterium glutamicum and E. coli, mainly after engineering genetic modification. Fungi, like Rhizopus spp. can metabolize different renewable carbon resources, with advantageously amylolytic properties to produce lactic acid. Additionally, yeasts can tolerate environmental restrictions (for example acidic conditions), being the wild-type low lactic acid producers that have been improved by genetic manipulation. Microalgae and cyanobacteria, as photosynthetic microorganisms can be an alternative lactic acid producer without carbohydrate feed costs. For lactic acid production, it is necessary to have substrates in the fermentation medium. Different carbohydrate sources can be used, from plant waste as molasses, starchy, lignocellulosic materials as agricultural and forestry residues. Dairy waste also can be used by the addition of supplementary components with a nitrogen source.
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Affiliation(s)
- Elahe Abedi
- Department of Food Science and Technology, College of Agriculture, Fasa University, Fasa, Iran
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29
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Miscevic D, Mao JY, Kefale T, Abedi D, Moo-Young M, Perry Chou C. Strain engineering for high-level 5-aminolevulinic acid production in Escherichia coli. Biotechnol Bioeng 2020; 118:30-42. [PMID: 32860420 DOI: 10.1002/bit.27547] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022]
Abstract
Herein, we report the development of a microbial bioprocess for high-level production of 5-aminolevulinic acid (5-ALA), a valuable non-proteinogenic amino acid with multiple applications in medical, agricultural, and food industries, using Escherichia coli as a cell factory. We first implemented the Shemin (i.e., C4) pathway for heterologous 5-ALA biosynthesis in E. coli. To reduce, but not to abolish, the carbon flux toward essential tetrapyrrole/porphyrin biosynthesis, we applied clustered regularly interspersed short palindromic repeats interference (CRISPRi) to repress hemB expression, leading to extracellular 5-ALA accumulation. We then applied metabolic engineering strategies to direct more dissimilated carbon flux toward the key precursor of succinyl-CoA for enhanced 5-ALA biosynthesis. Using these engineered E. coli strains for bioreactor cultivation, we successfully demonstrated high-level 5-ALA biosynthesis from glycerol (~30 g L-1 ) under both microaerobic and aerobic conditions, achieving up to 5.95 g L-1 (36.9% of the theoretical maximum yield) and 6.93 g L-1 (50.9% of the theoretical maximum yield) 5-ALA, respectively. This study represents one of the most effective bio-based production of 5-ALA from a structurally unrelated carbon to date, highlighting the importance of integrated strain engineering and bioprocessing strategies to enhance bio-based production.
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Affiliation(s)
- Dragan Miscevic
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Canada
| | - Teshager Kefale
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.,Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Daryoush Abedi
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.,Department of Drug & Food Control, Tehran University of Medical Sciences, Tehran, Iran
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
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Miscevic D, Srirangan K, Kefale T, Kilpatrick S, Chung DA, Moo-Young M, Chou CP. Heterologous production of 3-hydroxyvalerate in engineered Escherichia coli. Metab Eng 2020; 61:141-151. [DOI: 10.1016/j.ymben.2019.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 11/09/2019] [Indexed: 10/25/2022]
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Kittler S, Kopp J, Veelenturf PG, Spadiut O, Delvigne F, Herwig C, Slouka C. The Lazarus Escherichia coli Effect: Recovery of Productivity on Glycerol/Lactose Mixed Feed in Continuous Biomanufacturing. Front Bioeng Biotechnol 2020; 8:993. [PMID: 32903513 PMCID: PMC7438448 DOI: 10.3389/fbioe.2020.00993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
Continuous cultivation with Escherichia coli has several benefits compared to classical fed-batch cultivation. The economic benefits would be a stable process, which leads to time independent quality of the product, and hence ease the downstream process. However, continuous biomanufacturing with E. coli is known to exhibit a drop of productivity after about 4–5 days of cultivation depending on dilution rate. These cultivations are generally performed on glucose, being the favorite carbon source for E. coli and used in combination with isopropyl β-D-1 thiogalactopyranoside (IPTG) for induction. In recent works, harsh induction with IPTG was changed to softer induction using lactose for T7-based plasmids, with the result of reducing the metabolic stress and tunability of productivity. These mixed feed systems based on glucose and lactose result in high amounts of correctly folded protein. In this study we used different mixed feed systems with glucose/lactose and glycerol/lactose to investigate productivity of E. coli based chemostats. We tested different strains producing three model proteins, with the final aim of a stable long-time protein expression. While glucose fed chemostats showed the well-known drop in productivity after a certain process time, glycerol fed cultivations recovered productivity after about 150 h of induction, which corresponds to around 30 generation times. We want to further highlight that the cellular response upon galactose utilization in E. coli BL21(DE3), might be causing fluctuating productivity, as galactose is referred to be a weak inducer. This “Lazarus” phenomenon has not been described in literature before and may enable a stabilization of continuous cultivation with E. coli using different carbon sources.
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Affiliation(s)
- Stefan Kittler
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Patrick Gwen Veelenturf
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech - Université de Liège, Gembloux, Belgium
| | - Christoph Herwig
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Christoph Slouka
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
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Engineering bacteria-seaweed symbioses for modulating the photosynthate content of Ulva (Chlorophyta): Significant for the feedstock of bioethanol production. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101945] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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33
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Szczerba H, Dudziak K, Krawczyk M, Targoński Z. A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. Int J Mol Sci 2020; 21:ijms21144835. [PMID: 32650546 PMCID: PMC7402333 DOI: 10.3390/ijms21144835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022] Open
Abstract
Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.
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Affiliation(s)
- Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
- Correspondence: ; Tel.: +48-81-462-3402
| | - Karolina Dudziak
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland;
| | | | - Zdzisław Targoński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
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Magalhães CP, Ribeiro JA, Guedes AP, Arantes AL, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Co-cultivation of Thermoanaerobacter strains with a methanogenic partner enhances glycerol conversion. Microb Biotechnol 2020; 13:962-973. [PMID: 32154666 PMCID: PMC7264899 DOI: 10.1111/1751-7915.13506] [Citation(s) in RCA: 1] [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: 07/23/2019] [Revised: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 11/30/2022] Open
Abstract
Glycerol-rich waste streams produced by the biodiesel, bioethanol and oleochemical industries can be treated and valorized by anaerobic microbial communities to produce methane. As current knowledge of the microorganisms involved in thermophilic glycerol conversion to methane is scarce, thermophilic glycerol-degrading methanogenic communities were enriched. A co-culture of Thermoanaerobacter and Methanothermobacter species was obtained, pointing to a non-obligately syntrophic glycerol degradation. This hypothesis was further studied by incubating Thermoanaerobacter brockii subsp. finnii and T. wiegelii with glycerol (10 mM) in pure culture and with different hydrogenotrophic methanogens. The presence of the methanogen accelerated glycerol fermentation by the two Thermoanaerobacter strains up to 3.3 mM day-1 , corresponding to 12 times higher volumetric glycerol depletion rates in the methanogenic co-cultures than in the pure bacterial cultures. The catabolic pathways of glycerol conversion were identified by genome analysis of the two Thermoanaerobacter strains. NADH and reduced ferredoxin formed in the pathway are linked to proton reduction, which becomes thermodynamically favourable when the hydrogen partial pressure is kept low by the hydrogenotrophic methanogenic partner.
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Affiliation(s)
| | - Joaquim A. Ribeiro
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Optimizer ‐ Serviços e Consultadoria Informática Lda.PortoPortugal
| | - Ana P. Guedes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Agricultural Superior School of Ponte de LimaPolytechnic Institute of Viana do CasteloViana do CasteloPortugal
| | - Ana L. Arantes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
| | - Diana Z. Sousa
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Alfons J. M. Stams
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Maria M. Alves
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
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Grimalt-Alemany A, Łężyk M, Asimakopoulos K, Skiadas IV, Gavala HN. Cryopreservation and fast recovery of enriched syngas-converting microbial communities. WATER RESEARCH 2020; 177:115747. [PMID: 32283432 DOI: 10.1016/j.watres.2020.115747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Over the last decades, the use of mixed microbial communities has attracted increasing scientific attention due to their potential biotechnological applications in several emerging technological platforms such as the carboxylate, bioplastic, syngas and bio-electrochemical synthesis platforms. However, this increasing interest has not been accompanied by a parallel development of suitable cryopreservation techniques for microbial communities. While cryopreservation methods for the long-term storage of axenic cultures are well established, their effectiveness in preserving the microbial diversity and functionality of microbial communities has rarely been studied. In this study, the effect of the addition of different cryopreservation agents on the long-term storage of microbial communities at -80 °C was studied using a stable enrichment culture converting syngas into acetate and ethanol. The cryopreservation agents considered in the study were glycerol, dimethylsulfoxide, polyvinylpyrrolidone, Tween 80 and yeast extract, as well as with no addition of cryopreservation agent. Their effectiveness was evaluated based on the microbial activity recovery and the maintenance of the microbial diversity and community structure upon revival of the microbial community. The results showed that the commonly used glycerol and no addition of cryopreservation agent were the least recommendable methods for the long-term frozen storage of microbial communities, while Tween 80 and polyvinylpyrrolidone were overall the most effective. Among the cryoprotectants studied, polyvinylpyrrolidone and especially Tween 80 were the only ones assuring reproducible results in terms of microbial activity recovery and microbial community structure preservation.
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Affiliation(s)
- Antonio Grimalt-Alemany
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Mateusz Łężyk
- Institute of Environmental Engineering and Building Installations, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Konstantinos Asimakopoulos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Ioannis V Skiadas
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Hariklia N Gavala
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark.
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Kubannek F, Thiel S, Bunk B, Huber K, Overmann J, Krewer U, Biedendieck R, Jahn D. Performance Modelling of the Bioelectrochemical Glycerol Oxidation by a Co‐Culture of
Geobacter Sulfurreducens
and
Raoultella Electrica. ChemElectroChem 2020. [DOI: 10.1002/celc.202000027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fabian Kubannek
- Institute of Energy and Process Systems EngineeringTechnische Universität Braunschweig Franz-Liszt-Straße 35 38106 Braunschweig Germany
| | - Simone Thiel
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Katharina Huber
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of MicroorganismsCell Cultures GmbH Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Ulrike Krewer
- Institute of Energy and Process Systems EngineeringTechnische Universität Braunschweig Franz-Liszt-Straße 35 38106 Braunschweig Germany
| | - Rebekka Biedendieck
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
| | - Dieter Jahn
- Institute of Microbiology Braunschweig Integrated Centre of Systems Biology (BRICS)Technische Universität Braunschweig Rebenring 56 38106 Braunschweig Germany
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Integrated strain engineering and bioprocessing strategies for high-level bio-based production of 3-hydroxyvalerate in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:5259-5272. [PMID: 32291486 DOI: 10.1007/s00253-020-10580-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022]
Abstract
As petro-based production generates numerous environmental impacts and their associated technological concerns, bio-based production has been well recognized these days as a modern alternative to manufacture chemical products in a more renewable, environmentally friendly, and sustainable manner. Herein, we report the development of a microbial bioprocess for high-level and potentially economical production of 3-hydroxyvalerate (3-HV), a valuable special chemical with multiple applications in chemical, biopolymer, and pharmaceutical industries, from glycerol, which can be cheaply and renewably refined as a byproduct from biodiesel production. We used our recently derived 3-HV-producing Escherichia coli strains for bioreactor characterization under various culture conditions. In the parental strain, 3-HV biosynthesis was limited by the intracellular availability of propionyl-CoA, whose formation was favored by anaerobic conditions, which often compromised cell growth. With appropriate strain engineering, we demonstrated that 3-HV can be effectively produced under both microaerobic (close to anaerobic) and aerobic conditions, which determine the direction of dissimilated carbon flux toward the succinate node in the tricarboxylic acid (TCA) cycle. We first used the ∆sdhA single mutant strain, in which the dissimilated carbon flux was primarily directed to the Sleeping beauty mutase (Sbm) pathway (via the reductive TCA branch, with enhanced cell growth under microaerobic conditions, achieving 3.08 g L-1 3-HV in a fed-batch culture. In addition, we used the ∆sdhA-∆iclR double mutant strain, in which the dissimilated carbon flux was directed from the TCA cycle to the Sbm pathway via the deregulated glyoxylate shunt, for cultivation under rather aerobic conditions. In addition to demonstrating effective cell growth, this strain has shown impressive 3-HV biosynthesis (up to 10.6 g L-1), equivalent to an overall yield of 18.8% based on consumed glycerol, in aerobic fed-batch culture. This study not only represents one of the most effective bio-based production of 3-HV from structurally unrelated carbons to date, but also highlights the importance of integrated strain engineering and bioprocessing strategies to enhance bio-based production.Key points• TCA cycle engineering was applied to enhance 3-HV biosynthesis in E. coli. • Effects of oxygenic conditions on 3-HV in E. coli biosynthesis were investigated. • Bioreactor characterization of 3-HV biosynthesis in E. coli was performed.
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Behera P, Nikhil KC, Kumar A, Gali JM, De A, Mohanty AK, Ali MA, Sharma B. Comparative proteomic analysis of Salmonella Typhimurium wild type and its isogenic fnr null mutant during anaerobiosis reveals new insight into bacterial metabolism and virulence. Microb Pathog 2019; 140:103936. [PMID: 31862389 DOI: 10.1016/j.micpath.2019.103936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 11/19/2022]
Abstract
AIM The aim of this study was to understand the role of anaerobic regulator FNR (Fumarate Nitrate Reduction) in Salmonella Typhimurium through proteomic approach. METHODS AND RESULTS We did label free quantitative proteomic analysis of Salmonella Typhimurium PM45 wild type and the fnr null mutant cultured under anaerobic conditions. The data revealed 153 significantly differentially expressed proteins (DEPs) in the mutant out of 1798 total proteins identified. Out of 153 DEPs, 94 proteins were up-regulated (repressed by FNR) and 59 proteins were down-regulated (activated by FNR) in the mutant. The network analysis indicated up-regulation of TCA cycle, electron transport chain and ethanolamine metabolism and down regulation of pyruvate metabolism and glycerol and glycerophospholipid metabolism. CONCLUSIONS Our study showed that FNR represses ethanolamine utilization. The different metabolic pathways such as pyruvate metabolism, glycerol metabolism and glycerophospholipid metabolism were activated by FNR. Further, FNR positively regulated the DNA binding protein Fis, one of the global regulators of virulence in Salmonella Typhimurium. Thus, our finding highlights the pivotal role of FNR in regulating bacterial metabolism and virulence during anaerobiosis for systemic infection of the host.
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Affiliation(s)
- Parthasarathi Behera
- Department of Veterinary Physiology & Biochemistry, College of Veterinary Sciences & A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, 796014, India.
| | - K C Nikhil
- Division of Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Ajay Kumar
- Division of Animal Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Jagan Mohanarao Gali
- Department of Veterinary Physiology & Biochemistry, College of Veterinary Sciences & A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, 796014, India
| | - A De
- Department of Veterinary Physiology & Biochemistry, College of Veterinary Sciences & A.H., R. K. Nagar, West Tripura, Tripura, 799008, India
| | - A K Mohanty
- Proteomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - M Ayub Ali
- Department of Veterinary Physiology & Biochemistry, College of Veterinary Sciences & A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, 796014, India
| | - Bhaskar Sharma
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
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Aßkamp MR, Klein M, Nevoigt E. Involvement of the external mitochondrial NADH dehydrogenase Nde1 in glycerol metabolism by wild-type and engineered Saccharomyces cerevisiae strains. FEMS Yeast Res 2019; 19:5420478. [PMID: 30915433 DOI: 10.1093/femsyr/foz026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/20/2019] [Indexed: 12/17/2022] Open
Abstract
Glycerol is an attractive substrate for microbial fermentations due to its higher degree of reduction compared to glucose. The replacement of the native FAD-dependent glycerol catabolic pathway in Saccharomyces cerevisiae by an artificial NADH-delivering dihydroxyacetone (DHA) pathway is supposed to facilitate the capturing of electrons in fermentation products. This requires that the electrons from the cytosolic NADH are not exclusively transferred to oxygen. However, the external NADH dehydrogenases (Nde1/2) and the L-glycerol 3-phosphate shuttle (composed of Gpd1/2 and Gut2), both coupled to the respiratory chain, are known to contribute to cytosolic NAD+ regeneration during growth on non-fermentable carbon sources. In order to evaluate the role of these mechanisms during growth on glycerol, we deleted GPD1/2, GUT2 as well as NDE1/2, separately and in combinations in both the glycerol-utilizing wild-type strain CBS 6412-13A and the corresponding engineered strain CBS DHA in which glycerol is catabolized by the DHA pathway. Particularly, the nde1Δ mutants showed a significant reduction in growth rate and the nde1∆ nde2∆ double deletion mutants did not grow at all in synthetic glycerol medium. The current work also demonstrates a positive impact of deleting NDE1 on the production of the fermentation product 1,2-propanediol in an accordingly engineered S. cerevisiae strain.
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Affiliation(s)
- Maximilian R Aßkamp
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Biodiesel’s trash is a biorefineries’ treasure: the use of “dirty” glycerol as an industrial fermentation substrate. World J Microbiol Biotechnol 2019; 36:2. [DOI: 10.1007/s11274-019-2776-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/22/2019] [Indexed: 10/25/2022]
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Valle A, Cantero D, Bolívar J. Metabolic engineering for the optimization of hydrogen production in Escherichia coli: A review. Biotechnol Adv 2019; 37:616-633. [DOI: 10.1016/j.biotechadv.2019.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/29/2022]
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Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP. Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 2019; 37:538-568. [DOI: 10.1016/j.biotechadv.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
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Lenzen C, Wynands B, Otto M, Bolzenius J, Mennicken P, Blank LM, Wierckx N. High-Yield Production of 4-Hydroxybenzoate From Glucose or Glycerol by an Engineered Pseudomonas taiwanensis VLB120. Front Bioeng Biotechnol 2019; 7:130. [PMID: 31245364 PMCID: PMC6581684 DOI: 10.3389/fbioe.2019.00130] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/14/2019] [Indexed: 12/19/2022] Open
Abstract
Aromatic compounds such as 4-hydroxybenzoic acid are broadly applied in industry for a myriad of applications used in everyday life. However, their industrial production currently relies heavily on fossil resources and involves environmentally unfriendly production conditions, thus creating the need for more sustainable biotechnological alternatives. In this study, synthetic biology was applied to metabolically engineer Pseudomonas taiwanensis VLB120 to produce 4-hydroxybenzoate from glucose, xylose, or glycerol as sole carbon sources. Genes encoding a 4-hydroxybenzoate production pathway were integrated into the host genome and the flux toward the central precursor tyrosine was enhanced by overexpressing genes encoding key enzymes of the shikimate pathway. The flux toward tryptophan biosynthesis was decreased by introducing a P290S point mutation in the trpE gene, and degradation pathways for 4-hydroxybenzoate, 4-hydroxyphenylpyruvate and 3-dehydroshikimate were knocked out. The resulting production strains were tailored for the utilization of glucose and glycerol through the rational modification of central carbon metabolism. In batch cultivations with a completely mineral medium, the best strain produced 1.37 mM 4-hydroxybenzoate from xylose with a C-mol yield of 8% and 3.3 mM from glucose with a C-mol yield of 19.0%. Using glycerol as a sole carbon source, the C-mol yield increased to 29.6%. To our knowledge, this is the highest yield achieved by any species in a fully mineral medium. In all, the efficient conversion of bio-based substrates into 4-hydroxybenzoate by these deeply engineered P. taiwanensis strains brings the renewable production of aromatics one step closer.
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Affiliation(s)
- Christoph Lenzen
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Benedikt Wynands
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Maike Otto
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Johanna Bolzenius
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Philip Mennicken
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
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Glycerol metabolism and its regulation in lactic acid bacteria. Appl Microbiol Biotechnol 2019; 103:5079-5093. [DOI: 10.1007/s00253-019-09830-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 01/09/2023]
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Yan Q, Robert S, Brooks JP, Fong SS. Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. BMC Bioinformatics 2019; 20:227. [PMID: 31060515 PMCID: PMC6501404 DOI: 10.1186/s12859-019-2826-1] [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: 04/08/2019] [Accepted: 04/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications. Results In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle. Conclusions Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens. Electronic supplementary material The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA.
| | - Seth Robert
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA
| | - J Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA, 23284, USA.,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Stephen S Fong
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, West Hall, Room 422, 601 West Main Street, P.O. Box 843028, Richmond, VA, 23284-3028, USA. .,Center for the study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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Li Y, Qiu Y, Zhang X, Zhu M, Tan W. Strain screening and optimization of biohydrogen production by Enterobacter aerogenes EB-06 from glycerol fermentation. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0250-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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Formate-removing inoculum dominated by Methanobacterium congolense supports succinate production from crude glycerol fermentation. J Ind Microbiol Biotechnol 2019; 46:625-634. [PMID: 30783892 DOI: 10.1007/s10295-019-02154-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
Abstract
We developed a formate-removing methanogenic inoculum (FRI) to facilitate succinate production from crude glycerol by Escherichia coli. FRI converted formate to methane, thereby enabling glycerol fermentation without additional electron acceptors under neutral pH. FRI was selectively enriched from sludge from the anaerobic digester of the Seonam sewage treatment plant (Seoul); this process was assessed via Illumina sequencing and scanning electron microscopy imaging. Methanobacterium congolense species occupied only 0.3% of the archaea community in the sludge and was enriched to 99.5% in complete FRI, wherein succinate-degrading bacteria were successfully eliminated. Co-culture with FRI improved glycerol fermentation and yielded 7.3 mM succinate from 28.7 mM crude glycerol, whereby FRI completely converted formate into methane. This study is the first to demonstrate methane production by M. congolense species, using formate. M. congolense-dominated FRI can serve as a renewable facilitator of waste feedstock fermentation and enable the production of commercially important compounds.
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Wang XL, Zhou JJ, Sun YQ, Xiu ZL. Bioconversion of Raw Glycerol From Waste Cooking-Oil-Based Biodiesel Production to 1,3-Propanediol and Lactate by a Microbial Consortium. Front Bioeng Biotechnol 2019; 7:14. [PMID: 30834245 PMCID: PMC6387908 DOI: 10.3389/fbioe.2019.00014] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/18/2019] [Indexed: 01/04/2023] Open
Abstract
Waste cooking oil (WCO) is a sustainable alternative to raw vegetable oils and fats for biodiesel production considering both environmental and economic benefits. Raw glycerol from WCO-based biodiesel production (GWCO) is difficult to utilize via biological method, as multiple toxic impurities have inhibitory effects on microbial growth especially for pure cultures. In this work, four microbial consortia were selected from activated sludge by 30 serial transfers under different conditions. The obtained consortia exhibited lower diversity and species difference with the transfers. The consortium LS30 exhibited unique advantages for bioconversion of GWCO to 1,3-propanediol (1,3-PDO) and lactate (LA). Moreover, the fermentation could be performed economically under microaerobic and non-sterile conditions. The consortium consisted of 57.97% Enterobacter and 39.25% Escherichia could effectively convert 60 g/L GWCO to 1,3-PDO and LA in batch fermentation. In addition, this consortium exhibited better tolerance to fatty acid-derived crude glycerol (100 g/L), which demonstrated that specific toxic impurities in GWCO did pose a great challenge to microbial growth and metabolism. In fed batch fermentation, 27.77 g/L 1,3-PDO and 14.68 g/L LA were achieved. Compared with the consortium, a long lag phase in cell growth associated with a decreased glycerol consumption was observed in four single-strain fermentations. Furthermore, neither the consortium DL38 with excellent glycerol tolerance nor consortium C2-2M with high yield of 1,3-PDO could effectively transform GWCO into valuable products. The results demonstrated that the selected microbial consortium has the advanced adaptability to the toxic impurities in GWCO compared with other reported consortia and isolated single strain. This process can contribute to added-value use of GWCO.
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Affiliation(s)
| | | | | | - Zhi-Long Xiu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
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Slouka C, Kopp J, Spadiut O, Herwig C. Perspectives of inclusion bodies for bio-based products: curse or blessing? Appl Microbiol Biotechnol 2019; 103:1143-1153. [PMID: 30569219 PMCID: PMC6394472 DOI: 10.1007/s00253-018-9569-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022]
Abstract
The bacterium Escherichia coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant protein can be located intracellularly, which often leads to protein aggregates inside of the cytoplasm, forming so the called inclusion bodies (IBs). When compared to other protein expression strategies, inclusion body formation allows high product titers and also the possibility of expressing proteins being toxic for the host. In the past years, the comprehension of inclusion bodies being only inactive protein aggregates changed, and the new term of non-classical inclusion bodies emerged. These inclusion bodies are believed to contain a reasonable amount of active protein within their structure. However, subsequent downstream processing, such as homogenisation of cells, centrifugation or solubilisation of IBs, is prone to variable process performance and is often known to result in low extraction yields. It is hypothesised that variations in IB quality attributes are responsible for those effects and that such attributes can be controlled by upstream process conditions. In this review, we address the impact of process design (process parameters) in the upstream on defined inclusion body quality attributes. The following topics are therefore addressed: (i) an overview of the range of inclusion body applications (including emerging technologies); (ii) analytical methods to determine quality attributes; and (iii) screws in process engineering to achieve the desired quality attributes for different inclusion body-based applications. Process parameters in the upstream can be used to trigger different quality attributes including protein activity, but are not exploited to a satisfying content yet. Design by quality approaches in the upstream are already considered for a multitude of existing processes. Further intensifying this approach may pave the industrial application for new IB-based products and improves IB processing, as discussed within this review.
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Affiliation(s)
- Christoph Slouka
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria.
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria.
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