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Laux M, Ciapina LP, de Carvalho FM, Gerber AL, Guimarães APC, Apolinário M, Paes JES, Jonck CR, de Vasconcelos ATR. Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome. BMC Microbiol 2024; 24:228. [PMID: 38943070 PMCID: PMC11212195 DOI: 10.1186/s12866-024-03390-6] [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: 12/22/2023] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove. RESULTS Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified. CONCLUSION The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.
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Affiliation(s)
- Marcele Laux
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Luciane Prioli Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil.
| | - Fabíola Marques de Carvalho
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Ana Paula C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Moacir Apolinário
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Jorge Eduardo Santos Paes
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Célio Roberto Jonck
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
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Brito HA, Napp AP, Pereira E, Bach E, Borowski JVB, Passaglia LMP, Melo VMM, Moreira R, Foster EJ, Lopes FC, Vainstein MH. Enhanced low-cost lipopeptide biosurfactant production by Bacillus velezensis from residual glycerin. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03051-y. [PMID: 38916653 DOI: 10.1007/s00449-024-03051-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Biosurfactants (BSFs) are molecules produced by microorganisms from various carbon sources, with applications in bioremediation and petroleum recovery. However, the production cost limits large-scale applications. This study optimized BSFs production by Bacillus velezensis (strain MO13) using residual glycerin as a substrate. The spherical quadratic central composite design (CCD) model was used to standardize carbon source concentration (30 g/L), temperature (34 °C), pH (7.2), stirring (239 rpm), and aeration (0.775 vvm) in a 5-L bioreactor. Maximum BSFs production reached 1527.6 mg/L of surfactins and 176.88 mg/L of iturins, a threefold increase through optimization. Microbial development, substrate consumption, concentration of BSFs, and surface tension were also evaluated on the bioprocess dynamics. Mass spectrometry Q-TOF-MS identified five surfactin and two iturin isoforms produced by B. velezensis MO13. This study demonstrates significant progress on BSF production using industrial waste as a microbial substrate, surpassing reported concentrations in the literature.
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Affiliation(s)
- Henrique A Brito
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Amanda P Napp
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Evandro Pereira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Evelise Bach
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - João V B Borowski
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Luciane M P Passaglia
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Vania M M Melo
- Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal Do Ceará, Fortaleza, Brasil
| | - Raphael Moreira
- Institute for Applied and Physical Chemistry, University of Bremen, 28359, Bremen, Germany
| | - E Johan Foster
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, Canada
| | - Fernanda C Lopes
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
- Departamento de Biofísica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Marilene H Vainstein
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil.
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil.
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Xu Z, Zhu X, Mohsin A, Guo J, Zhuang Y, Chu J, Guo M, Wang G. A machine learning-based approach for improving plasmid DNA production in Escherichia coli fed-batch fermentations. Biotechnol J 2024; 19:e2400140. [PMID: 38896410 DOI: 10.1002/biot.202400140] [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: 03/07/2024] [Revised: 04/29/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Artificial Intelligence (AI) technology is spearheading a new industrial revolution, which provides ample opportunities for the transformational development of traditional fermentation processes. During plasmid fermentation, traditional subjective process control leads to highly unstable plasmid yields. In this study, a multi-parameter correlation analysis was first performed to discover a dynamic metabolic balance among the oxygen uptake rate, temperature, and plasmid yield, whilst revealing the heating rate and timing as the most important optimization factor for balanced cell growth and plasmid production. Then, based on the acquired on-line parameters as well as outputs of kinetic models constructed for describing process dynamics of biomass concentration, plasmid yield, and substrate concentration, a machine learning (ML) model with Random Forest (RF) as the best machine learning algorithm was established to predict the optimal heating strategy. Finally, the highest plasmid yield and specific productivity of 1167.74 mg L-1 and 8.87 mg L-1/OD600 were achieved with the optimal heating strategy predicted by the RF model in the 50 L bioreactor, respectively, which was 71% and 21% higher than those obtained in the control cultures where a traditional one-step temperature upshift strategy was applied. In addition, this study transformed empirical fermentation process optimization into a more efficient and rational self-optimization method. The methodology employed in this study is equally applicable to predict the regulation of process dynamics for other products, thereby facilitating the potential for furthering the intelligent automation of fermentation processes.
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Affiliation(s)
- Zhixian Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Xiaofeng Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Jianfei Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
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Mittra D, Mahalik S. Improving the production of recombinant L-Asparaginase-II in Escherichia coli by co-expressing catabolite repressor activator ( cra) gene. Prep Biochem Biotechnol 2024; 54:709-719. [PMID: 38692288 DOI: 10.1080/10826068.2023.2279097] [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: 05/03/2024]
Abstract
Identification of a single genetic target for microbial strain improvement is difficult due to the complexity of the genetic regulatory network. Hence, a more practical approach is to identify bottlenecks in the regulatory networks that control critical metabolic pathways. The present work focuses on enhancing cellular physiology by increasing the metabolic flux through the central carbon metabolic pathway. Global regulator cra (catabolite repressor activator), a DNA-binding transcriptional dual regulator was selected for the study as it controls the expression of a large number of operons that modulate central carbon metabolism. To upregulate the activity of central carbon metabolism, the cra gene was co-expressed using a plasmid-based system. Co-expression of cra led to a 17% increase in the production of model recombinant protein L-Asparaginase-II. A pulse addition of 0.36% of glycerol every two hours post-induction, further increased the production of L-Asparaginase-II by 35% as compared to the control strain expressing only recombinant protein. This work exemplifies that upregulating the activity of central carbon metabolism by tuning the expression of regulatory genes like cra can relieve the host from cellular stress and thereby promote the growth as well as expression of recombinant hosts.
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Affiliation(s)
- Debashrita Mittra
- Post Graduate Department of Biosciences & Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, India
| | - Shubhashree Mahalik
- Post Graduate Department of Biosciences & Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, India
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Pause L, Weimer A, Wirth NT, Nguyen AV, Lenz C, Kohlstedt M, Wittmann C, Nikel PI, Lai B, Krömer JO. Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system. Microb Biotechnol 2024; 17:e14375. [PMID: 37990843 PMCID: PMC10832537 DOI: 10.1111/1751-7915.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Providing an anodic potential in a bio-electrochemical system to the obligate aerobe Pseudomonas putida enables anaerobic survival and allows the cells to overcome redox imbalances. In this setup, the bacteria could be exploited to produce chemicals via oxidative pathways at high yield. However, the absence of anaerobic growth and low carbon turnover rates remain as obstacles for the application of such an electro-fermentation technology. Growth and carbon turnover start with carbon uptake into the periplasm and cytosol. P. putida KT2440 has three native transporting systems for glucose, each differing in energy and redox demand. This architecture previously led to the hypothesis that internal redox and energy constraints ultimately limit cytoplasmic carbon utilization in a bio-electrochemical system. However, it remains largely unclear which uptake route is predominantly used by P. putida under electro-fermentative conditions. To elucidate this, we created three gene deletion mutants of P. putida KT2440, forcing the cells to exclusively utilize one of the routes. When grown in a bio-electrochemical system, the pathway mutants were heavily affected in terms of sugar consumption, current output and product formation. Surprisingly, however, we found that about half of the acetate formed in the cytoplasm originated from carbon that was put into the system via the inoculation biomass, while the other half came from the consumption of substrate. The deletion of individual sugar uptake routes did not alter significantly the secreted acetate concentrations among different strains even with different carbon sources. This means that the stoichiometry of the sugar uptake routes is not a limiting factor during electro-fermentation and that the low rates might be caused by other reasons, for example energy limitations or a yet-to-be-identified oxygen-dependent regulatory mechanism.
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Affiliation(s)
- Laura Pause
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Anna Weimer
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Nicolas T. Wirth
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Anh Vu Nguyen
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Claudius Lenz
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | | | - Pablo I. Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Bin Lai
- BMBF Junior Research Group BiophotovoltaicsHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Jens O. Krömer
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
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Asin-Garcia E, Garcia-Morales L, Bartholet T, Liang Z, Isaacs F, Martins dos Santos VP. Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species. Nucleic Acids Res 2023; 51:12522-12536. [PMID: 37941137 PMCID: PMC10711431 DOI: 10.1093/nar/gkad1024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 10/14/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
The widespread Pseudomonas genus comprises a collection of related species with remarkable abilities to degrade plastics and polluted wastes and to produce a broad set of valuable compounds, ranging from bulk chemicals to pharmaceuticals. Pseudomonas possess characteristics of tolerance and stress resistance making them valuable hosts for industrial and environmental biotechnology. However, efficient and high-throughput genetic engineering tools have limited metabolic engineering efforts and applications. To improve their genome editing capabilities, we first employed a computational biology workflow to generate a genus-specific library of potential single-stranded DNA-annealing proteins (SSAPs). Assessment of the library was performed in different Pseudomonas using a high-throughput pooled recombinase screen followed by Oxford Nanopore NGS analysis. Among different active variants with variable levels of allelic replacement frequency (ARF), efficient SSAPs were found and characterized for mediating recombineering in the four tested species. New variants yielded higher ARFs than existing ones in Pseudomonas putida and Pseudomonas aeruginosa, and expanded the field of recombineering in Pseudomonas taiwanensisand Pseudomonas fluorescens. These findings will enhance the mutagenesis capabilities of these members of the Pseudomonas genus, increasing the possibilities for biotransformation and enhancing their potential for synthetic biology applications. .
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
| | - Luis Garcia-Morales
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Tessa Bartholet
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Zhuobin Liang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Vitor A P Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen 6700 AA, The Netherlands
- LifeGlimmer GmbH, Berlin 12163, Germany
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Tong Y, Li Y, Qin W, Wu S, Xu W, Jin P, Zheng Z. New insight into the metabolic mechanism of a novel lipid-utilizing and denitrifying bacterium capable of simultaneous removal of nitrogen and grease through transcriptome analysis. Front Microbiol 2023; 14:1258003. [PMID: 37965562 PMCID: PMC10642853 DOI: 10.3389/fmicb.2023.1258003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction Issues related to fat, oil, and grease from kitchen waste (KFOG) in lipid-containing wastewater are intensifying globally. We reported a novel denitrifying bacterium Pseudomonas CYCN-C with lipid-utilizing activity and high nitrogen-removal efficiency. The aim of the present study was aim to explore the metabolic mechanism of the simultaneous lipid-utilizing and denitrifying bacterium CYCN-C at transcriptome level. Methods We comparatively investigated the cell-growth and nitrogen-removal performances of newly reported Pseudomonas glycinae CYCN-C under defined cultivation conditions. Transcriptome analysis was further used to investigate all pathway genes involved in nitrogen metabolism, lipid degradation and utilization, and cell growth at mRNA levels. Results CYCN-C could directly use fat, oil, and grease from kitchen waste (KFOG) as carbon source with TN removal efficiency of 73.5%, significantly higher than that (60.9%) with sodium acetate. The change levels of genes under defined KFOG and sodium acetate were analyzed by transcriptome sequencing. Results showed that genes cyo, CsrA, PHAs, and FumC involved in carbon metabolism under KFOG were significantly upregulated by 6.9, 0.7, 26.0, and 19.0-folds, respectively. The genes lipA, lipB, glpD, and glpK of lipid metabolic pathway were upregulated by 0.6, 0.4, 21.5, and 1.3-folds, respectively. KFOG also improved the denitrification efficiency by inducing the expression of the genes nar, nirB, nirD, and norR of denitrification pathways. Conclusion In summary, this work firstly provides valuable insights into the genes expression of lipid-utilizing and denitrifying bacterium, and provides a new approach for sewage treatment with reuse of KFOG wastes.
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Affiliation(s)
- Yaobin Tong
- School of Environmental & Resource, Zhejiang A & F University, Hangzhou, China
| | - Yiyi Li
- Zhejiang Sunda Public Environmental Protection Co., Ltd., Hangzhou, China
| | - Wenpan Qin
- Zhejiang Sunda Public Environmental Protection Co., Ltd., Hangzhou, China
| | - Shengchun Wu
- School of Environmental & Resource, Zhejiang A & F University, Hangzhou, China
- Zhejiang Sunda Public Environmental Protection Co., Ltd., Hangzhou, China
| | - Weiping Xu
- Zhejiang Sunda Public Environmental Protection Co., Ltd., Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang A & F University, Hangzhou, China
| | - Zhanwang Zheng
- School of Environmental & Resource, Zhejiang A & F University, Hangzhou, China
- Zhejiang Sunda Public Environmental Protection Co., Ltd., Hangzhou, China
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Ciurko D, Chebbi A, Kruszelnicki M, Czapor-Irzabek H, Urbanek AK, Polowczyk I, Franzetti A, Janek T. Production and characterization of lipopeptide biosurfactant from a new strain of Pseudomonas antarctica 28E using crude glycerol as a carbon source. RSC Adv 2023; 13:24129-24139. [PMID: 37577095 PMCID: PMC10415746 DOI: 10.1039/d3ra03408a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023] Open
Abstract
Pseudomonas is a cosmopolitan genus of bacteria found in soil, water, organic matter, plants and animals and known for the production of glycolipid and lipopeptide biosurfactants. In this study bacteria (laboratory collection number 28E) isolated from soil collected in Spitsbergen were used for biosurfactant production. 16S rRNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) revealed that this isolate belongs to the species Pseudomonas antarctica. In the present study, crude glycerol, a raw material obtained from several industrial processes, was evaluated as a potential low-cost carbon source to reduce the costs of lipopeptide production. Among several tested glycerols, a waste product of stearin production, rich in nitrogen, iron and calcium, ensured optimal conditions for bacterial growth. Biosurfactant production was evidenced by a reduction of surface tension (ST) and an increase in the emulsification index (E24%). According to Fourier-transform infrared spectroscopy (FTIR) and electrospray ionization mass spectrometry (ESI-MS), the biosurfactant was identified as viscosin. The critical micelle concentration (CMC) of lipopeptide was determined to be 20 mg L-1. Interestingly, viscosin production has been reported previously for Pseudomonas viscosa, Pseudomonas fluorescens and Pseudomonas libanensis. To the best of our knowledge, this is the first report on viscosin production by a P. antarctica 28E. The results indicated the potential of crude glycerol as a low-cost substrate to produce a lipopeptide biosurfactant with promising tensioactive and emulsifying properties.
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Affiliation(s)
- Dominika Ciurko
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences 51-630 Wrocław Poland +48-71-320-7734
| | - Alif Chebbi
- Department of Science, Roma Tre University 00146 Rome Italy
| | - Mateusz Kruszelnicki
- Department of Process Engineering and Technology of Polymers and Carbon Materials, Wroclaw University of Science and Technology 50-370 Wrocław Poland
| | - Hanna Czapor-Irzabek
- Laboratory of Elemental Analysis and Structural Research, Wroclaw Medical University 50-556 Wroclaw Poland
| | - Aneta K Urbanek
- Faculty of Biotechnology, University of Wroclaw 50-383 Wroclaw Poland
| | - Izabela Polowczyk
- Department of Process Engineering and Technology of Polymers and Carbon Materials, Wroclaw University of Science and Technology 50-370 Wrocław Poland
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences - DISAT, University of Milano-Bicocca 20126 Milano Italy
| | - Tomasz Janek
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences 51-630 Wrocław Poland +48-71-320-7734
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Tang Y, Shi Y, Jia B, Zhang Y, Wang Q. Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa. Biochem Biophys Res Commun 2023; 645:30-39. [PMID: 36680934 DOI: 10.1016/j.bbrc.2022.12.060] [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: 12/02/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium capable of widespread niches, which is also one of the main bacteria that cause patient infection. The metabolic diversity of Pseudomonas aeruginosa is an essential factor in adapting to a variety of environments. Based on the previous studies, adaptive genetic variation in the glycerol kinase GlpK, the glycerol 3-phosphotransferase, contributes to the fitness of bacteria in human bodies, such as Mycobacterium tuberculosis and Escherichia coli. Thus, this study aimed to explore the molecular evolution and function of glpK in P. aeruginosa. Using extensive population genomic data, we have identified the prevalence of two glpK copies in P. aeruginosa that clustered into distinct branches, which were later known as Clade 1 and 2. The evolution analysis revealed that glpK in Clade 1 derived from an ancestral P. aeruginosa species and the other from an ancient horizontal gene transfer event. In addition, we confirmed that the GlpK in Clade 2 still retained glycerol kinase activity but was much weaker than that of GlpK in Clade 1. We demonstrated the importance of the critical amino acid Q70 in GlpK glycerol kinase activity by point mutation. Furthermore, Co-expression network analysis implied that the two glpK copies of P. aeruginosa regulate separate networks and may be a strategy to improve fitness in P. aeruginosa.
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Affiliation(s)
- Yao Tang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yuqi Shi
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Boshuang Jia
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yunhua Zhang
- School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, 230000, China.
| | - Qiang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
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Ziegler AL, Grütering C, Poduschnick L, Mitsos A, Blank LM. Co-feeding enhances the yield of methyl ketones. J Ind Microbiol Biotechnol 2023; 50:kuad029. [PMID: 37704397 PMCID: PMC10521942 DOI: 10.1093/jimb/kuad029] [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: 04/12/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
The biotechnological production of methyl ketones is a sustainable alternative to fossil-derived chemical production. To date, the best host for microbial production of methyl ketones is a genetically engineered Pseudomonas taiwanensis VLB120 ∆6 pProd strain, achieving yields of 101 mgg-1 on glucose in batch cultivations. For competitiveness with the petrochemical production pathway, however, higher yields are necessary. Co-feeding can improve the yield by fitting the carbon-to-energy ratio to the organism and the target product. In this work, we developed co-feeding strategies for P. taiwanensis VLB120 ∆6 pProd by combined metabolic modeling and experimental work. In a first step, we conducted flux balance analysis with an expanded genome-scale metabolic model of iJN1463 and found ethanol as the most promising among five cosubstrates. Next, we performed cultivations with ethanol and found the highest reported yield in batch production of methyl ketones with P. taiwanensis VLB120 to date, namely, 154 mg g-1 methyl ketones. However, ethanol is toxic to the cell, which reflects in a lower substrate consumption and lower product concentrations when compared to production on glucose. Hence, we propose cofeeding ethanol with glucose and find that, indeed, higher concentrations than in ethanol-fed cultivation (0.84 g Laq-1 with glucose and ethanol as opposed to 0.48 g Laq-1 with only ethanol) were achieved, with a yield of 85 mg g-1. In a last step, comparing experimental with computational results suggested the potential for improving the methyl ketone yield by fed-batch cultivation, in which cell growth and methyl ketone production are separated into two phases employing optimal ethanol to glucose ratios. ONE-SENTENCE SUMMARY By combining computational and experimental work, we demonstrate that feeding ethanol in addition to glucose improves the yield of biotechnologically produced methyl ketones.
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Affiliation(s)
- Anita L Ziegler
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Carolin Grütering
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Leon Poduschnick
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Mitsos
- JARA-ENERGY, 52056 Aachen, Germany
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
- Institute of Energy and Climate Research: Energy Systems Engineering (IEK-10), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
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11
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Metabolic Mechanism and Physiological Role of Glycerol 3-Phosphate in Pseudomonas aeruginosa PAO1. mBio 2022; 13:e0262422. [PMID: 36218368 PMCID: PMC9765544 DOI: 10.1128/mbio.02624-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen that is lethal to cystic fibrosis (CF) patients. Glycerol generated during the degradation of phosphatidylcholine, the major lung surfactant in CF patients, could be utilized by P. aeruginosa. Previous studies have indicated that metabolism of glycerol by this bacterium contributes to its adaptation to and persistence in the CF lung environment. Here, we investigated the metabolic mechanisms of glycerol and its important metabolic intermediate glycerol 3-phosphate (G3P) in P. aeruginosa PAO1. We found that G3P homeostasis plays an important role in the growth and virulence factor production of P. aeruginosa PAO1. The G3P accumulation caused by the mutation of G3P dehydrogenase (GlpD) and exogenous glycerol led to impaired growth and reductions in pyocyanin synthesis, motilities, tolerance to oxidative stress, and resistance to kanamycin. Transcriptomic analysis indicates that the growth retardation caused by G3P stress is associated with reduced glycolysis and adenosine triphosphate (ATP) generation. Furthermore, two haloacid dehalogenase-like phosphatases (PA0562 and PA3172) that play roles in the dephosphorylation of G3P in strain PAO1 were identified, and their enzymatic properties were characterized. Our findings reveal the importance of G3P homeostasis and indicate that GlpD, the key enzyme for G3P catabolism, is a potential therapeutic target for the prevention and treatment of infections by this pathogen. IMPORTANCE In view of the intrinsic resistance of Pseudomonas aeruginosa to antibiotics and its potential to acquire resistance to current antibiotics, there is an urgent need to develop novel therapeutic options for the treatment of infections caused by this bacterium. Bacterial metabolic pathways have recently become a focus of interest as potential targets for the development of new antibiotics. In this study, we describe the mechanism of glycerol utilization in P. aeruginosa PAO1, which is an available carbon source in the lung environment. Our results reveal that the homeostasis of glycerol 3-phosphate (G3P), a pivotal intermediate in glycerol catabolism, is important for the growth and virulence factor production of P. aeruginosa PAO1. The mutation of G3P dehydrogenase (GlpD) and the addition of glycerol were found to reduce the tolerance of P. aeruginosa PAO1 to oxidative stress and to kanamycin. The findings highlight the importance of G3P homeostasis and suggest that GlpD is a potential drug target for the treatment of P. aeruginosa infections.
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12
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Duque E, Udaondo Z, Molina L, de la Torre J, Godoy P, Ramos JL. Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:934-946. [PMID: 35651318 PMCID: PMC9795978 DOI: 10.1111/1758-2229.13097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 05/17/2023]
Abstract
The extensive use of petrochemicals has produced serious environmental pollution problems; fortunately, bioremediation is considered an efficient way to fight against pollution. In line with Synthetic Biology is that robust microbial chassis with an expanded ability to remove environmental pollutants are desirable. Pseudomonas putida KT2440 is a robust lab microbe that has preserved the ability to survive in the environment and is the natural host for the self-transmissible TOL plasmid, which allows metabolism of toluene and xylenes to central metabolism. We show that the P. putida KT2440 (pWW0) acquired the ability to use octane as the sole C-source after acquisition of an almost 62-kb ICE from a microbial community that harbours an incomplete set of octane metabolism genes. The ICE bears genes for an alkane monooxygenase, a PQQ-dependent alcohol dehydrogenase and aldehyde dehydrogenase but lacks the electron donor enzymes required for the monooxygenase to operate. Host rubredoxin and rubredoxin reductase allow metabolism of octane to octanol. Proteomic assays and mutants unable to grow on octane or octanoic acid revealed that metabolism of octane is mediated by redundant host and ICE enzymes. Octane is oxidized to octanol, octanal and octanoic acid, the latter is subsequently acylated and oxidized to yield acetyl-CoA that is assimilated via the glyoxylate shunt; in fact, a knockout mutant in the aceA gene, encoding isocitrate lyase was unable to grow on octane or octanoic acid.
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Affiliation(s)
- Estrella Duque
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical ScienceLittle RockArkansasUSA
| | - Lázaro Molina
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Jesús de la Torre
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Patricia Godoy
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
| | - Juan L. Ramos
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICGranadaSpain
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13
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Zhang C, Zhao Y, Li Z, Wang W, Huang Y, Pan G, Fan K. Molecular mechanism of GylR-mediated regulation of glycerol metabolism in Streptomyces clavuligerus NRRL 3585. Front Microbiol 2022; 13:1078293. [PMID: 36504789 PMCID: PMC9732521 DOI: 10.3389/fmicb.2022.1078293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Glycerol is a readily available and low-cost simple polyol compound, which can be used as a carbon source for microorganisms to produce various value-added products. Understanding the underlying regulatory mechanism in glycerol metabolism is critical for making better use of glycerol for diverse applications. In a few reported Streptomyces strains, the glycerol utilization gene cluster (glp operon) was shown to be regulated by the IclR family transcriptional regulator GylR. However, the molecular regulatory mechanism mediated by GylR has not been fully elucidated. In this study, we first analyzed the available Actinobacteria genomes in the NCBI Genome database, and found that the glp operon-like gene clusters are conserved in Streptomyces and several other genera of Actinobacteria. By taking Streptomyces clavuligerus NRRL 3585 as a model system, we identified that GylR represses the expressions of glp operon and gylR by directly binding to their promoter regions. Both glycerol-3-phosphate and dihydroxyacetone phosphate can induce the dissociation of GylR from its binding sequences. Furthermore, we identified a minimal essential operator site (a palindromic 18-bp sequence) of GylR-like regulators in Streptomyces. Our study for the first time reported the binding sequences and effector molecules of GylR-like proteins in Streptomyces. The molecular regulatory mechanism mediated by GylR presumably exists widely in Streptomyces. Our findings would facilitate the design of glycerol utilization pathways for producing valuable products. Moreover, our study provided new basic elements for the development of glycerol-inducible regulatory tools for synthetic biology research in the future.
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Affiliation(s)
- Chaobo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Youbao Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Keqiang Fan,
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14
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Santamaria G, Liao C, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J, Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife 2022; 11:e76119. [PMID: 36409069 PMCID: PMC9708071 DOI: 10.7554/elife.76119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations.
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Affiliation(s)
- Guillem Santamaria
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Zhe Wang
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francisco Rodrigues Pinto
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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15
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From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440. Int Microbiol 2022; 26:243-255. [PMID: 36357545 PMCID: PMC9649394 DOI: 10.1007/s10123-022-00282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their high costs still impose some barriers for industrial scalability, requiring solutions that could be both greener and cost-effective. Since Pseudomonas putida KT2440 is a powerful degrader of gallic acid, its metabolism offers pathways that can be engineered to produce it from cheap and renewable carbon sources, such as the crude glycerol generated in biodiesel units. In this study, a synthetic operon with the heterologous genes aroG4, quiC and pobA* was developed and expressed in P. putida, based on an in silico analysis of possible metabolic routes, resulting in no production. Then, the sequences pcaHG and galTAPR were deleted from the genome of this strain to avoid the degradation of gallic acid and its main intermediate, the protocatechuic acid. This mutant was transformed with the vector containing the synthetic operon and was finally able to convert glycerol into gallic acid. Production assays in shaker showed a final concentration of 346.7 ± 0.004 mg L-1 gallic acid after 72 h.
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16
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Olicón-Hernández DR, Guerra-Sánchez G, Porta CJ, Santoyo-Tepole F, Hernández-Cortez C, Tapia-García EY, Chávez-Camarillo GM. Fundaments and Concepts on Screening of Microorganisms for Biotechnological Applications. Mini Review. Curr Microbiol 2022; 79:373. [PMID: 36302918 DOI: 10.1007/s00284-022-03082-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/08/2022] [Indexed: 11/25/2022]
Abstract
Microbial biotechnology uses microorganisms and their derivatives to generate industrial and/or environmental products that impact daily life. Modern biotechnology uses proteomics, metabolomics, quantum processors, and massive sequencing methods to yield promising results with microorganisms. However, the fundamental concepts of microbial biotechnology focus on the specific search for microorganisms from natural sources and their correct analysis to implement large-scale processes. This mini-review focuses on the methods used for the isolation and selection of microorganisms with biotechnological potential to empathize the importance of these concepts in microbial biotechnology. In this work, a review of the state of the art in recent years on the selection and characterization of microorganisms with a basic approach to understanding the importance of fundamental concepts in the field of biotechnology was carried out. The proper selection of isolation sources and the design of suitable selection criteria according to the desired activity have generated substantial changes in the development of biotechnology for more than three decades. Some examples include Taq polymerase in the PCR method and CRISPR technology. The objective of this mini review is to establish general ideas for the screening of microorganisms based on basic concepts of biotechnology that are left aside in several articles and maintain the importance of the basic concepts that this implies in the development of modern biotechnology.
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Affiliation(s)
- Dario R Olicón-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México.
| | - Guadalupe Guerra-Sánchez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
| | - Carla J Porta
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
| | - Fortunata Santoyo-Tepole
- Departamento de Investigación, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
| | - Cecilia Hernández-Cortez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
| | - Erika Y Tapia-García
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
| | - Griselda Ma Chávez-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Colonia Santo Tomas, 11340, Ciudad de México, México
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17
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Zubkov IN, Bukin YS, Sorokoumov PN, Shishlyannikov SM. Preparation of polyhydroxyalkanoates using <i>Pseudomonas helmanticensis</i> in non-sterile media containing glycerol and sodium dodecyl sulfate. PROCEEDINGS OF UNIVERSITIES. APPLIED CHEMISTRY AND BIOTECHNOLOGY 2022. [DOI: 10.21285/2227-2925-2022-12-3-479-484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Biosynthetically-produced Pseudomonas poly-3-hydroxyalkanoates (PHAs) are a promising substitute for conventional plastics. Costs involved with the production of PHAs can be reduced by optimizing power consumption, which can be achieved using nutrient media without preliminary steam sterilization. Cultivation of Pseudomonas bacteria resistant to sodium dodecyl sulfate (SDS) on SDS-containing non-sterile media yields a biomass consisting predominantly of a PHA producer. SDS plays the role of an antimicrobial agent that inhibits the growth of foreign microorganisms. In this work, an SDS-resistant culture of Pseudomonas helmanticensis and media containing glycerol and SDS were used. The concentrations of carbon (glycerol) and nitrogen sources were optimized using an experiment performed according to a central composite rotatable design. The concentration of substrate C and the C/N ratio between the glycerol and nitrogen content were varied. The dependence of the degree of substrate conversion in PHA on C and C/N was derived in the R programming environment. The constructed model adequately describes the experimental data at a significance level of 0.05 (adequacy variance of the regression equation 4.1×10-2; R2 =0.98). According to the constructed model, the conversion of glycerol to PHA equals 6.9±0.4%. Under optimized conditions (0.61 g/L nitrogen source; 8.4 g/L glycerol; 96 h), P. helmanticensis converts 7.0% of the substrate to PHA with an average monomer unit length. Using a 16S rRNA metagenomic assay, the proportion of foreign bacteria in P. helmanticensis cultures on non-sterile media containing 0.5 g/L SDS was shown to be 2%.
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Affiliation(s)
- I. N. Zubkov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS)
| | | | - P. N. Sorokoumov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS)
| | - S. M. Shishlyannikov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS)
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18
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Schoppel K, Trachtmann N, Korzin EJ, Tzanavari A, Sprenger GA, Weuster-Botz D. Metabolic control analysis enables rational improvement of E. coli L-tryptophan producers but methylglyoxal formation limits glycerol-based production. Microb Cell Fact 2022; 21:201. [PMID: 36195869 PMCID: PMC9531422 DOI: 10.1186/s12934-022-01930-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background Although efficient l-tryptophan production using engineered Escherichia coli is established from glucose, the use of alternative carbon sources is still very limited. Through the application of glycerol as an alternate, a more sustainable substrate (by-product of biodiesel preparation), the well-studied intracellular glycolytic pathways are rerouted, resulting in the activity of different intracellular control sites and regulations, which are not fully understood in detail. Metabolic analysis was applied to well-known engineered E. coli cells with 10 genetic modifications. Cells were withdrawn from a fed-batch production process with glycerol as a carbon source, followed by metabolic control analysis (MCA). This resulted in the identification of several additional enzymes controlling the carbon flux to l-tryptophan. Results These controlling enzyme activities were addressed stepwise by the targeted overexpression of 4 additional enzymes (trpC, trpB, serB, aroB). Their efficacy regarding l-tryptophan productivity was evaluated under consistent fed-batch cultivation conditions. Although process comparability was impeded by process variances related to a temporal, unpredictable break-off in l-tryptophan production, process improvements of up to 28% with respect to the l-tryptophan produced were observed using the new producer strains. The intracellular effects of these targeted genetic modifications were revealed by metabolic analysis in combination with MCA and expression analysis. Furthermore, it was discovered that the E. coli cells produced the highly toxic metabolite methylglyoxal (MGO) during the fed-batch process. A closer look at the MGO production and detoxification on the metabolome, fluxome, and transcriptome level of the engineered E. coli indicated that the highly toxic metabolite plays a critical role in the production of aromatic amino acids with glycerol as a carbon source. Conclusions A detailed process analysis of a new l-tryptophan producer strain revealed that several of the 4 targeted genetic modifications of the E. colil-tryptophan producer strain proved to be effective, and, for others, new engineering approaches could be derived from the results. As a starting point for further strain and process optimization, the up-regulation of MGO detoxifying enzymes and a lowering of the feeding rate during the last third of the cultivation seems reasonable. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01930-1.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Emil J Korzin
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Angelina Tzanavari
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany.
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19
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Nanoemulsified clove essential oils-based edible coating controls Pseudomonas spp.-causing spoilage of tilapia (Oreochromis niloticus) fillets: Working mechanism and bacteria metabolic responses. Food Res Int 2022; 159:111594. [DOI: 10.1016/j.foodres.2022.111594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022]
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20
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Koller M, Obruča S. Biotechnological production of polyhydroxyalkanoates from glycerol: A review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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Khandelwal H, Mutyala S, Kim M, Eun Song Y, Li S, Jang M, Oh SE, Rae Kim J. Colorimetric isolation of a novel electrochemically active Pseudomonas strain using tungsten nanorods for bioelectrochemical applications. Bioelectrochemistry 2022; 146:108136. [DOI: 10.1016/j.bioelechem.2022.108136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/15/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022]
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Wirth NT, Nikel PI. Combinatorial pathway balancing provides biosynthetic access to 2-fluoro- cis, cis-muconate in engineered Pseudomonas putida. CHEM CATALYSIS 2021; 1:1234-1259. [PMID: 34977847 PMCID: PMC8711041 DOI: 10.1016/j.checat.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022]
Abstract
The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Perdigão R, Almeida CMR, Magalhães C, Ramos S, Carolas AL, Ferreira BS, Carvalho MF, Mucha AP. Bioremediation of Petroleum Hydrocarbons in Seawater: Prospects of Using Lyophilized Native Hydrocarbon-Degrading Bacteria. Microorganisms 2021; 9:2285. [PMID: 34835411 PMCID: PMC8617842 DOI: 10.3390/microorganisms9112285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/16/2022] Open
Abstract
This work aimed to develop a bioremediation product of lyophilized native bacteria to respond to marine oil spills. Three oil-degrading bacterial strains (two strains of Rhodococcus erythropolis and one Pseudomonas sp.), isolated from the NW Portuguese coast, were selected for lyophilization after biomass growth optimization (tested with alternative carbon sources). Results indicated that the bacterial strains remained viable after the lyophilization process, without losing their biodegradation potential. The biomass/petroleum ratio was optimized, and the bioremediation efficiency of the lyophilized bacterial consortium was tested in microcosms with natural seawater and petroleum. An acceleration of the natural oil degradation process was observed, with an increased abundance of oil-degraders after 24 h, an emulsion of the oil/water layer after 7 days, and an increased removal of total petroleum hydrocarbons (47%) after 15 days. This study provides an insight into the formulation and optimization of lyophilized bacterial agents for application in autochthonous oil bioremediation.
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Affiliation(s)
- Rafaela Perdigão
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - C. Marisa R. Almeida
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
| | - Catarina Magalhães
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
- Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre 790, 4150-171 Porto, Portugal
| | - Sandra Ramos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
| | - Ana L. Carolas
- Biotrend S.A., Biocant Park, Núcleo 04 Lote 2, 3060-197 Cantanhede, Portugal; (A.L.C.); (B.S.F.)
| | - Bruno S. Ferreira
- Biotrend S.A., Biocant Park, Núcleo 04 Lote 2, 3060-197 Cantanhede, Portugal; (A.L.C.); (B.S.F.)
| | - Maria F. Carvalho
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Ana P. Mucha
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; (C.M.R.A.); (C.M.); (S.R.); (M.F.C.); (A.P.M.)
- Faculty of Sciences, University of Porto (FCUP), Rua do Campo Alegre 790, 4150-171 Porto, Portugal
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25
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Zhao F, Wu Y, Wang Q, Zheng M, Cui Q. Glycerol or crude glycerol as substrates make Pseudomonas aeruginosa achieve anaerobic production of rhamnolipids. Microb Cell Fact 2021; 20:185. [PMID: 34556134 PMCID: PMC8461908 DOI: 10.1186/s12934-021-01676-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The anaerobic production of rhamnolipids is significant in research and application, such as foamless fermentation and in situ production of rhamnolipids in the anoxic environments. Although a few studies reported that some rare Pseudomonas aeruginosa strains can produce rhamnolipids anaerobically, the decisive factors for anaerobic production of rhamnolipids were unknown. RESULTS Two possible hypotheses on the decisive factors for anaerobic production of rhamnolipids by P. aeruginosa were proposed, the strains specificity of rare P. aeruginosa (hypothesis 1) and the effect of specific substrates (hypothesis 2). This study assessed the anaerobic growth and rhamnolipids synthesis of three P. aeruginosa strains using different substrates. P. aeruginosa strains anaerobically grew well using all the tested substrates, but glycerol was the only carbon source that supported anaerobic production of rhamnolipids. Other carbon sources with different concentrations still failed for anaerobic production of rhamnolipids by P. aeruginosa. Nitrate was the excellent nitrogen source for anaerobic production of rhamnolipids. FTIR spectra analysis confirmed the anaerobically produced rhamnolipids by P. aeruginosa using glycerol. The anaerobically produced rhamnolipids decreased air-water surface tension to below 29.0 mN/m and emulsified crude oil with EI24 above 65%. Crude glycerol and 1, 2-propylene glycol also supported the anaerobic production of rhamnolipids by all P. aeruginosa strains. Prospects and bottlenecks to anaerobic production of rhamnolipids were also discussed. CONCLUSIONS Glycerol substrate was the decisive factor for anaerobic production of rhamnolipids by P. aeruginosa. Strain specificity resulted in the different anaerobic yield of rhamnolipids. Crude glycerol was one low cost substrate for anaerobic biosynthesis of rhamnolipids by P. aeruginosa. Results help advance the research on anaerobic production of rhamnolipids, deepen the biosynthesis theory of rhamnolipids and optimize the anaerobic production of rhamnolipids.
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Affiliation(s)
- Feng Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Yuting Wu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Qingzhi Wang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Mengyao Zheng
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Qingfeng Cui
- Research Institute of Petroleum Exploration and Development (Langfang), Langfang, 065007, Hebei, China
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Schoppel K, Trachtmann N, Mittermeier F, Sprenger GA, Weuster-Botz D. Metabolic control analysis of L-tryptophan producing Escherichia coli applying targeted perturbation with shikimate. Bioprocess Biosyst Eng 2021; 44:2591-2613. [PMID: 34519841 PMCID: PMC8536597 DOI: 10.1007/s00449-021-02630-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022]
Abstract
L-tryptophan production from glycerol with Escherichia coli was analysed by perturbation studies and metabolic control analysis. The insertion of a non-natural shikimate transporter into the genome of an Escherichia coli L-tryptophan production strain enabled targeted perturbation within the product pathway with shikimate during parallelised short-term perturbation experiments with cells withdrawn from a 15 L fed-batch production process. Expression of the shikimate/H+-symporter gene (shiA) from Corynebacterium glutamicum did not alter process performance within the estimation error. Metabolic analyses and subsequent extensive data evaluation were performed based on the data of the parallel analysis reactors and the production process. Extracellular rates and intracellular metabolite concentrations displayed evident deflections in cell metabolism and particularly in chorismate biosynthesis due to the perturbations with shikimate. Intracellular flux distributions were estimated using a thermodynamics-based flux analysis method, which integrates thermodynamic constraints and intracellular metabolite concentrations to restrain the solution space. Feasible flux distributions, Gibbs reaction energies and concentration ranges were computed simultaneously for the genome-wide metabolic model, with minimum bias in relation to the direction of metabolic reactions. Metabolic control analysis was applied to estimate elasticities and flux control coefficients, predicting controlling sites for L-tryptophan biosynthesis. The addition of shikimate led to enhanced deviations in chorismate biosynthesis, revealing a so far not observed control of 3-dehydroquinate synthase on L-tryptophan formation. The relative expression of the identified target genes was analysed with RT-qPCR. Transcriptome analysis revealed disparities in gene expression and the localisation of target genes to further improve the microbial L-tryptophan producer by metabolic engineering.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Fabian Mittermeier
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany.
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Genetic and Biochemical Characterization of the Na +/H + Antiporters of Pseudomonas aeruginosa. J Bacteriol 2021; 203:e0028421. [PMID: 34280000 DOI: 10.1128/jb.00284-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa has four Na+/H+ antiporters that interconvert and balance Na+ and H+ gradients across the membrane. These gradients are important for bioenergetics and ionic homeostasis. To understand these transporters, we constructed four strains, each of which has only one antiporter, i.e., NhaB, NhaP, NhaP2, and Mrp. We also constructed a quadruple deletion mutant that has no Na+/H+ antiporters. Although the antiporters of P. aeruginosa have been studied previously, the strains constructed here present the opportunity to characterize their kinetic properties in their native membranes and their roles in the physiology of P. aeruginosa. The strains expressing only NhaB or Mrp, the two electrogenic antiporters, were able to grow essentially like the wild-type strain across a range of Na+ concentrations and pH values. Strains with only NhaP or NhaP2, which are electroneutral, grew more poorly at increasing Na+ concentrations, especially at high pH values, with the strain expressing NhaP being more sensitive. The strain with no Na+/H+ antiporters was extremely sensitive to the Na+ concentration and showed essentially no Na+(Li+)/H+ antiporter activity, but it retained most K+/H+ antiporter activity of the wild-type strain at pH 7.5 and approximately one-half at pH 8.5. We also used the four strains that each express one of the four antiporters to characterize the kinetic properties of each transporter. Transcriptome sequencing analysis of the quadruple deletion strain showed widespread changes, including changes in pyocyanin synthesis, biofilm formation, and nitrate and glycerol metabolism. Thus, the strains constructed for this study will open a new door to understanding the physiological roles of these proteins and their activities in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa has four Na+/H+ antiporters that connect and interconvert its Na+ and H+ gradients. We have constructed four deletion mutants, each of which has only one of the four Na+/H+ antiporters. These strains made it possible to study the properties and physiological roles of each antiporter independently in its native membrane. Mrp and NhaB are each able to sustain growth over a wide range of pH values and Na+ concentrations, whereas the two electroneutral antiporters, NhaP and NhaP2, are most effective at low pH values. We also constructed a quadruple mutant lacking all four antiporters, in which the H+ and Na+ gradients are disconnected. This will make it possible to study the role of the two gradients independently.
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Kozaeva E, Volkova S, Matos MRA, Mezzina MP, Wulff T, Volke DC, Nielsen LK, Nikel PI. Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A-dependent bioproduction in rewired Pseudomonas putida. Metab Eng 2021; 67:373-386. [PMID: 34343699 DOI: 10.1016/j.ymben.2021.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 01/16/2023]
Abstract
Pseudomonas putida is evolutionarily endowed with features relevant for bioproduction, especially under harsh operating conditions. The rich metabolic versatility of this species, however, comes at the price of limited formation of acetyl-coenzyme A (CoA) from sugar substrates. Since acetyl-CoA is a key metabolic precursor for a number of added-value products, in this work we deployed an in silico-guided rewiring program of central carbon metabolism for upgrading P. putida as a host for acetyl-CoA-dependent bioproduction. An updated kinetic model, integrating fluxomics and metabolomics datasets in addition to manually-curated information of enzyme mechanisms, identified targets that would lead to increased acetyl-CoA levels. Based on these predictions, a set of plasmids based on clustered regularly interspaced short palindromic repeats (CRISPR) and dead CRISPR-associated protein 9 (dCas9) was constructed to silence genes by CRISPR interference (CRISPRi). Dynamic reduction of gene expression of two key targets (gltA, encoding citrate synthase, and the essential accA gene, encoding subunit A of the acetyl-CoA carboxylase complex) mediated an 8-fold increase in the acetyl-CoA content of rewired P. putida. Poly(3-hydroxybutyrate) (PHB) was adopted as a proxy of acetyl-CoA availability, and two synthetic pathways were engineered for biopolymer accumulation. By including cell morphology as an extra target for the CRISPRi approach, fully rewired P. putida strains programmed for PHB accumulation had a 5-fold increase in PHB titers in bioreactor cultures using glucose. Thus, the strategy described herein allowed for rationally redirecting metabolic fluxes in P. putida from central metabolism towards product biosynthesis-especially relevant when deletion of essential pathways is not an option.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Svetlana Volkova
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Marta R A Matos
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mariela P Mezzina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Lars K Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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30
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Matuszewska M, Maciąg T, Rajewska M, Wierzbicka A, Jafra S. The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. Sci Rep 2021; 11:10994. [PMID: 34040089 PMCID: PMC8154892 DOI: 10.1038/s41598-021-90488-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.
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Affiliation(s)
- Marta Matuszewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Aldona Wierzbicka
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
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31
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Fernández-Cabezón L, Cros A, Nikel PI. Spatiotemporal Manipulation of the Mismatch Repair System of Pseudomonas putida Accelerates Phenotype Emergence. ACS Synth Biol 2021; 10:1214-1226. [PMID: 33843192 DOI: 10.1021/acssynbio.1c00031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of complex phenotypes in industrially relevant bacteria is a major goal of metabolic engineering, which encompasses the implementation of both rational and random approaches. In the latter case, several tools have been developed toward increasing mutation frequencies, yet the precise control of mutagenesis processes in cell factories continues to represent a significant technical challenge. Pseudomonas species are endowed with one of the most efficient DNA mismatch repair (MMR) systems found in the bacterial domain. Here, we investigated if the endogenous MMR system could be manipulated as a general strategy to artificially alter mutation rates in Pseudomonas species. To bestow a conditional mutator phenotype in the platform bacterium Pseudomonas putida, we constructed inducible mutator devices to modulate the expression of the dominant-negative mutLE36K allele. Regulatable overexpression of mutLE36K in a broad-host-range, easy-to-cure plasmid format resulted in a transitory inhibition of the MMR machinery, leading to a significant increase (up to 438-fold) in DNA mutation frequencies and a heritable fixation of mutations in the genome. Following such an accelerated mutagenesis-followed by selection approach, three phenotypes were successfully evolved: resistance to antibiotics streptomycin and rifampicin (either individually or combined) and reversion of a synthetic uracil auxotrophy. Thus, these mutator devices could be applied to accelerate the evolution of metabolic pathways in long-term evolutionary experiments, alternating cycles of (inducible) mutagenesis coupled to selection schemes toward the desired phenotype(s).
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Affiliation(s)
- Lorena Fernández-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Borrero-de Acuña JM, Rohde M, Saldias C, Poblete-Castro I. Fed-Batch mcl- Polyhydroxyalkanoates Production in Pseudomonas putida KT2440 and Δ phaZ Mutant on Biodiesel-Derived Crude Glycerol. Front Bioeng Biotechnol 2021; 9:642023. [PMID: 33796510 PMCID: PMC8007980 DOI: 10.3389/fbioe.2021.642023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel industry. Pseudomonas bacteria metabolize the polyol into several biopolymers, including alginate and medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs). Although P. putida is a suited platform to derive these polyoxoesters from crude glycerol, the attained concentrations in batch and fed-batch cultures are still low. In this study, we employed P. putida KT2440 and the hyper-PHA producer ΔphaZ mutant in two different fed-batch modes to synthesize mcl-PHAs from raw glycerol. Initially, the cells grew in a batch phase (μmax 0.21 h–1) for 22 h followed by a carbon-limiting exponential feeding, where the specific growth rate was set at 0.1 (h–1), resulting in a cell dry weight (CDW) of nearly 50 (g L–1) at 40 h cultivation. During the PHA production stage, we supplied the substrate at a constant rate of 50 (g h–1), where the KT2440 and the ΔphaZ produced 9.7 and 12.7 gPHA L–1, respectively, after 60 h cultivation. We next evaluated the PHA production ability of the P. putida strains using a DO-stat approach under nitrogen depletion. Citric acid was the main by-product secreted by the cells, accumulating in the culture broth up to 48 (g L–1) under nitrogen limitation. The mutant ΔphaZ amassed 38.9% of the CDW as mcl-PHA and exhibited a specific PHA volumetric productivity of 0.34 (g L–1 h–1), 48% higher than the parental KT2440 under the same growth conditions. The biosynthesized mcl-PHAs had average molecular weights ranging from 460 to 505 KDa and a polydispersity index (PDI) of 2.4–2.6. Here, we demonstrated that the DO-stat feeding approach in high cell density cultures enables the high yield production of mcl-PHA in P. putida strains using the industrial crude glycerol, where the fed-batch process selection is essential to exploit the superior biopolymer production hallmarks of engineered bacterial strains.
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Affiliation(s)
- José Manuel Borrero-de Acuña
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility of Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cesar Saldias
- Departamento de Química Física, Facultad de Química y Farmacia, Pontificia Universidad Católica de Chile, Macul, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Faculty of Life Sciences, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
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Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria. mSystems 2021; 6:6/2/e00014-21. [PMID: 33727391 PMCID: PMC8546961 DOI: 10.1128/msystems.00014-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PDH) is widely distributed in nature and catalyzes the first committing step in the oxidative branch of the pentose phosphate (PP) pathway, feeding either the reductive PP or the Entner-Doudoroff pathway. Besides its role in central carbon metabolism, this dehydrogenase provides reduced cofactors, thereby affecting redox balance. Although G6PDH is typically considered to display specificity toward NADP+, some variants accept NAD+ similarly or even preferentially. Furthermore, the number of G6PDH isozymes encoded in bacterial genomes varies from none to more than four orthologues. On this background, we systematically analyzed the interplay of the three G6PDH isoforms of the soil bacterium Pseudomonas putida KT2440 from genomic, genetic, and biochemical perspectives. P. putida represents an ideal model to tackle this endeavor, as its genome harbors gene orthologues for most dehydrogenases in central carbon metabolism. We show that the three G6PDHs of strain KT2440 have different cofactor specificities and that the isoforms encoded by zwfA and zwfB carry most of the activity, acting as metabolic “gatekeepers” for carbon sources that enter at different nodes of the biochemical network. Moreover, we demonstrate how multiplication of G6PDH isoforms is a widespread strategy in bacteria, correlating with the presence of an incomplete Embden-Meyerhof-Parnas pathway. The abundance of G6PDH isoforms in these species goes hand in hand with low NADP+ affinity, at least in one isozyme. We propose that gene duplication and relaxation in cofactor specificity is an evolutionary strategy toward balancing the relative production of NADPH and NADH. IMPORTANCE Protein families have likely arisen during evolution by gene duplication and divergence followed by neofunctionalization. While this phenomenon is well documented for catabolic activities (typical of environmental bacteria that colonize highly polluted niches), the coexistence of multiple isozymes in central carbon catabolism remains relatively unexplored. We have adopted the metabolically versatile soil bacterium Pseudomonas putida KT2440 as a model to interrogate the physiological and evolutionary significance of coexisting glucose-6-phosphate dehydrogenase (G6PDH) isozymes. Our results show that each of the three G6PDHs in this bacterium display distinct biochemical properties, especially at the level of cofactor preference, impacting bacterial physiology in a carbon source-dependent fashion. Furthermore, the presence of multiple G6PDHs differing in NAD+ or NADP+ specificity in bacterial species strongly correlates with their predominant metabolic lifestyle. Our findings support the notion that multiplication of genes encoding cofactor-dependent dehydrogenases is a general evolutionary strategy toward achieving redox balance according to the growth conditions.
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Bravakos P, Mandalakis M, Nomikou P, Anastasiou TI, Kristoffersen JB, Stavroulaki M, Kilias S, Kotoulas G, Magoulas A, Polymenakou PN. Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece. Sci Rep 2021; 11:1336. [PMID: 33446715 PMCID: PMC7809023 DOI: 10.1038/s41598-020-79359-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 12/05/2022] Open
Abstract
Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO2-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.
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Affiliation(s)
- Panos Bravakos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Paraskevi Nomikou
- Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Thekla I Anastasiou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Jon Bent Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Melanthia Stavroulaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Stephanos Kilias
- Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (IMBBC-HCMR), Gournes Pediados, Heraklion Crete, Greece.
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Xu Z, Pan C, Li X, Hao N, Zhang T, Gaffrey MJ, Pu Y, Cort JR, Ragauskas AJ, Qian WJ, Yang B. Enhancement of polyhydroxyalkanoate production by co-feeding lignin derivatives with glycerol in Pseudomonas putida KT2440. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:11. [PMID: 33413621 PMCID: PMC7792162 DOI: 10.1186/s13068-020-01861-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Efficient utilization of all available carbons from lignocellulosic biomass is critical for economic efficiency of a bioconversion process to produce renewable bioproducts. However, the metabolic responses that enable Pseudomonas putida to utilize mixed carbon sources to generate reducing power and polyhydroxyalkanoate (PHA) remain unclear. Previous research has mainly focused on different fermentation strategies, including the sequential feeding of xylose as the growth stage substrate and octanoic acid as the PHA-producing substrate, feeding glycerol as the sole carbon substrate, and co-feeding of lignin and glucose. This study developed a new strategy-co-feeding glycerol and lignin derivatives such as benzoate, vanillin, and vanillic acid in Pseudomonas putida KT2440-for the first time, which simultaneously improved both cell biomass and PHA production. RESULTS Co-feeding lignin derivatives (i.e. benzoate, vanillin, and vanillic acid) and glycerol to P. putida KT2440 was shown for the first time to simultaneously increase cell dry weight (CDW) by 9.4-16.1% and PHA content by 29.0-63.2%, respectively, compared with feeding glycerol alone. GC-MS results revealed that the addition of lignin derivatives to glycerol decreased the distribution of long-chain monomers (C10 and C12) by 0.4-4.4% and increased the distribution of short-chain monomers (C6 and C8) by 0.8-3.5%. The 1H-13C HMBC, 1H-13C HSQC, and 1H-1H COSY NMR analysis confirmed that the PHA monomers (C6-C14) were produced when glycerol was fed to the bacteria alone or together with lignin derivatives. Moreover, investigation of the glycerol/benzoate/nitrogen ratios showed that benzoate acted as an independent factor in PHA synthesis. Furthermore, 1H, 13C and 31P NMR metabolite analysis and mass spectrometry-based quantitative proteomics measurements suggested that the addition of benzoate stimulated oxidative-stress responses, enhanced glycerol consumption, and altered the intracellular NAD+/NADH and NADPH/NADP+ ratios by up-regulating the proteins involved in energy generation and storage processes, including the Entner-Doudoroff (ED) pathway, the reductive TCA route, trehalose degradation, fatty acid β-oxidation, and PHA biosynthesis. CONCLUSIONS This work demonstrated an effective co-carbon feeding strategy to improve PHA content/yield and convert lignin derivatives into value-added products in P. putida KT2440. Co-feeding lignin break-down products with other carbon sources, such as glycerol, has been demonstrated as an efficient way to utilize biomass to increase PHA production in P. putida KT2440. Moreover, the involvement of aromatic degradation favours further lignin utilization, and the combination of proteomics and metabolomics with NMR sheds light on the metabolic and regulatory mechanisms for cellular redox balance and potential genetic targets for a higher biomass carbon conversion efficiency.
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Affiliation(s)
- Zhangyang Xu
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
| | - Chunmei Pan
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
- College of Food and Bioengineering, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, Henan, China
| | - Xiaolu Li
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
| | - Naijia Hao
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yunqiao Pu
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John R Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bin Yang
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA.
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Zhang B, Jiang Y, Li Z, Wang F, Wu XY. Recent Progress on Chemical Production From Non-food Renewable Feedstocks Using Corynebacterium glutamicum. Front Bioeng Biotechnol 2021; 8:606047. [PMID: 33392171 PMCID: PMC7775722 DOI: 10.3389/fbioe.2020.606047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/31/2020] [Indexed: 11/13/2022] Open
Abstract
Due to the non-renewable nature of fossil fuels, microbial fermentation is considered a sustainable approach for chemical production using glucose, xylose, menthol, and other complex carbon sources represented by lignocellulosic biomass. Among these, xylose, methanol, arabinose, glycerol, and other alternative feedstocks have been identified as superior non-food sustainable carbon substrates that can be effectively developed for microbe-based bioproduction. Corynebacterium glutamicum is a model gram-positive bacterium that has been extensively engineered to produce amino acids and other chemicals. Recently, in order to reduce production costs and avoid competition for human food, C. glutamicum has also been engineered to broaden its substrate spectrum. Strengthening endogenous metabolic pathways or assembling heterologous ones enables C. glutamicum to rapidly catabolize a multitude of carbon sources. This review summarizes recent progress in metabolic engineering of C. glutamicum toward a broad substrate spectrum and diverse chemical production. In particularly, utilization of lignocellulosic biomass-derived complex hybrid carbon source represents the futural direction for non-food renewable feedstocks was discussed.
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Affiliation(s)
- Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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Molecular Network and Culture Media Variation Reveal a Complex Metabolic Profile in Pantoea cf. eucrina D2 Associated with an Acidified Marine Sponge. Int J Mol Sci 2020; 21:ijms21176307. [PMID: 32878176 PMCID: PMC7504411 DOI: 10.3390/ijms21176307] [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: 08/05/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative Pantoea eucrina D2 was isolated from the marine sponge Chondrosia reniformis. Sponges were collected in a shallow volcanic vents system in Ischia island (South Italy), influenced by CO2 emissions and lowered pH. The chemical diversity of the secondary metabolites produced by this strain, under different culture conditions, was explored by a combined approach including molecular networking, pure compound isolation and NMR spectroscopy. The metabolome of Pantoea cf. eucrina D2 yielded a very complex molecular network, allowing the annotation of several metabolites, among them two biosurfactant clusters: lipoamino acids and surfactins. The production of each class of metabolites was highly dependent on the culture conditions, in particular, the production of unusual surfactins derivatives was reported for the first time from this genus; interestingly the production of these metabolites only arises by utilizing inorganic nitrogen as a sole nitrogen source. Major components of the extract obtained under standard medium culture conditions were isolated and identified as N-lipoamino acids by a combination of 1D and 2D NMR spectroscopy and HRESI-MS analysis. Assessment of the antimicrobial activity of the pure compounds towards some human pathogens, indicated a moderate activity of leucine containing N-lipoamino acids towards Staphylococcus aureus, Staphylococcus epidermidis and a clinical isolate of the emerging food pathogen Listeria monocytogenes.
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metab Eng Commun 2020; 10:e00126. [PMID: 32215253 PMCID: PMC7090339 DOI: 10.1016/j.mec.2020.e00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding β-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering. Plasmid-curing is the most time-consuming step in genome engineering approaches. We have developed a system for easy target- and self-curing of plasmid DNA. Synthetic control of replication and highly-specific in vivo DNA digestion were used. Plasmid curing with this system displays an efficiency >90% in a 24-h cultivation. Quick genome engineering facilitated genome reduction of P. putida.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Laura Friis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources. mBio 2020; 11:mBio.02684-19. [PMID: 32184246 PMCID: PMC7078475 DOI: 10.1128/mbio.02684-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is well known for causing infections in the airways of people with cystic fibrosis. Although it is clear that P. aeruginosa is metabolically well adapted to life in the CF lung, little is currently known about how the organism metabolizes the nutrients available in the airways. In this work, we used a combination of gene expression and isotope tracer (“fluxomic”) analyses to find out exactly where the input carbon goes during growth on two CF-relevant carbon sources, acetate and glycerol (derived from the breakdown of lung surfactant). We found that carbon is routed (“fluxed”) through very different pathways during growth on these substrates and that this is accompanied by an unexpected remodeling of the cell’s electron transfer pathways. Having access to this “blueprint” is important because the metabolism of P. aeruginosa is increasingly being recognized as a target for the development of much-needed antimicrobial agents. Pseudomonas aeruginosa is an opportunistic human pathogen, particularly noted for causing infections in the lungs of people with cystic fibrosis (CF). Previous studies have shown that the gene expression profile of P. aeruginosa appears to converge toward a common metabolic program as the organism adapts to the CF airway environment. However, we still have only a limited understanding of how these transcriptional changes impact metabolic flux at the systems level. To address this, we analyzed the transcriptome, proteome, and fluxome of P. aeruginosa grown on glycerol or acetate. These carbon sources were chosen because they are the primary breakdown products of an airway surfactant, phosphatidylcholine, which is known to be a major carbon source for P. aeruginosa in CF airways. We show that the fluxes of carbon throughout central metabolism are radically different among carbon sources. For example, the newly recognized “EDEMP cycle” (which incorporates elements of the Entner-Doudoroff [ED] pathway, the Embden-Meyerhof-Parnas [EMP] pathway, and the pentose phosphate [PP] pathway) plays an important role in supplying NADPH during growth on glycerol. In contrast, the EDEMP cycle is attenuated during growth on acetate, and instead, NADPH is primarily supplied by the reaction catalyzed by isocitrate dehydrogenase(s). Perhaps more importantly, our proteomic and transcriptomic analyses revealed a global remodeling of gene expression during growth on the different carbon sources, with unanticipated impacts on aerobic denitrification, electron transport chain architecture, and the redox economy of the cell. Collectively, these data highlight the remarkable metabolic plasticity of P. aeruginosa; that plasticity allows the organism to seamlessly segue between different carbon sources, maximizing the energetic yield from each.
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Engineering of glycerol utilization in Pseudomonas chlororaphis GP72 for enhancing phenazine-1-carboxylic acid production. World J Microbiol Biotechnol 2020; 36:49. [PMID: 32157439 DOI: 10.1007/s11274-020-02824-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022]
Abstract
Glycerol is a by-product of biodiesel, and it has a great application prospect to be transformed to synthesize high value-added compounds. Pseudomonas chlororaphis GP72 isolated from the green pepper rhizosphere is a plant growth promoting rhizobacteria that can utilize amount of glycerol to synthesize phenazine-1-carboxylic acid (PCA). PCA has been commercially registered as "Shenqinmycin" in China due to its characteristics of preventing pepper blight and rice sheath blight. The aim of this study was to engineer glycerol utilization pathway in P. chlororaphis GP72. First, the two genes glpF and glpK from the glycerol metabolism pathway were overexpressed in GP72ANO separately. Then, the two genes were co-expressed in GP72ANO, improving PCA production from 729.4 mg/L to 993.4 mg/L at 36 h. Moreover, the shunt pathway was blocked to enhance glycerol utilization, resulting in 1493.3 mg/L PCA production. Additionally, we confirmed the inhibition of glpR on glycerol metabolism pathway in P. chlororaphis GP72. This study provides a good example for improving the utilization of glycerol to synthesize high value-added compounds in Pseudomonas.
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Poblete-Castro I, Aravena-Carrasco C, Orellana-Saez M, Pacheco N, Cabrera A, Borrero-de Acuña JM. Engineering the Osmotic State of Pseudomonas putida KT2440 for Efficient Cell Disruption and Downstream Processing of Poly(3-Hydroxyalkanoates). Front Bioeng Biotechnol 2020; 8:161. [PMID: 32211393 PMCID: PMC7066983 DOI: 10.3389/fbioe.2020.00161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/17/2020] [Indexed: 11/17/2022] Open
Abstract
In the last decade, the development of novel programmable cell lytic systems based on different inducible genetic constructs like the holin–endolysin and lysozyme appears as a promising alternative to circumvent the use of costly enzymes and mechanical disrupters for downstream processing of intracellular microbial products. Despite the advances, upon activation of these systems the cellular disruption of the biocatalyst occurs in an extended period, thus delaying the recovery of poly(3-hydroxyalkanoate) (PHA). Herein the osmotic state of Pseudomonas putida KT2440 was engineered by inactivating the inner-membrane residing rescue valve MscL, which is responsible mainly for circumventing low-osmolarity challenges. Then the major outer membrane porin OprF and the specific porin OprE were overproduced during PHA producing conditions on decanoate-grown cells. The engineered P. putida strains carrying each porin showed no impairment on growth rate and final biomass and PHA yield after 48 h cultivation. Expression of both porins in tandem in the mutant strain KTΔmscL-oprFE led to a slight reduction of the biomass synthesis (∼10%) but higher PHA accumulation (%wt) relative to the cell dry mass. Each strain was then challenged to an osmotic upshift for 1 h and subsequently to a rapid passage to a hypotonic condition where the membrane stability of the KTΔmscL-oprFE suffered damage, resulting in a rapid reduction of cell viability. Cell disruption accounted for >95% of the cell population within 3 h as reported by colony forming units (CFU), FACS analyses, and transmission electron microscopy. PHA recovery yielded 94.2% of the biosynthesized biopolymer displaying no significant alterations on the final monomer composition. This study can serve as an efficient genetic platform for the recovery of any microbial intracellular compound allowing less unit operation steps for cellular disruption.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Carla Aravena-Carrasco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Alex Cabrera
- Unidad de Citometría de Flujo, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Manuel Borrero-de Acuña
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
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45
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Gajdoš P, Hambalko J, Slaný O, Čertík M. Conversion of waste materials into very long chain fatty acids by the recombinant yeast Yarrowia lipolytica. FEMS Microbiol Lett 2020; 367:5780224. [DOI: 10.1093/femsle/fnaa042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/03/2020] [Indexed: 01/17/2023] Open
Abstract
ABSTRACT
Erucic acid (C22:1Δ13) has several industrial applications including its use as a lubricant, surfactant and biodiesel and composite material constituent. It is produced by plants belonging to the Brassicaceae family, especially by the high erucic acid rapeseed. The ability to convert oleic acid into erucic acid is facilitated by FAE1. In this study, FAD2 (encoding Δ12-desaturase) was deleted in the strain Po1d to increase oleic acid content. Subsequently, FAE1 from Thlaspi arvense was overexpressed in Yarrowia lipolytica with the Δfad2 genotype. This resulted in the YL10 strain producing very long chain fatty acids, especially erucic acid. The YL10 strain was cultivated in media containing crude glycerol and waste cooking oil as carbon substrates. The cells grown using glycerol produced microbial oil devoid of linoleic acid, which was enriched with very long chain fatty acids, mainly erucic acid (9% of the total fatty acids). When cells were grown using waste cooking oil, the highest yield of erucic acid was obtained (887 mg L–1). However, external linoleic and α-linolenic were accumulated in cellular lipids when yeasts were grown in an oil medium. This study describes the possibility of conversion of waste material into erucic acid by a recombinant yeast strain.
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Affiliation(s)
- Peter Gajdoš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, Bratislava 81237, Slovak Republic
| | - Jaroslav Hambalko
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, Bratislava 81237, Slovak Republic
| | - Ondrej Slaný
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, Bratislava 81237, Slovak Republic
| | - Milan Čertík
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, Bratislava 81237, Slovak Republic
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46
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Batianis C, Kozaeva E, Damalas SG, Martín‐Pascual M, Volke DC, Nikel PI, Martins dos Santos VA. An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida. Microb Biotechnol 2020; 13:368-385. [PMID: 32045111 PMCID: PMC7017828 DOI: 10.1111/1751-7915.13533] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/26/2019] [Indexed: 01/15/2023] Open
Abstract
Owing to its wide metabolic versatility and physiological robustness, together with amenability to genetic manipulations and high resistance to stressful conditions, Pseudomonas putida is increasingly becoming the organism of choice for a range of applications in both industrial and environmental applications. However, a range of applied synthetic biology and metabolic engineering approaches are still limited by the lack of specific genetic tools to effectively and efficiently regulate the expression of target genes. Here, we present a single-plasmid CRISPR-interference (CRISPRi) system expressing a nuclease-deficient cas9 gene under the control of the inducible XylS/Pm expression system, along with the option of adopting constitutively expressed guide RNAs (either sgRNA or crRNA and tracrRNA). We showed that the system enables tunable, tightly controlled gene repression (up to 90%) of chromosomally expressed genes encoding fluorescent proteins, either individually or simultaneously. In addition, we demonstrate that this method allows for suppressing the expression of the essential genes pyrF and ftsZ, resulting in significantly low growth rates or morphological changes respectively. This versatile system expands the capabilities of the current CRISPRi toolbox for efficient, targeted and controllable manipulation of gene expression in P. putida.
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Affiliation(s)
- Christos Batianis
- Laboratory of Systems and Synthetic BiologyWageningen & Research University6708WageningenThe Netherlands
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Stamatios G. Damalas
- Laboratory of Systems and Synthetic BiologyWageningen & Research University6708WageningenThe Netherlands
| | - María Martín‐Pascual
- Laboratory of Systems and Synthetic BiologyWageningen & Research University6708WageningenThe Netherlands
| | - Daniel C. Volke
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Vitor A.P. Martins dos Santos
- Laboratory of Systems and Synthetic BiologyWageningen & Research University6708WageningenThe Netherlands
- Lifeglimmer GmbH12163BerlinGermany
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Otto M, Wynands B, Lenzen C, Filbig M, Blank LM, Wierckx N. Rational Engineering of Phenylalanine Accumulation in Pseudomonas taiwanensis to Enable High-Yield Production of Trans-Cinnamate. Front Bioeng Biotechnol 2019; 7:312. [PMID: 31824929 PMCID: PMC6882275 DOI: 10.3389/fbioe.2019.00312] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Microbial biocatalysis represents a promising alternative for the production of a variety of aromatic chemicals, where microorganisms are engineered to convert a renewable feedstock under mild production conditions into a valuable chemical building block. This study describes the rational engineering of the solvent-tolerant bacterium Pseudomonas taiwanensis VLB120 toward accumulation of L-phenylalanine and its conversion into the chemical building block t-cinnamate. We recently reported rational engineering of Pseudomonas toward L-tyrosine accumulation by the insertion of genetic modifications that allow both enhanced flux and prevent aromatics degradation. Building on this knowledge, three genes encoding for enzymes involved in the degradation of L-phenylalanine were deleted to allow accumulation of 2.6 mM of L-phenylalanine from 20 mM glucose. The amino acid was subsequently converted into the aromatic model compound t-cinnamate by the expression of a phenylalanine ammonia-lyase (PAL) from Arabidopsis thaliana. The engineered strains produced t-cinnamate with yields of 23 and 39% Cmol Cmol−1 from glucose and glycerol, respectively. Yields were improved up to 48% Cmol Cmol−1 from glycerol when two enzymes involved in the shikimate pathway were additionally overexpressed, however with negative impact on strain performance and reproducibility. Production titers were increased in fed-batch fermentations, in which 33.5 mM t-cinnamate were produced solely from glycerol, in a mineral medium without additional complex supplements. The aspect of product toxicity was targeted by the utilization of a streamlined, genome-reduced strain, which improves upon the already high tolerance of P. taiwanensis VLB120 toward t-cinnamate.
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Affiliation(s)
- Maike Otto
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christoph Lenzen
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Melanie Filbig
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
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Alhasawi AA, Thomas SC, Tharmalingam S, Legendre F, Appanna VD. Isocitrate Lyase and Succinate Semialdehyde Dehydrogenase Mediate the Synthesis of α-Ketoglutarate in Pseudomonas fluorescens. Front Microbiol 2019; 10:1929. [PMID: 31507554 PMCID: PMC6716453 DOI: 10.3389/fmicb.2019.01929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/05/2019] [Indexed: 01/04/2023] Open
Abstract
Glycerol is an important by-product of the biodiesel industry and its transformation into value-added products like keto acids is being actively pursued in order to improve the efficacy of this renewable energy sector. Here, we report that the enhanced production of α-ketoglutarate (KG) effected by Pseudomonas fluorescens in a mineral medium supplemented with manganese (Mn) is propelled by the increased activities of succinate semialdehyde dehydrogenase (SSADH), γ-aminobutyric acid aminotransaminase (GABAT), and isocitrate lyase (ICL). The latter generates glyoxylate and succinate two key metabolites involved in this process. Fumarate reductase (FRD) also aids in augmenting the pool of succinate, a precursor of succinate semialdehyde (SSA). The latter is then carboxylated to KG with the assistance of α-ketoglutarate decarboxylase (KDC). These enzymes work in tandem to ensure copious secretion of the keto acid. When incubated with glycerol in the presence of bicarbonate (HCO3−), cell-free extracts readily produce KG with a metabolite fingerprint attributed to glutamate, γ-aminobutyric acid (GABA), succinate and succinate semialdehyde. Further targeted metabolomic and functional proteomic studies with high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and gel electrophoresis techniques provided molecular insights into this KG-generating machinery. Real-time quantitative polymerase chain reaction (RT-qPCR) analyses revealed the transcripts responsible for ICL and SSADH were elevated in the Mn-supplemented cultures. This hitherto unreported metabolic network where ICL and SSADH orchestrate the enhanced production of KG from glycerol, provides an elegant means of converting an industrial waste into a keto acid with wide-ranging application in the medical, cosmetic, and chemical sectors.
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Affiliation(s)
- Azhar A Alhasawi
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sean C Thomas
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sujeethar Tharmalingam
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada.,Department of Biology, Laurentian University, Sudbury, ON, Canada.,Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada.,Northern Ontario School of Medicine, Laurentian University, Sudbury, ON, Canada
| | - Felix Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Vasu D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
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Exploiting the natural poly(3-hydroxyalkanoates) production capacity of Antarctic Pseudomonas strains: from unique phenotypes to novel biopolymers. ACTA ACUST UNITED AC 2019; 46:1139-1153. [DOI: 10.1007/s10295-019-02186-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/07/2019] [Indexed: 12/11/2022]
Abstract
Abstract
Extreme environments are a unique source of microorganisms encoding metabolic capacities that remain largely unexplored. In this work, we isolated two Antarctic bacterial strains able to produce poly(3-hydroxyalkanoates) (PHAs), which were classified after 16S rRNA analysis as Pseudomonas sp. MPC5 and MPC6. The MPC6 strain presented nearly the same specific growth rate whether subjected to a temperature of 4 °C 0.18 (1/h) or 30 °C 0.2 (1/h) on glycerol. Both Pseudomonas strains produced high levels of PHAs and exopolysaccharides from glycerol at 4 °C and 30 °C in batch cultures, an attribute that has not been previously described for bacteria of this genus. The MPC5 strain produced the distinctive medium-chain-length-PHA whereas Pseudomonas sp. MPC6 synthesized a novel polyoxoester composed of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate-co-3-hydroxydecanoate-co-3-hydroxydodecanoate). Batch bioreactor production of PHAs in MPC6 resulted in a titer of 2.6 (g/L) and 1.3 (g/L), accumulating 47.3% and 34.5% of the cell dry mass as PHA, at 30 and 4 °C, respectively. This study paves the way for using Antarctic Pseudomonas strains for biosynthesizing novel PHAs from low-cost substrates such as glycerol and the possibility to carry out the bioconversion process for biopolymer synthesis without the need for temperature control.
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50
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Sánchez-Pascuala A, Fernández-Cabezón L, de Lorenzo V, Nikel PI. Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida. Metab Eng 2019; 54:200-211. [DOI: 10.1016/j.ymben.2019.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 01/23/2023]
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