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Guo Q, Dong ZX, Luo X, Zheng LJ, Fan LH, Zheng HD. Engineering Escherichia coli for D-allulose biosynthesis from glycerol. J Biotechnol 2024; 394:103-111. [PMID: 39181208 DOI: 10.1016/j.jbiotec.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/07/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
D-allulose, a naturally occurring monosaccharide, is present in small quantities in nature. It is considered a valuable low-calorie sweetener due to its low absorption in the digestive tract and zero energy for growth. Most of the recent efforts to produce D-allulose have focused on in vitro enzyme catalysis. However, microbial fermentation is emerging as a promising alternative that offers the advantage of combining enzyme manufacturing and product synthesis within a single bioreactor. Here, a novel approach was proposed for the efficient biosynthesis of D-allulose from glycerol using metabolically engineered Escherichia coli. FbaA, Fbp, AlsE, and A6PP were used to construct the D-allulose synthesis pathway. Subsequently, PfkA, PfkB, and Pgi were disrupted to block the entry of the intermediate fructose-6-phosphate (F6P) into the Embden-Meyerhof-Parnas (EMP) and pentose phosphate (PP) pathways. Additionally, GalE and FryA were inactivated to reduce D-allulose consumption by the cells. Finally, a fed-batch fermentation process was implemented to optimize the performance of the cell factory. As a result, the titer of D-allulose reached 7.02 g/L with a maximum yield of 0.287 g/g.
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Affiliation(s)
- Qiang Guo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China
| | - Zhen-Xing Dong
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China
| | - Xuan Luo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China
| | - Ling-Jie Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China; Qingyuan Innovation Laboratory, Quanzhou 362801, China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China; Qingyuan Innovation Laboratory, Quanzhou 362801, China.
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, China; Qingyuan Innovation Laboratory, Quanzhou 362801, China.
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2
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Shin J, Zielinski DC, Palsson BO. Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering. Metab Eng 2024; 84:34-47. [PMID: 38825177 DOI: 10.1016/j.ymben.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of Vibrio natriegens to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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3
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Lara AR, Kunert F, Vandenbroucke V, Taymaz-Nikerel H, Martínez LM, Sigala JC, Delvigne F, Gosset G, Büchs J. Transport-controlled growth decoupling for self-induced protein expression with a glycerol-repressible genetic circuit. Biotechnol Bioeng 2024; 121:1789-1802. [PMID: 38470342 DOI: 10.1002/bit.28697] [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: 12/04/2023] [Revised: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Decoupling cell formation from recombinant protein synthesis is a potent strategy to intensify bioprocesses. Escherichia coli strains with mutations in the glucose uptake components lack catabolite repression, display low growth rate, no overflow metabolism, and high recombinant protein yields. Fast growth rates were promoted by the simultaneous consumption of glucose and glycerol, and this was followed by a phase of slow growth, when only glucose remained in the medium. A glycerol-repressible genetic circuit was designed to autonomously induce recombinant protein expression. The engineered strain bearing the genetic circuit was cultured in 3.9 g L-1 glycerol + 18 g L-1 glucose in microbioreactors with online oxygen transfer rate monitoring. The growth was fast during the simultaneous consumption of both carbon sources (C-sources), while expression of the recombinant protein was low. When glycerol was depleted, the growth rate decreased, and the specific fluorescence reached values 17% higher than those obtained with a strong constitutive promoter. Despite the relatively high amount of C-source used, no oxygen limitation was observed. The proposed approach eliminates the need for the substrate feeding or inducers addition and is set as a simple batch culture while mimicking fed-batch performance.
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Affiliation(s)
- Alvaro R Lara
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Flavio Kunert
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Vincent Vandenbroucke
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Turkey
| | - Luz María Martínez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Guillermo Gosset
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jochen Büchs
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
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4
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Zion S, Katz S, Hershberg R. Escherichia coli adaptation under prolonged resource exhaustion is characterized by extreme parallelism and frequent historical contingency. PLoS Genet 2024; 20:e1011333. [PMID: 38885285 PMCID: PMC11213340 DOI: 10.1371/journal.pgen.1011333] [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: 01/10/2024] [Revised: 06/28/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Like many other non-sporulating bacterial species, Escherichia coli is able to survive prolonged periods of resource exhaustion, by entering a state of growth called long-term stationary phase (LTSP). In July 2015, we initiated a set of evolutionary experiments aimed at characterizing the dynamics of E. coli adaptation under LTSP. In these experiments populations of E. coli were allowed to initially grow on fresh rich media, but were not provided with any new external growth resources since their establishment. Utilizing whole genome sequencing data obtained for hundreds of clones sampled at 12 time points spanning the first six years of these experiments, we reveal several novel aspects of the dynamics of adaptation. First, we show that E. coli continuously adapts genetically, up to six years under resource exhaustion, through the highly convergent accumulation of mutations. We further show that upon entry into LTSP, long-lasting lineages are established. This lineage structure is in itself convergent, with similar lineages arising across independently evolving populations. The high parallelism with which adaptations occur under LTSP, combined with the LTSP populations' lineage structure, enable us to screen for pairs of loci displaying a significant association in the occurrence of mutations, suggestive of a historical contingency. We find that such associations are highly frequent and that a third of convergently mutated loci are involved in at least one such association. Combined our results demonstrate that LTSP adaptation is characterized by remarkably high parallelism and frequent historical contingency.
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Affiliation(s)
- Shira Zion
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sophia Katz
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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5
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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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6
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Allaert Y, Leyder A, Franceus J, Desmet T. Strategies for the synthesis of the osmolyte glucosylglycerate and its precursor glycerate. Appl Microbiol Biotechnol 2024; 108:297. [PMID: 38607564 PMCID: PMC11009771 DOI: 10.1007/s00253-024-13139-w] [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: 02/20/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Glycosidic osmolytes are widespread natural compounds that protect microorganisms and their macromolecules from the deleterious effects of various environmental stresses. Their protective properties have attracted considerable interest for industrial applications, especially as active ingredients in cosmetics and healthcare products. In that regard, the osmolyte glucosylglycerate is somewhat overlooked. Glucosylglycerate is typically accumulated by certain organisms when they are exposed to high salinity and nitrogen starvation, and its potent stabilizing effects have been demonstrated in vitro. However, the applications of this osmolyte have not been thoroughly explored due to the lack of a cost-efficient production process. Here, we present an overview of the progress that has been made in developing promising strategies for the synthesis of glucosylglycerate and its precursor glycerate, and discuss the remaining challenges. KEY POINTS: • Bacterial milking could be explored for fermentative production of glucosylglycerate • Glycoside phosphorylases of GH13_18 represent attractive alternatives for biocatalytic production • Conversion of glycerol with alditol oxidase is a promising strategy for generating the precursor glycerate.
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Affiliation(s)
- Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Arthur Leyder
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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7
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Dodia H, Mishra V, Nakrani P, Muddana C, Kedia A, Rana S, Sahasrabuddhe D, Wangikar PP. Dynamic flux balance analysis of high cell density fed-batch culture of Escherichia coli BL21 (DE3) with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2024; 121:1394-1406. [PMID: 38214104 DOI: 10.1002/bit.28654] [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: 08/23/2023] [Revised: 12/08/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
Dynamic flux balance analysis (FBA) allows estimation of intracellular reaction rates using organism-specific genome-scale metabolic models (GSMM) and by assuming instantaneous pseudo-steady states for processes that are inherently dynamic. This technique is well-suited for industrial bioprocesses employing complex media characterized by a hierarchy of substrate uptake and product secretion. However, knowledge of exchange rates of many components of the media would be required to obtain meaningful results. Here, we performed spent media analysis using mass spectrometry coupled with liquid and gas chromatography for a fed-batch, high-cell density cultivation of Escherichia coli BL21(DE3) expressing a recombinant protein. Time course measurements thus obtained for 246 metabolites were converted to instantaneous exchange rates. These were then used as constraints for dynamic FBA using a previously reported GSMM, thus providing insights into how the flux map evolves through the process. Changes in tri-carboxylic acid cycle fluxes correlated with the increased demand for energy during recombinant protein production. The results show how amino acids act as hubs for the synthesis of other cellular metabolites. Our results provide a deeper understanding of an industrial bioprocess and will have implications in further optimizing the process.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vivek Mishra
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | | | | | - Anant Kedia
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Sneha Rana
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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8
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [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] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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9
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Park T, Kang JY, Jin M, Yang J, Kim H, Noh C, Jung CH, Eom SH. Structural insights into the octamerization of glycerol dehydrogenase. PLoS One 2024; 19:e0300541. [PMID: 38483875 PMCID: PMC10939272 DOI: 10.1371/journal.pone.0300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Glycerol dehydrogenase (GDH) catalyzes glycerol oxidation to dihydroxyacetone in a NAD+-dependent manner. As an initiator of the oxidative pathway of glycerol metabolism, a variety of functional and structural studies of GDH have been conducted previously. Structural studies revealed intriguing features of GDH, like the flexible β-hairpin and its significance. Another commonly reported structural feature is the enzyme's octameric oligomerization, though its structural details and functional significance remained unclear. Here, with a newly reported GDH structure, complexed with both NAD+ and glycerol, we analyzed the octamerization of GDH. Structural analyses revealed that octamerization reduces the structural dynamics of the N-domain, which contributes to more consistently maintaining a distance required for catalysis between the cofactor and substrate. This suggests that octamerization may play a key role in increasing the likelihood of the enzyme reaction by maintaining the ligands in an appropriate configuration for catalysis. These findings expand our understanding of the structure of GDH and its relation to the enzyme's activity.
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Affiliation(s)
- Taein Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Minwoo Jin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jihyeong Yang
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyunwoo Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Chaemin Noh
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Che-Hun Jung
- Department of Molecular Medicine, Chonnam National University, Gwangju, Republic of Korea
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Soo Hyun Eom
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [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: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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Smith JJ, Valentino TR, Ablicki AH, Banerjee R, Colligan AR, Eckert DM, Desjardins GA, Diehl KL. A genetically-encoded fluorescent biosensor for visualization of acetyl-CoA in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573774. [PMID: 38260544 PMCID: PMC10802309 DOI: 10.1101/2023.12.31.573774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Acetyl-coenzyme A is a central metabolite that participates in many cellular pathways. Evidence suggests that acetyl-CoA production and consumption are highly compartmentalized in mammalian cells. Yet methods to measure acetyl-CoA in living cells are lacking. In this work, we engineer an acetyl-CoA biosensor from the bacterial protein PanZ and circularly permuted green fluorescent protein (cpGFP). We biochemically characterize the sensor and demonstrate its selectivity for acetyl-CoA over other CoA species. We then deploy the biosensor in E. coli and HeLa cells to demonstrate its utility in living cells. In E. coli, we show that the biosensor enables detection of rapid changes in acetyl-CoA levels. In human cells, we show that the biosensor enables subcellular detection and reveals the compartmentalization of acetyl-CoA metabolism.
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12
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Lee JH, Lee SR, Lee SY, Lee PC. Complete microbial synthesis of crocetin and crocins from glycerol in Escherichia coli. Microb Cell Fact 2024; 23:10. [PMID: 38178149 PMCID: PMC10765794 DOI: 10.1186/s12934-023-02287-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Crocin, a glycosylated apocarotenoid pigment predominantly found in saffron, has garnered significant interest in the field of biotechnology for its bioactive properties. Traditional production of crocins and their aglycone, crocetin, typically involves extraction from crocin-producing plants. This study aimed to develop an alternative biosynthetic method for these compounds by engineering the metabolic pathways of zeaxanthin, crocetin, and crocin in Escherichia coli strains. RESULTS Employing a series of genetic modifications and the strategic overexpression of key enzymes, we successfully established a complete microbial pathway for synthesizing crocetin and four glycosylated derivatives of crocetin, utilizing glycerol as the primary carbon source. The overexpression of zeaxanthin cleavage dioxygenase and a novel variant of crocetin dialdehyde dehydrogenase resulted in a notable yield of crocetin (34.77 ± 1.03 mg/L). Further optimization involved the overexpression of new types of crocetin and crocin-2 glycosyltransferases, facilitating the production of crocin-1 (6.29 ± 0.19 mg/L), crocin-2 (5.29 ± 0.24 mg/L), crocin-3 (1.48 ± 0.10 mg/L), and crocin-4 (2.72 ± 0.13 mg/L). CONCLUSIONS This investigation introduces a pioneering and integrated microbial synthesis method for generating crocin and its derivatives, employing glycerol as a sustainable carbon feedstock. The substantial yields achieved highlight the commercial potential of microbial-derived crocins as an eco-friendly alternative to plant extraction methods. The development of these microbial processes not only broadens the scope for crocin production but also suggests significant implications for the exploitation of bioengineered compounds in pharmaceutical and food industries.
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Affiliation(s)
- Jun Ho Lee
- Department of Molecular Science and Technology, Department of Applied Chemical and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Seong-Rae Lee
- Department of Molecular Science and Technology, Department of Applied Chemical and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Department of Applied Chemical and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 16499, Republic of Korea.
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Park T, Hoang HN, Kang JY, Park J, Mun SA, Jin M, Yang J, Jung CH, Eom SH. Structural and functional insights into the flexible β-hairpin of glycerol dehydrogenase. FEBS J 2023; 290:4342-4355. [PMID: 37165682 DOI: 10.1111/febs.16813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/17/2023] [Accepted: 05/09/2023] [Indexed: 05/12/2023]
Abstract
During glycerol metabolism, the initial step of glycerol oxidation is catalysed by glycerol dehydrogenase (GDH), which converts glycerol to dihydroxyacetone in a NAD+ -dependent manner via an ordered Bi-Bi kinetic mechanism. Structural studies conducted with GDH from various species have mainly elucidated structural details of the active site and ligand binding. However, the structure of the full GDH complex with both cofactor and substrate bound is not determined, and thus, the structural basis of the kinetic mechanism of GDH remains unclear. Here, we report the crystal structures of Escherichia coli GDH with a substrate analogue bound in the absence or presence of NAD+ . Structural analyses including molecular dynamics simulations revealed that GDH possesses a flexible β-hairpin, and that during the ordered progression of the kinetic mechanism, the flexibility of the β-hairpin is reduced after NAD+ binding. It was also observed that this alterable flexibility of the β-hairpin contributes to the cofactor binding and possibly to the catalytic efficiency of GDH. These findings suggest the importance of the flexible β-hairpin to GDH enzymatic activity and shed new light on the kinetic mechanism of GDH.
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Affiliation(s)
- Taein Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
| | - Huyen Nga Hoang
- Department of Molecular Medicine, Chonnam National University, Gwangju, Korea
- Hanoi Medical University, Hanoi, Vietnam
| | - Jung Youn Kang
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jongseo Park
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
| | - Sang A Mun
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
| | - Minwoo Jin
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
| | - Jihyeong Yang
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
| | - Che-Hun Jung
- Department of Molecular Medicine, Chonnam National University, Gwangju, Korea
- Department of Chemistry, Chonnam National University, Gwangju, Korea
| | - Soo Hyun Eom
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Korea
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14
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Van Zyl WF, Van Staden AD, Dicks LMT, Trindade M. Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli. Microb Cell Fact 2023; 22:149. [PMID: 37559122 PMCID: PMC10413542 DOI: 10.1186/s12934-023-02162-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/29/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Lanthipeptides are a rapidly expanding family of ribosomally synthesized and post-translationally modified natural compounds with diverse biological functions. Lanthipeptide structural and biosynthetic genes can readily be identified in genomic datasets, which provides a substantial repository for unique peptides with a wide range of potentially novel bioactivities. To realize this potential efficiently optimized heterologous production systems are required. However, only a few class I lanthipeptides have been successfully expressed using Escherichia coli as heterologous producer. This may be attributed to difficulties experienced in the co-expression of structural genes and multiple processing genes as well as complex optimization experiments. RESULTS Here, an optimized modular plasmid system is presented for the complete biosynthesis for each of the class I lanthipeptides nisin and clausin, in E. coli. Genes encoding precursor lanthipeptides were fused to the gene encoding the mCherry red fluorescent protein and co-expressed along with the required synthetases from the respective operons. Antimicrobially active nisin and clausin were proteolytically liberated from the expressed mCherry fusions. The mCherry-NisA expression system combined with in vivo fluorescence monitoring was used to elucidate the effect of culture media composition, promoter arrangement, and culture conditions including choice of growth media and inducer agents on the heterologous expression of the class I lanthipeptides. To evaluate the promiscuity of the clausin biosynthetic enzymes, the optimized clausin expression system was used for the heterologous expression of epidermin. CONCLUSION We succeeded in developing novel mCherry-fusion based plug and play heterologous expression systems to produce two different subgroups of class I lanthipeptides. Fully modified Pre-NisA, Pre-ClausA and Pre-EpiA fused to the mCherry fluorescence gene was purified from the Gram-negative host E. coli BL21 (DE3). Our study demonstrates the potential of using in vivo fluorescence as a platform to evaluate the expression of mCherry-fused lanthipeptides in E. coli. This allowed a substantial reduction in optimization time, since expression could be monitored in real-time, without the need for extensive and laborious purification steps or the use of in vitro activity assays. The optimized heterologous expression systems developed in this study may be employed in future studies for the scalable expression of novel NisA derivatives, or novel genome mined derivatives of ClausA and other class I lanthipeptides in E. coli.
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Affiliation(s)
- Winschau F Van Zyl
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa.
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa.
| | - Anton D Van Staden
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
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15
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Molinari PE, Krapp AR, Weiner A, Beyer HM, Kondadi AK, Blomeier T, López M, Bustos-Sanmamed P, Tevere E, Weber W, Reichert AS, Calcaterra NB, Beller M, Carrillo N, Zurbriggen MD. NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems. Nat Commun 2023; 14:3277. [PMID: 37280202 DOI: 10.1038/s41467-023-38739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
NADP(H) is a central metabolic hub providing reducing equivalents to multiple biosynthetic, regulatory and antioxidative pathways in all living organisms. While biosensors are available to determine NADP+ or NADPH levels in vivo, no probe exists to estimate the NADP(H) redox status, a determinant of the cell energy availability. We describe herein the design and characterization of a genetically-encoded ratiometric biosensor, termed NERNST, able to interact with NADP(H) and estimate ENADP(H). NERNST consists of a redox-sensitive green fluorescent protein (roGFP2) fused to an NADPH-thioredoxin reductase C module which selectively monitors NADP(H) redox states via oxido-reduction of the roGFP2 moiety. NERNST is functional in bacterial, plant and animal cells, and organelles such as chloroplasts and mitochondria. Using NERNST, we monitor NADP(H) dynamics during bacterial growth, environmental stresses in plants, metabolic challenges to mammalian cells, and wounding in zebrafish. NERNST estimates the NADP(H) redox poise in living organisms, with various potential applications in biochemical, biotechnological and biomedical research.
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Affiliation(s)
- Pamela E Molinari
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Adriana R Krapp
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Andrea Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Hannes M Beyer
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - Arun Kumar Kondadi
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - Melina López
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Pilar Bustos-Sanmamed
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Evelyn Tevere
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- INM - Leibniz Institute for New Materials and Department of Materials Sciences and Engineering, Saarland University, Saarbrücken, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Mathias Beller
- Institute of Mathematical Modeling of Biological Systems, University of Düsseldorf, Düsseldorf, Germany
| | - Nestor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina.
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.
- CEPLAS - Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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16
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Stinson LF, George AD. Human Milk Lipids and Small Metabolites: Maternal and Microbial Origins. Metabolites 2023; 13:metabo13030422. [PMID: 36984862 PMCID: PMC10054125 DOI: 10.3390/metabo13030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Although there has been limited application in the field to date, human milk omics research continues to gain traction. Human milk lipidomics and metabolomics research is particularly important, given the significance of milk lipids and metabolites for infant health. For researchers conducting compositional milk analyses, it is important to consider the origins of these compounds. The current review aims to provide a summary of the existing evidence on the sources of human milk lipids and small metabolites. Here, we describe five major sources of milk lipids and metabolites: de novo synthesis from mammary cells, production by the milk microbiota, dietary consumption, release from non-mammary tissue, and production by the gut microbiota. We synthesize the literature to provide evidence and understanding of these pathways in the context of mammary gland biology. We recommend future research focus areas to elucidate milk lipid and small metabolite synthesis and transport pathways. Better understanding of the origins of human milk lipids and metabolites is important to improve translation of milk omics research, particularly regarding the modulation of these important milk components to improve infant health outcomes.
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Affiliation(s)
- Lisa F. Stinson
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
| | - Alexandra D. George
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne 3004, Australia
- Correspondence:
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17
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de Divitiis M, Ami D, Pessina A, Palmioli A, Sciandrone B, Airoldi C, Regonesi ME, Brambilla L, Lotti M, Natalello A, Brocca S, Mangiagalli M. Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:30. [PMID: 36823649 PMCID: PMC9948444 DOI: 10.1186/s13068-023-02281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose. RESULTS The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness. CONCLUSIONS CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
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Affiliation(s)
- Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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18
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Wagner N, Bade F, Straube E, Rabe K, Frazão CJR, Walther T. In vivo implementation of a synthetic metabolic pathway for the carbon-conserving conversion of glycolaldehyde to acetyl-CoA. Front Bioeng Biotechnol 2023; 11:1125544. [PMID: 36845174 PMCID: PMC9947464 DOI: 10.3389/fbioe.2023.1125544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Ethylene glycol (EG) derived from plastic waste or CO2 can serve as a substrate for microbial production of value-added chemicals. Assimilation of EG proceeds though the characteristic intermediate glycolaldehyde (GA). However, natural metabolic pathways for GA assimilation have low carbon efficiency when producing the metabolic precursor acetyl-CoA. In alternative, the reaction sequence catalyzed by EG dehydrogenase, d-arabinose 5-phosphate aldolase, d-arabinose 5-phosphate isomerase, d-ribulose 5-phosphate 3-epimerase (Rpe), d-xylulose 5-phosphate phosphoketolase, and phosphate acetyltransferase may enable the conversion of EG into acetyl-CoA without carbon loss. We investigated the metabolic requirements for in vivo function of this pathway in Escherichia coli by (over)expressing constituting enzymes in different combinations. Using 13C-tracer experiments, we first examined the conversion of EG to acetate via the synthetic reaction sequence and showed that, in addition to heterologous phosphoketolase, overexpression of all native enzymes except Rpe was required for the pathway to function. Since acetyl-CoA could not be reliably quantified by our LC/MS-method, the distribution of isotopologues in mevalonate, a stable metabolite that is exclusively derived from this intermediate, was used to probe the contribution of the synthetic pathway to biosynthesis of acetyl-CoA. We detected strong incorporation of 13C carbon derived from labeled GA in all intermediates of the synthetic pathway. In presence of unlabeled co-substrate glycerol, 12.4% of the mevalonate (and therefore acetyl-CoA) was derived from GA. The contribution of the synthetic pathway to acetyl-CoA production was further increased to 16.1% by the additional expression of the native phosphate acyltransferase enzyme. Finally, we demonstrated that conversion of EG to mevalonate was feasible albeit at currently extremely small yields.
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Affiliation(s)
- Nils Wagner
- TU Dresden, Institute of Natural Materials Technology, Dresden, Germany
| | - Frederik Bade
- TU Dresden, Institute of Natural Materials Technology, Dresden, Germany
| | - Elly Straube
- TU Dresden, Institute of Natural Materials Technology, Dresden, Germany
| | - Kenny Rabe
- TU Dresden, Institute of Natural Materials Technology, Dresden, Germany
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19
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Lozano-Terol G, Gallego-Jara J, Sola-Martínez RA, Ortega Á, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Regulation of the pyrimidine biosynthetic pathway by lysine acetylation of E. coli OPRTase. FEBS J 2023; 290:442-464. [PMID: 35989594 PMCID: PMC10087573 DOI: 10.1111/febs.16598] [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: 02/21/2022] [Revised: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 02/05/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is an important route due to the relevance of its products, its implications in health and its conservation among organisms. Here, we investigated the regulation by lysine acetylation of this pathway. To this aim, intracellular and extracellular metabolites of the route were quantified, revealing a possible blockage of the pathway by acetylation of the OPRTase enzyme (orotate phosphoribosyltransferase). Chemical acetylation of OPRTase by acetyl-P involved a decrease in enzymatic activity. To test the effect of acetylation in this enzyme, K26 and K103 residues were selected to generate site-specific acetylated proteins. Several differences were observed in kinetic parameters, emphasizing that the kcat of these mutants showed a strong decrease of 300 and 150-fold for OPRTase-103AcK and 19 and 6.3-fold for OPRTase-26AcK, for forward and reverse reactions. In vivo studies suggested acetylation of this enzyme by a nonenzymatic acetyl-P-dependent mechanism and a reversion of this process by the CobB deacetylase. A complementation assay of a deficient strain in the pyrE gene with OPRTase-26AcK and OPRTase-103AcK was performed, and curli formation, stoichiometric parameters and orotate excretion were measured. Complementation with acetylated enzymes entailed a profile very similar to that of the ∆pyrE strain, especially in the case of complementation with OPRTase-103AcK. These results suggest regulation of the de novo pyrimidine biosynthesis pathway by lysine acetylation of OPRTase in Escherichia coli. This finding is of great relevance due to the essential role of this route and the OPRTase enzyme as a target for antimicrobial, antiviral and cancer treatments.
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
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20
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Yeast Mannan-Rich Fraction Modulates Endogenous Reactive Oxygen Species Generation and Antibiotic Sensitivity in Resistant E. coli. Int J Mol Sci 2022; 24:ijms24010218. [PMID: 36613662 PMCID: PMC9820725 DOI: 10.3390/ijms24010218] [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: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Mannan-rich fraction (MRF) isolated from Saccharomyces cerevisiae has been studied for its beneficial impact on animal intestinal health. Herein, we examined how MRF affected the formation of reactive oxygen species (ROS), impacting antibiotic susceptibility in resistant Escherichia coli through the modulation of bacterial metabolism. The role of MRF in effecting proteomic change was examined using a proteomics-based approach. The results showed that MRF, when combined with bactericidal antibiotic treatment, increased ROS production in resistant E. coli by 59.29 ± 4.03% compared to the control (p ≤ 0.05). We further examined the effect of MRF alone and in combination with antibiotic treatment on E. coli growth and explored how MRF potentiates bacterial susceptibility to antibiotics via proteomic changes in key metabolic pathways. Herein we demonstrated that MRF supplementation in the growth media of ampicillin-resistant E. coli had a significant impact on the normal translational control of the central metabolic pathways, including those involved in the glycolysis-TCA cycle (p ≤ 0.05).
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21
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Ortiz-Padilla M, Portillo-Calderón I, Velázquez-Escudero A, Rodríguez-Baño J, Pascual Á, Rodríguez-Martínez JM, Docobo-Pérez F. Effect of Glycerol on Fosfomycin Activity against Escherichia coli. Antibiotics (Basel) 2022; 11:antibiotics11111612. [PMID: 36421256 PMCID: PMC9686493 DOI: 10.3390/antibiotics11111612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Fosfomycin is an antimicrobial that inhibits the biosynthesis of peptidoglycan by entering the bacteria through two channels (UhpT and GlpT). Glycerol is clinically used as a treatment for elevated intracranial pressure and induces the expression of glpT in Escherichia coli. Glycerol might offer synergistic activity by increasing fosfomycin uptake. The present study evaluates the use of glycerol at physiological concentrations in combination with fosfomycin against a collection of isogenic mutants of fosfomycin-related genes in E. coli strains. Induction of fosfomycin transporters, susceptibility tests, interaction assays, and time-kill assays were performed. Our results support the notion that glycerol allows activation of the GlpT transporter, but this induction is delayed over time and is not homogeneous across the bacterial population, leading to contradictory results regarding the enhancement of fosfomycin activity. The susceptibility assays showed an increase in fosfomycin activity with glycerol in the disk diffusion assay but not in the agar dilution or broth microdilution assays. Similarly, in the time-kill assays, the effect of glycerol was absent by the emergence of fosfomycin-resistant subpopulations. In conclusion, glycerol may not be a good candidate for use as an adjuvant with fosfomycin.
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Affiliation(s)
- Miriam Ortiz-Padilla
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
| | - Inés Portillo-Calderón
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - Ana Velázquez-Escudero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - José Manuel Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
- Correspondence: (J.M.R.-M.); (F.D.-P.); Tel.: +34-95-455-6100 (J.M.R.-M. & F.D.-P.)
| | - Fernando Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
- Correspondence: (J.M.R.-M.); (F.D.-P.); Tel.: +34-95-455-6100 (J.M.R.-M. & F.D.-P.)
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22
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Wang Z, Li X, Dai Y, Yin L, Azi F, Zhou J, Dong M, Xia X. Sustainable production of genistin from glycerol by constructing and optimizing Escherichia coli. Metab Eng 2022; 74:206-219. [DOI: 10.1016/j.ymben.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/05/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
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Development of a Glycerol-Inducible Expression System for High-Yield Heterologous Protein Production in Bacillus subtilis. Microbiol Spectr 2022; 10:e0132222. [PMID: 36036634 PMCID: PMC9604022 DOI: 10.1128/spectrum.01322-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The development of efficient, low-cost, and robust expression systems is important for the mass production of proteins and natural products in large amounts using cell factories. Glycerol is an ideal carbon source for large-scale fermentation due to its low cost and favorable maintenance of the fermentation process. Here, we used the antiterminator protein GlpP and its target promoter PglpD to construct a highly efficient glycerol-inducible expression system (GIES) in Bacillus subtilis. This system was able to express heterologous genes in an autoinducible manner based on the sequential utilization of glucose and glycerol under the regulation of carbon catabolite repression. In such a system, the concentration of glycerol regulated the strength of gene expression, and the concentration of glucose affected both the timing of induction and the strength of gene expression. By enhancing GlpP, the GIES was further strengthened for high-level intracellular expression of aspartase and secretory expression of nattokinase. High yields of nattokinase in a 5-L fermenter through batch and fed-batch fermentation demonstrated the potential to apply the GIES for large-scale enzyme production. Through the evolution of the -10 box of PglpD, mutants with gradient activities were obtained. In addition, hybrid glycerol-inducible promoters were successfully constructed by combining the constitutive promoters and the 5' untranslated region of PglpD. Collectively, this study developed a GIES to obtain high-value products from inexpensive glycerol. More importantly, the great potential of the pair of inherent terminator and antiterminator protein as a portable biological tool for various purposes in synthetic biology is proposed. IMPORTANCE In this study, a GIES was constructed in B. subtilis by employing the antiterminator protein GlpP and the GlpP-regulated promoter PglpD. Based on the sequential utilization of glucose and glycerol by B. subtilis, the GIES was able to express genes in an autoinducible manner. The amounts and ratio of glucose and glycerol can regulate the gene induction timing and expression strength. The GIES was further applied for high yields of nattokinase, and its robustness in production scale-up was confirmed in a 5-L fermenter. The high-level expression of heterologous proteins demonstrated the huge application potential of the GIES. Furthermore, mutants of PglpD with gradient activities and hybrid glycerol-inducible promoters were obtained through the evolution of the -10 box of PglpD and the combination of the constitutive promoters and the 5' untranslated region of PglpD, respectively. These results demonstrated the use of the antiterminator protein as a regulator for various purposes in synthetic biology.
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Effendi SSW, Ng IS. Reprogramming T7RNA Polymerase in Escherichia coli Nissle 1917 under Specific Lac Operon for Efficient p-Coumaric Acid Production. ACS Synth Biol 2022; 11:3471-3481. [PMID: 36087056 DOI: 10.1021/acssynbio.2c00363] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lac operon is the standard regulator used to control the orthogonality of T7RNA polymerase (T7RNAP) and T7 promoter inEscherichia coli BL21(DE3) strain for protein expression. However,E. coliNissle 1917 (EcN), the unique probiotic strain, has seldom been precisely adapted to the T7 system. Herein, we applied bioinformatics analysis on Lac operon from different strains, and it was observed that a weak promoter for LacI repressor existed in EcN. Furthermore, X-gal assay revealed a strong expression of lacZ in EcN. We demonstrated that Lac operon significantly affected the protein expression in the two T7-derived EcN, in which T7RNAP was integrated at lambda (ET7L) and HK022 (ET7H), respectively. Different combinations of replication origin, chaperonin GroELS, inducer, and medium were explored to fine-tune the best strain with tyrosine ammonia-lyase (TAL) for p-coumaric acid (pCA) production, which is one of the essential bioactive compounds for human health. Finally, the highest pCA conversion of 78.8% was achieved using RRtL (plasmid form) under the optimum condition, and a 51.5% conversion was obtained with L::Rt strain which has integrated T7-RtTAL at HK022 of ET7L in the simulated gut environment. The appropriate reprogramming of T7RNAP expedites EcN as an effective and promising cell factory for live bacterial therapeutics in the future.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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25
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Chiang CJ, Hu MC, Ta T, Chao YP. Glutamate as a non-conventional substrate for high production of the recombinant protein in Escherichia coli. Front Microbiol 2022; 13:991963. [PMID: 36187956 PMCID: PMC9515452 DOI: 10.3389/fmicb.2022.991963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
The economic viability of the biomass-based biorefinery is readily acknowledged by implementation of a cascade process that produces value-added products such as enzymes prior to biofuels. Proteins from the waste stream of biorefinery processes generally contain glutamate (Glu) in abundance. Accordingly, this study was initiated to explore the potential of Glu for production of recombinant proteins in Escherichia coli. The approach was first adopted by expression of D-hydantoinase (HDT) in commercially-available BL21(DE3) strain. Equipped with the mutant gltS (gltS*), the strain grown on Glu produced the maximum HDT as compared to the counterpart on glucose, glycerol, or acetate. The Glu-based production scheme was subsequently reprogrammed based on the L-arabinose-regulated T7 expression system. The strain with gltS* was further engineered by rewiring metabolic pathways. With low ammonium, the resulting strain produced 1.63-fold more HDT. The result indicates that Glu can serve as a carbon and nitrogen source. Overall, our proposed approach may open up a new avenue for the enzyme biorefinery platform based on Glu.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Mu-Chen Hu
- Department of Chemical Engineering, Feng Chia University, Taichung, Taiwan
| | - Thanh Ta
- Department of Chemical Engineering, Feng Chia University, Taichung, Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung, Taiwan
- *Correspondence: Yun-Peng Chao,
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26
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Lin WH, Jacobs-Wagner C. Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli. Curr Biol 2022; 32:3911-3924.e4. [PMID: 35961315 DOI: 10.1016/j.cub.2022.07.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 10/15/2022]
Abstract
Adenosine triphosphate (ATP) is an abundant and essential metabolite that cells consume and regenerate in large amounts to support growth. Although numerous studies have inferred the intracellular concentration of ATP in bacterial cultures, what happens in individual bacterial cells under stable growth conditions is less clear. Here, we use the QUEEN-2m biosensor to quantify ATP dynamics in single Escherichia coli cells in relation to their growth rate, metabolism, cell cycle, and cell lineage. We find that ATP dynamics are more complex than expected from population studies and are associated with growth-rate variability. Under stable nutrient-rich condition, cells can display large fluctuations in ATP level that are partially coordinated with the cell cycle. Abrogation of aerobic acetate fermentation (overflow metabolism) through genetic deletion considerably reduces both the amplitude of ATP level fluctuations and the cell-cycle trend. Similarly, growth in media in which acetate fermentation is lower or absent results in the reduction of ATP level fluctuation and cell-cycle trend. This suggests that overflow metabolism exhibits temporal dynamics, which contributes to fluctuating ATP levels during growth. Remarkably, at the single-cell level, growth rate negatively correlates with the amplitude of ATP fluctuation for each tested condition, linking ATP dynamics to growth-rate heterogeneity in clonal populations. Our work highlights the importance of single-cell analysis in studying metabolism and its implication to phenotypic diversity and cell growth.
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Affiliation(s)
- Wei-Hsiang Lin
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA.
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27
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Eghtesadi N, Olaifa K, Perna FM, Capriati V, Trotta M, Ajunwa O, Marsili E. Electroactivity of weak electricigen Bacillus subtilis biofilms in solution containing deep eutectic solvent components. Bioelectrochemistry 2022; 147:108207. [PMID: 35839687 DOI: 10.1016/j.bioelechem.2022.108207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022]
Abstract
Bacillus subtilis is a Gram-positive, spore-forming bacterium with a versatile and adaptable metabolism, which makes it a viable cell factory for microbial production. Electroactivity has recently been identified as a cellular characteristic linked with the metabolic activity of B. subtilis. The enhancement of B. subtilis electroactivity can positively enhance bioproduction of high-added value metabolites under electrofermentative conditions. Here, we explored the use of deep eutectic solvents (DESs) and DES components as biocompatible nutrient additives for enhancing electroactivity of B. subtilis. The strongest electroactivity was obtained in an aqueous choline chloride: glycerol (1:2 mol mol-1) eutectic mixture. At low concentration (50-500 mM), this mixture induced a pseudo-diauxic increase in planktonic growth and increased biofilm formation, likely due to a nutritional and osmoprotectant effect. Similarities in electroactivity enhancements of choline chloride-based eutectic mixtures and quinone redox metabolism in B. subtilis were detected using high performance liquid chromatography and differential pulse voltammetry. Results show that choline chloride-based aqueous eutectic mixtures can enhance biomass and productivity in biofilm-based electrofermentation. However, the specific mechanism needs to be fully elucidated.
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Affiliation(s)
- Neda Eghtesadi
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan
| | - Kayode Olaifa
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan
| | - Filippo Maria Perna
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro," via E. Orabona 4, I-70125 Bari, Italy
| | - Vito Capriati
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro," via E. Orabona 4, I-70125 Bari, Italy
| | - Massimo Trotta
- Istituto per i Processi Chimico Fisici, CNR, via E. Orabona 4, I-70125 Bari, Italy
| | - Obinna Ajunwa
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan; Department of Microbiology, Modibbo Adama University, Yola, Nigeria.
| | - Enrico Marsili
- Biofilm Laboratory, Nazarbayev University, 53 Kabanbay Batyr Avenue, Nur-Sultan 01000, Kazakhstan.
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González-López I, Medrano-Félix JA, Castro-Del Campo N, López-Cuevas O, Ibarra Rodríguez JR, Martinez-Rodríguez C, Valdez-Torres JB, Chaidez C. Metabolic plasticity of Salmonella enterica as adaptation strategy in river water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1529-1541. [PMID: 33706620 DOI: 10.1080/09603123.2021.1896682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
The survival of Salmonella in subtropical river water depends on genetic and metabolic reorganization for the expression of alternative metabolic pathways in response to starvation, which allows Salmonella to use environmental carbon sources (C-sources). However, knowledge regarding the metabolic plasticity of Salmonella serotypes for C-source utilization when exposed to these conditions remains unclear. The aim of this study was to evaluate the metabolic response and level of environmental C-source consumption by environmental Salmonella (Oranienburg and Saintpaul) and clinical Salmonella (Typhi) serotypes by comparing laboratory growth against exposure to river water conditions. Metabolic characterization was performed using a Biolog® EcoPlateTM containing 31 C-sources. The results obtained under laboratory growth conditions showed that environmental serotypes used 74.1% of the C-sources, whereas the clinical serotype used 45.1%. In contrast, in river water, all strains used up to 96.7% of the C-sources. Salmonella exposure to river water increases its capacity to use environmental C-sources.
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Affiliation(s)
- Irvin González-López
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | - José Andrés Medrano-Félix
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, CONACYT-Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | - Nohelia Castro-Del Campo
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | - Osvaldo López-Cuevas
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | | | - Celida Martinez-Rodríguez
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | - José Benigno Valdez-Torres
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
| | - Cristóbal Chaidez
- Environmental Microbiology, Laboratorio Nacional Para La Investigación En Inocuidad Alimentaria, Centro De Investigación En Alimentación Y Desarrollo A.C, Culiacán, Sinaloa, México
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29
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Hsiang CC, Diankristanti PA, Tan SI, Ke YC, Chen YC, Effendi SSW, Ng IS. Tailoring key enzymes for renewable and high-level itaconic acid production using genetic Escherichia coli via whole-cell bioconversion. Enzyme Microb Technol 2022; 160:110087. [DOI: 10.1016/j.enzmictec.2022.110087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/14/2022] [Accepted: 06/16/2022] [Indexed: 11/29/2022]
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30
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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors. Sci Rep 2022; 12:8788. [PMID: 35610252 PMCID: PMC9130244 DOI: 10.1038/s41598-022-12463-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.
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31
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Current Trends in Acetins Production: Green versus Non-Green Synthesis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072255. [PMID: 35408654 PMCID: PMC9000466 DOI: 10.3390/molecules27072255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
Abstract
To utilize excess glycerol produced from the biodiesel industry, researchers are developing innovative methods of transforming glycerol into value-added chemicals. One strategy adopted is the conversion of glycerol into acetins, which are esters of glycerol that have wide applications in cosmetics, pharmaceuticals, food and fuel additives, and plasticizers and serve as precursors for other chemical compounds. Acetins are synthesized either by traditional chemical methods or by biological processes. Although the chemical methods are efficient, productive, and commercialized, they are "non-green", meaning that they are unsafe for the environment and consumers. On the other hand, the biological process is "green" in the sense that it protects both the environment and consumers. It is, however, less productive and requires further effort to achieve commercialization. Thus, both methodologies have benefits and drawbacks, and this study aims to present and discuss these. In addition, we briefly discuss general strategies for optimizing biological processes that could apply to acetins production on an industrial scale.
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32
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Peng F, Ye M, Liu Y, Liu J, Lan Y, Luo A, Zhang T, Jiang Z, Song H. Comparative genomics reveals response of Rhodococcus pyridinivorans B403 to phenol after evolution. Appl Microbiol Biotechnol 2022; 106:2751-2761. [DOI: 10.1007/s00253-022-11858-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/24/2022]
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Chemosensory Proteins (CSPs) in the Cotton Bollworm Helicoverpa armigera. INSECTS 2021; 13:insects13010029. [PMID: 35055872 PMCID: PMC8780252 DOI: 10.3390/insects13010029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary The insect chemosensory system is crucial in regulating insect behaviors. Chemosensory proteins (CSPs) are a family of small, soluble proteins conventionally known to transport odorant molecules in insect chemosensory system. Besides chemosensation, CSPs have been reported to play important roles in development, nutrient metabolism, and insecticide resistance. Therefore, identification and characterization of previously unknown CSPs will be valuable for further investigation of this protein family. The cotton bollworm, Helicoverpa armigera (Hübner) is among the most serious insect pests in various agricultural and horticultural crops. In this study, 27 CSP genes were identified from H. armigera genome and transcriptome sequences, and their expression patterns were further examined by using transcriptomic data obtained from different tissues and stages. The results demonstrate that H. armigera CSP genes are highly expressed in both chemosensory and non-chemosensory tissues. Moreover, a new recombinant expression method was developed that can significantly increase H. armigera CSP expression levels as soluble proteins in Escherichia coli. This study improves our understanding of insect CSPs and developed a new approach to highly express recombinant CSPs, which can be expanded to examine CSPs in other species for functional characterization. Abstract Chemosensory proteins (CSPs) are a family of small, soluble proteins that play a crucial role in transporting odorant and pheromone molecules in the insect chemosensory system. Recent studies reveal that they also function in development, nutrient metabolism and insecticide resistance. In-depth and systematic characterization of previously unknown CSPs will be valuable to investigate more detailed functionalities of this protein family. Here, we identified 27 CSP genes from the genome and transcriptome sequences of cotton bollworm, Helicoverpa armigera (Hübner). The expression patterns of these genes were studied by using transcriptomic data obtained from different tissues and stages. The results demonstrate that H. armigera CSP genes are not only highly expressed in chemosensory tissues, such as antennae, mouthparts, and tarsi, but also in the salivary glands, cuticle epidermis, and hind gut. HarmCSP6 and 22 were selected as candidate CSPs for expression in Escherichia coli and purification. A new method was developed that significantly increased the HarmCSP6 and 22 expression levels as soluble recombinant proteins for purification. This study advances our understanding of insect CSPs and provides a new approach to highly express recombinant CSPs in E. coli.
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34
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Mehta D, Chirmade T, Tungekar AA, Gani K, Bhambure R. Cloning and expression of antibody fragment (Fab) I: Effect of expression construct and induction strategies on light and heavy chain gene expression. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Wang Y, Zhou S, Liu Q, Jeong SH, Zhu L, Yu X, Zheng X, Wei G, Kim SW, Wang C. Metabolic Engineering of Escherichia coli for Production of α-Santalene, a Precursor of Sandalwood Oil. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13135-13142. [PMID: 34709805 DOI: 10.1021/acs.jafc.1c05486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
α-Santalene belongs to a class of natural compounds with many physiological functions and medical applications. Advances in metabolic engineering enable non-native hosts (e.g., Escherichia coli) to produce α-santalene, the precursor of sandalwood oil. However, imbalances in enzymatic activity often result in a metabolic burden on hosts and repress the synthetic capacity of the desired product. In this work, we manipulated ribosome binding sites (RBSs) to optimize an α-santalene synthetic operon in E. coli, and the best engineered E. coli NA-IS3D strain could produce α-santalene at a titer of 412 mg·L-1. Concerning the observation of the inverse correlation between indole synthesis and α-santalene production, this study speculated that indole-associated amino acid metabolism would be competitive to the synthesis of α-santalene rather than indole toxicity itself. The deletion of tnaA could lead to a 1.5-fold increase in α-santalene production to a titer of 599 mg·L-1 in E. coli tnaA- NA-IS3D. Our results suggested that the optimization of RBS sets of the synthetic module and attenuation of the competitive pathway are promising approaches for improving the production of terpenoids including α-santalene.
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Affiliation(s)
- Yan Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Shenting Zhou
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Qian Liu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Seong-Hee Jeong
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Liyan Zhu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Xiangming Yu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Xiaojian Zheng
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215006, People's Republic of China
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36
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Clomburg JM, Cintolesi A, Gonzalez R. In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Microb Biotechnol 2021; 15:289-304. [PMID: 34699695 PMCID: PMC8719807 DOI: 10.1111/1751-7915.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2 , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Angela Cintolesi
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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An Escherichia coli FdrA Variant Derived from Syntrophic Coculture with a Methanogen Increases Succinate Production Due to Changes in Allantoin Degradation. mSphere 2021; 6:e0065421. [PMID: 34494882 PMCID: PMC8550087 DOI: 10.1128/msphere.00654-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wild-type Escherichia coli was adapted to syntrophic growth with Methanobacterium formicicum for glycerol fermentation over 44 weeks. Succinate production by E. coli started to increase in the early stages of syntrophic growth. Genetic analysis of the cultured E. coli population by pooled sequencing at eight time points suggests that (i) rapid evolution occurred through repeated emergence of mutators that introduced a large number of nucleotide variants and (ii) many mutators increased to high frequencies but remained polymorphic throughout the continuous cultivation. The evolved E. coli populations exhibited gains both in fitness and succinate production, but only for growth under glycerol fermentation with M. formicicum (the condition for this laboratory evolution) and not under other growth conditions. The mutant alleles of the 69 single nucleotide polymorphisms (SNPs) identified in the adapted E. coli populations were constructed individually in the ancestral wild-type E. coli. We analyzed the phenotypic changes caused by 84 variants, including 15 nonsense variants, and found that FdrAD296Y was the most significant variant leading to increased succinate production. Transcription of fdrA was induced under anaerobic allantoin degradation conditions, and FdrA was shown to play a crucial role in oxamate production. The FdrAD296Y variant increased glyoxylate conversion to malate by accelerating oxamate production, which promotes carbon flow through the C4 branch, leading to increased succinate production. IMPORTANCE Here, we demonstrate the ability of E. coli to perform glycerol fermentation in coculture with the methanogen M. formicicum to produce succinate. We found that the production of succinate by E. coli significantly increased during successive cocultivation. Genomic DNA sequencing, evaluation of relative fitness, and construction of SNPs were performed, from which FdrAD296Y was identified as the most significant variant to enable increased succinate production by E. coli. The function of FdrA is uncertain. In this study, experiments with gene expression assays and metabolic analysis showed for the first time that FdrA could be the “orphan enzyme” oxamate:carbamoyltransferase in anaerobic allantoin degradation. Furthermore, we demonstrate that the anaerobic allantoin degradation pathway is linked to succinate production via the glyoxylate pathway during glycerol fermentation.
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Identification of Optimal Expression Parameters and Purification of a Codon-Optimized Human GLIS1 Transcription Factor from Escherichia coli. Mol Biotechnol 2021; 64:42-56. [PMID: 34528219 DOI: 10.1007/s12033-021-00390-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
GLIS1 has multiple roles in embryonic development and in deriving induced pluripotent stem cells by aiding signaling pathways and chromatin assembly. An inexpensive and simple method to produce human GLIS1 protein from Escherichia coli (E. coli) is demonstrated in this study. Various parameters such as codon usage bias, E. coli strains, media, induction conditions (such as inducer concentration, cell density, time, and temperature), and genetic constructs were investigated to obtain soluble expression of human GLIS1 protein. Using identified expression conditions and an appropriate genetic construct, the human GLIS1 protein was homogeneously purified (purity > 90%) under native conditions. Importantly, the purified protein has upheld a stable secondary structure, as demonstrated by circular dichroism spectroscopy. To the best of our knowledge, this is the first study to report the ideal expression conditions of human GLIS1 protein in E. coli to achieve soluble expression and purification under native conditions, upholding its stable secondary structure post-purification. The biological activity of the purified GLIS1 fusion protein was further assessed in MDA-MB-231 cells. This biologically active human GLIS1 protein potentiates new avenues to understand its molecular mechanisms in different cellular functions in various cancers and in the generation of induced pluripotent stem cells.
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Multi-level rebalancing of the naringenin pathway using riboswitch-guided high-throughput screening. Metab Eng 2021; 67:417-427. [PMID: 34416365 DOI: 10.1016/j.ymben.2021.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022]
Abstract
Recombinant microbes have emerged as promising alternatives to natural sources of naringenin-a key molecular scaffold for flavonoids. In recombinant strains, expression levels of the pathway genes should be optimized at both transcription and the translation stages to precisely allocate cellular resources and maximize metabolite production. However, the optimization of the expression levels of naringenin generally relies on evaluating a small number of variants from libraries constructed by varying transcription efficiency only. In this study, we introduce a systematic strategy for the multi-level optimization of biosynthetic pathways. We constructed a multi-level combinatorial library covering both transcription and translation stages using synthetic T7 promoter variants and computationally designed 5'-untranslated regions. Furthermore, we identified improved strains through high-throughput screening based on a synthetic naringenin riboswitch. The most-optimized strain obtained using this approach exhibited a 3-fold increase in naringenin production, compared with the parental strain in which only the transcription efficiency was modulated. Furthermore, in a fed-batch bioreactor, the optimized strain produced 260.2 mg/L naringenin, which is the highest concentration reported to date using glycerol and p-coumaric acid as substrates. Collectively, this work provides an efficient strategy for the expression optimization of the biosynthetic pathways.
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Abstract
Recently, there has been a resurgence of interest in continuous bioprocessing as a cost-optimised production strategy, driven by a rising global requirement for recombinant proteins used as biological drugs. This strategy could provide several benefits over traditional batch processing, including smaller bioreactors, smaller facilities, and overall reduced plant footprints and investment costs. Continuous processes may also offer improved product quality and minimise heterogeneity, both in the culture and in the product. In this paper, a model protein, green fluorescent protein (GFP) mut3*, was used to test the recombinant protein expression in an Escherichia coli strain with industrial relevance grown in chemostat. An important factor in enabling stable productivity in continuous cultures is the carbon source. We have studied the viability and heterogeneity of the chemostat cultures using a chemically defined medium based on glucose or glycerol as the single carbon source. As a by-product of biodiesel production, glycerol is expected to become a sustainable alternative substrate to glucose. We have found that although glycerol gives a higher cell density, it also generates higher heterogeneity in the culture and a less stable recombinant protein production. We suggest that manipulating the balance between different subpopulations to increase the proportion of productive cells may be a possible solution for making glycerol a successful alternative to glucose.
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Vaud S, Pearcy N, Hanževački M, Van Hagen AMW, Abdelrazig S, Safo L, Ehsaan M, Jonczyk M, Millat T, Craig S, Spence E, Fothergill J, Bommareddy RR, Colin PY, Twycross J, Dalby PA, Minton NP, Jäger CM, Kim DH, Yu J, Maness PC, Lynch S, Eckert CA, Conradie A, Bryan SJ. Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution. Metab Eng 2021; 67:308-320. [PMID: 34245888 DOI: 10.1016/j.ymben.2021.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/26/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene-forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including Escherichia coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate-limiting steps in biological ethylene production. We employed a combination of genome-scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to EFE (wild type versus mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges.
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Affiliation(s)
- Sophie Vaud
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nicole Pearcy
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marko Hanževački
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander M W Van Hagen
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Laudina Safo
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Magdalene Jonczyk
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Thomas Millat
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sean Craig
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Edward Spence
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James Fothergill
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rajesh Reddy Bommareddy
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Pierre-Yves Colin
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Jamie Twycross
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK; School of Computer Science, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Jianping Yu
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Sean Lynch
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA; Somalogic, Inc., Boulder, CO, USA
| | - Carrie A Eckert
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA
| | - Alex Conradie
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Samantha J Bryan
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK.
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Wang Y, Hou Y, Wang Q, Wang Y. The elucidation of the biodegradation of nitrobenzene and p-nitrophenol of nitroreductase from Antarctic psychrophile Psychrobacter sp. ANT206 under low temperature. JOURNAL OF HAZARDOUS MATERIALS 2021; 413:125377. [PMID: 33609870 DOI: 10.1016/j.jhazmat.2021.125377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/06/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Psychrobacter is one important typical strain in the Antarctic environment. In our previous study, Psychrobacter sp. ANT206 from Antarctica with novel cold-adapted nitroreductase (PsNTR) could biodegrade nitrobenzene and p-nitrophenol in low temperature environment. In this study, the in-frame deletion mutant of psntr (Δpsntr-ANT206) that displayed well genetic stability and kanamycin resistance stability was constructed using allelic replacement method. Additionally, Δpsntr-ANT206 was more sensitive to nitrobenzene and p-nitrophenol in the comparison of heat and hyperosmolarity, suggesting that psntr gene participated in the regulation of the tolerance against nitro-aromatic compounds (NACs). Further analysis was conducted by integrated gas chromatography-mass spectrometry (GC-MS), and several metabolites were identified. Among them, ethylbenzene, L-Alanine, citric acid, aniline, 4-aminophenol and other metabolites were different between the wild-type strain and Δpsntr-ANT206 under nitrobenzene and p-nitrophenol stress at different time periods under low temperature, respectively. These data could increase the knowledge of the construction of deletion mutant strains and biodegradation mechanism of NACs of typical strains Psychrobacter from Antarctica, which would also provide the basis of the molecular technique on the regulation of bioremediation of the contaminants under low temperature in the future.
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Affiliation(s)
- Yifan Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yanhua Hou
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Quanfu Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Yatong Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Kumar J, Chauhan AS, Gupta JA, Rathore AS. Supplementation of critical amino acids improves glycerol and lactose uptake and enhances recombinant protein production in Escherichia coli. Biotechnol J 2021; 16:e2100143. [PMID: 34047499 DOI: 10.1002/biot.202100143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Lactose-based induction strategy in E. coli cultivation has several advantages over IPTG as it is cheap, does not impart metabolic stress to cells, and is non-toxic to cells. However, complexity of lactose as an inducer limits its application in fed-batch cultivation. A mixed glycerol-lactose based induction strategy is generally opted during fed-batch cultivation of E. coli. However, slow growth of E. coli in glycerol and lactose results in slower induction of heterologous protein. MAIN METHODS AND MAJOR RESULTS In this study, initially we have demonstrated supplementation of critical amino acids (AAs) improves uptake rate of glycerol and lactose in wildtype E. coli BL21(DE3) in defined medium. A feeding strategy of mixed glycerol-lactose feed along with supplement of critical AAs enhances recombinant production of pramlintide multimer (rPramlintide). High cell density cultivation of E. coli using mixed glycerol-lactose feed and critical AAs supplement resulted in final cell density of 52.2 ± 0.90 g L-1 and rPramlintide titer of 7.8 g L-1 . RT-qPCR analysis of genes involved in glycerol and lactose metabolism of recombinant culture showed upregulation with AAs supplementation. CONCLUSIONS AND IMPLICATIONS We hypothesize that supplementation of critical AAs serves dual purpose: (i) faster assimilation of carbon sources, and (ii) combating metabolic stress arises due to AAs starvation. The substrate uptake and gene expression profiles demonstrate that AAs addition enhances glycerol and lactose assimilation due to overall improvement in their metabolism governed by global regulators of carbon metabolism.
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Affiliation(s)
- Jashwant Kumar
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Ashish S Chauhan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Jaya A Gupta
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
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44
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Cascaded processing enables continuous upstream processing with E. coli BL21(DE3). Sci Rep 2021; 11:11477. [PMID: 34075099 PMCID: PMC8169658 DOI: 10.1038/s41598-021-90899-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
In many industrial sectors continuous processing is already the golden standard to maximize productivity. However, when working with living cells, subpopulation formation causes instabilities in long-term cultivations. In cascaded continuous cultivation, biomass formation and recombinant protein expression can be spatially separated. This cultivation mode was found to facilitate stable protein expression using microbial hosts, however mechanistic knowledge of this cultivation strategy is scarce. In this contribution we present a method workflow to reduce workload and accelerate the establishment of stable continuous processes with E. coli BL21(DE3) exclusively based on bioengineering methods.
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45
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Vichi J, Salazar E, Jacinto VJ, Rodriguez LO, Grande R, Dantán-González E, Morett E, Hernández-Mendoza A. High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth. PLoS One 2021; 16:e0248513. [PMID: 33730068 PMCID: PMC7968713 DOI: 10.1371/journal.pone.0248513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
In spite of increased complexity in eukaryotes compared to prokaryotes, several basic metabolic and regulatory processes are conserved. Here we explored analogies in the eubacteria Escherichia coli and the unicellular fission yeast Schizosaccharomyces pombe transcriptomes under two carbon sources: 2% glucose; or a mix of 2% glycerol and 0.2% sodium acetate using the same growth media and growth phase. Overall, twelve RNA-seq libraries were constructed. A total of 593 and 860 genes were detected as differentially expressed for E. coli and S. pombe, respectively, with a log2 of the Fold Change ≥ 1 and False Discovery Rate ≤ 0.05. In aerobic glycolysis, most of the expressed genes were associated with cell proliferation in both organisms, including amino acid metabolism and glycolysis. In contrast in glycerol/acetate condition, genes related to flagellar assembly and membrane proteins were differentially expressed such as the general transcription factors fliA, flhD, flhC, and flagellum assembly genes were detected in E. coli, whereas in S. pombe genes for hexose transporters, integral membrane proteins, galactose metabolism, and ncRNAs related to cellular stress were overexpressed. In general, our study shows that a conserved "foraging behavior" response is observed in these eukaryotic and eubacterial organisms in gluconeogenic carbon sources.
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Affiliation(s)
- Joivier Vichi
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Verónica Jiménez Jacinto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Leticia Olvera Rodriguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ricardo Grande
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Dantán-González
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
- * E-mail:
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46
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Millard P, Enjalbert B, Uttenweiler-Joseph S, Portais JC, Létisse F. Control and regulation of acetate overflow in Escherichia coli. eLife 2021; 10:63661. [PMID: 33720011 PMCID: PMC8021400 DOI: 10.7554/elife.63661] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
Overflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli – global control of the central metabolism and local control of the acetate pathway – but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviours and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control, and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.
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Affiliation(s)
- Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Brice Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Jean-Charles Portais
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, INSERM U1031, CNRS 5070, Université Toulouse III - Paul Sabatier, EFS, Toulouse, France
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,Université Toulouse III - Paul Sabatier, Toulouse, France
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Pedebos C, Smith IPS, Boags A, Khalid S. The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli. Structure 2021; 29:444-456.e2. [PMID: 33577754 DOI: 10.1016/j.str.2021.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/11/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022]
Abstract
The periplasm of Gram-negative bacteria is a complex, highly crowded molecular environment. Little is known about how antibiotics move across the periplasm and the interactions they experience. Here, atomistic molecular dynamics simulations are used to study the antibiotic polymyxin B1 within models of the periplasm, which are crowded to different extents. We show that PMB1 is likely to be able to "hitchhike" within the periplasm by binding to lipoprotein carriers-a previously unreported passive transport route. The simulations reveal that PMB1 forms both transient and long-lived interactions with proteins, osmolytes, lipids of the outer membrane, and the cell wall, and is rarely uncomplexed when in the periplasm. Furthermore, it can interfere in the conformational dynamics of native proteins. These are important considerations for interpreting its mechanism of action and are likely to also hold for other antibiotics that rely on diffusion to cross the periplasm.
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Affiliation(s)
- Conrado Pedebos
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Iain Peter Shand Smith
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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Metabolic engineering of E. coli for pyocyanin production. Metab Eng 2021; 64:15-25. [PMID: 33454430 DOI: 10.1016/j.ymben.2021.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 11/17/2020] [Accepted: 01/10/2021] [Indexed: 01/07/2023]
Abstract
Pyocyanin is a secondary metabolite from Pseudomonas aeruginosa that belongs to the class of phenazines, which are aromatic nitrogenous compounds with numerous biological functions. Besides its antifungal and antimicrobial activities, pyocyanin is a remarkable redox-active molecule with potential applications ranging from the pharma industry to the development of microbial fuel cells. Nevertheless, pyocyanin production has been restricted to P. aeruginosa strains, limiting its practical applicability. In this study, the pyocyanin biosynthetic pathway was engineered for the first time for high level production of this compound in a heterologous host. Escherichia coli cells harboring the nine-gene pathway divided into two plasmids were able to produce and secrete pyocyanin at higher levels than some Pseudomonas aeruginosa strains. The influence of culture and induction parameters were evaluated, and the optimized conditions led to an increase of 3.5-fold on pyocyanin accumulation. Pathway balancing was achieved by testing a set of plasmids with different copy numbers to optimize the expression levels of pyocyanin biosynthetic genes, resulting in a fourfold difference in product titer among the engineered strains. Further improvements were achieved by co-expression of Vitreoscilla hemoglobin Vhb, which relieved oxygen limitations and led to a final titer of 18.8 mg/L pyocyanin. These results show promise to use E. coli for phenazines production, and the engineered strain developed here has the potential to be used in electro-fermentation systems where pyocyanin plays a role as electron-shuttle.
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49
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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: 23] [Impact Index Per Article: 7.7] [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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Chiang CJ, Ho YJ, Hu MC, Chao YP. Rewiring of glycerol metabolism in Escherichia coli for effective production of recombinant proteins. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:205. [PMID: 33317614 PMCID: PMC7737366 DOI: 10.1186/s13068-020-01848-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The economic viability of a protein-production process relies highly on the production titer and the price of raw materials. Crude glycerol coming from the production of biodiesel is a renewable and cost-effective resource. However, glycerol is inefficiently utilized by Escherichia coli. RESULTS This issue was addressed by rewiring glycerol metabolism for redistribution of the metabolic flux. Key steps in central metabolism involving the glycerol dissimilation pathway, the pentose phosphate pathway, and the tricarboxylic acid cycle were pinpointed and manipulated to provide precursor metabolites and energy. As a result, the engineered E. coli strain displayed a 9- and 30-fold increase in utilization of crude glycerol and production of the target protein, respectively. CONCLUSIONS The result indicates that the present method of metabolic engineering is useful and straightforward for efficient adjustment of the flux distribution in glycerol metabolism. The practical application of this methodology in biorefinery and the related field would be acknowledged.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yi-Jing Ho
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
| | - Mu-Chen Hu
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung, 41354 Taiwan
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