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Baumann PT, Dal Molin M, Aring H, Krumbach K, Müller MF, Vroling B, van Summeren-Wesenhagen PV, Noack S, Marienhagen J. Beyond rational-biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes. BMC Biol 2023; 21:183. [PMID: 37667306 PMCID: PMC10478468 DOI: 10.1186/s12915-023-01688-x] [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: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND In contrast to modern rational metabolic engineering, classical strain development strongly relies on random mutagenesis and screening for the desired production phenotype. Nowadays, with the availability of biosensor-based FACS screening strategies, these random approaches are coming back into fashion. In this study, we employ this technology in combination with comparative genome analyses to identify novel mutations contributing to product formation in the genome of a Corynebacterium glutamicum L-histidine producer. Since all known genetic targets contributing to L-histidine production have been already rationally engineered in this strain, identification of novel beneficial mutations can be regarded as challenging, as they might not be intuitively linkable to L-histidine biosynthesis. RESULTS In order to identify 100 improved strain variants that had each arisen independently, we performed > 600 chemical mutagenesis experiments, > 200 biosensor-based FACS screenings, isolated > 50,000 variants with increased fluorescence, and characterized > 4500 variants with regard to biomass formation and L-histidine production. Based on comparative genome analyses of these 100 variants accumulating 10-80% more L-histidine, we discovered several beneficial mutations. Combination of selected genetic modifications allowed for the construction of a strain variant characterized by a doubled L-histidine titer (29 mM) and product yield (0.13 C-mol C-mol-1) in comparison to the starting variant. CONCLUSIONS This study may serve as a blueprint for the identification of novel beneficial mutations in microbial producers in a more systematic manner. This way, also previously unexplored genes or genes with previously unknown contribution to the respective production phenotype can be identified. We believe that this technology has a great potential to push industrial production strains towards maximum performance.
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Affiliation(s)
- Philipp T Baumann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Michael Dal Molin
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
- Department I of Internal Medicine, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Hannah Aring
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Moritz-Fabian Müller
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Bas Vroling
- Bioprodict GmbH, Nieuwe Marktstraat 54E, 6511AA, Nijmegen, The Netherlands
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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2
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Rusu AV, Trif M, Rocha JM. Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation Formulations. Molecules 2023; 28:6020. [PMID: 37630272 PMCID: PMC10458110 DOI: 10.3390/molecules28166020] [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: 05/25/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Food supplementation formulations refer to products that are designed to provide additional nutrients to the diet. Vitamins, dietary fibers, minerals and other functional compounds (such as antioxidants) are concentrated in dietary supplements. Specific amounts of dietary compounds are given to the body through food supplements, and these include as well so-called non-essential compounds such as secondary plant bioactive components or microbial natural products in addition to nutrients in the narrower sense. A significant social challenge represents how to moderately use the natural resources in light of the growing world population. In terms of economic production of (especially natural) bioactive molecules, ways of white biotechnology production with various microorganisms have recently been intensively explored. In the current review other relevant dietary supplements and natural substances (e.g., vitamins, amino acids, antioxidants) used in production of dietary supplements formulations and their microbial natural production via fermentative biotechnological approaches are briefly reviewed. Biotechnology plays a crucial role in optimizing fermentation conditions to maximize the yield and quality of the target compounds. Advantages of microbial production include the ability to use renewable feedstocks, high production yields, and the potential for cost-effective large-scale production. Additionally, it can be more environmentally friendly compared to chemical synthesis, as it reduces the reliance on petrochemicals and minimizes waste generation. Educating consumers about the benefits, safety, and production methods of microbial products in general is crucial. Providing clear and accurate information about the science behind microbial production can help address any concerns or misconceptions consumers may have.
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Affiliation(s)
- Alexandru Vasile Rusu
- CENCIRA Agrofood Research and Innovation Centre, Ion Meșter 6, 400650 Cluj-Napoca, Romania;
| | - Monica Trif
- Food Research Department, Centre for Innovative Process Engineering (CENTIV) GmbH, 28857 Syke, Germany
| | - João Miguel Rocha
- Universidade Católica Portuguesa, CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
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3
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Wizrah MS, Chua SM, Luo Z, Manik MK, Pan M, Whyte JM, Robertson AA, Kappler U, Kobe B, Fraser JA. AICAR transformylase/IMP cyclohydrolase (ATIC) is essential for de novo purine biosynthesis and infection by Cryptococcus neoformans. J Biol Chem 2022; 298:102453. [PMID: 36063996 PMCID: PMC9525906 DOI: 10.1016/j.jbc.2022.102453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 01/27/2023] Open
Abstract
The fungal pathogen Cryptococcus neoformans is a leading cause of meningoencephalitis in the immunocompromised. As current antifungal treatments are toxic to the host, costly, limited in their efficacy, and associated with drug resistance, there is an urgent need to identify vulnerabilities in fungal physiology to accelerate antifungal discovery efforts. Rational drug design was pioneered in de novo purine biosynthesis as the end products of the pathway, ATP and GTP, are essential for replication, transcription, and energy metabolism, and the same rationale applies when considering the pathway as an antifungal target. Here, we describe the identification and characterization of C. neoformans 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/5'-inosine monophosphate cyclohydrolase (ATIC), a bifunctional enzyme that catalyzes the final two enzymatic steps in the formation of the first purine base inosine monophosphate. We demonstrate that mutants lacking the ATIC-encoding ADE16 gene are adenine and histidine auxotrophs that are unable to establish an infection in a murine model of virulence. In addition, our assays employing recombinantly expressed and purified C. neoformans ATIC enzyme revealed Km values for its substrates AICAR and 5-formyl-AICAR are 8-fold and 20-fold higher, respectively, than in the human ortholog. Subsequently, we performed crystallographic studies that enabled the determination of the first fungal ATIC protein structure, revealing a key serine-to-tyrosine substitution in the active site, which has the potential to assist the design of fungus-specific inhibitors. Overall, our results validate ATIC as a promising antifungal drug target.
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Affiliation(s)
- Maha S.I. Wizrah
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Sheena M.H. Chua
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Zhenyao Luo
- School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mohammad K. Manik
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Mengqi Pan
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Jessica M.L. Whyte
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Avril A.B. Robertson
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, Queensland, Australia,School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia,For correspondence: James A. Fraser
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Kasari M, Kasari V, Kärmas M, Jõers A. Decoupling Growth and Production by Removing the Origin of Replication from a Bacterial Chromosome. ACS Synth Biol 2022; 11:2610-2622. [PMID: 35798328 DOI: 10.1021/acssynbio.1c00618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Efficient production of biochemicals and proteins in cell factories frequently benefits from a two-stage bioprocess in which growth and production phases are decoupled. Here, we describe a novel growth switch based on the permanent removal of the origin of replication (oriC) from the Escherichia coli chromosome. Without oriC, cells cannot initiate a new round of replication, and they stop growing while their metabolism remains active. Our system relies on a serine recombinase from bacteriophage phiC31 whose expression is controlled by the temperature-sensitive cI857 repressor from phage lambda. The reporter protein expression in switched cells continues after cessation of growth, leading to protein levels up to 5 times higher compared to nonswitching cells. Switching induces a unique physiological state that is different from both normal exponential and stationary phases. The switched cells remain in this state even when not growing, retain their protein synthesis capacity, and do not induce proteins associated with the stationary phase. Our switcher technology is potentially useful for a range of products and applicable in many bacterial species for decoupling growth and production.
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Affiliation(s)
- Marje Kasari
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Villu Kasari
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Mirjam Kärmas
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Arvi Jõers
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
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5
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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6
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Moulaee K, Neri G. Electrochemical Amino Acid Sensing: A Review on Challenges and Achievements. BIOSENSORS 2021; 11:502. [PMID: 34940259 PMCID: PMC8699811 DOI: 10.3390/bios11120502] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 05/05/2023]
Abstract
The rapid growth of research in electrochemistry in the last decade has resulted in a significant advancement in exploiting electrochemical strategies for assessing biological substances. Among these, amino acids are of utmost interest due to their key role in human health. Indeed, an unbalanced amino acid level is the origin of several metabolic and genetic diseases, which has led to a great need for effective and reliable evaluation methods. This review is an effort to summarize and present both challenges and achievements in electrochemical amino acid sensing from the last decade (from 2010 onwards) to show where limitations and advantages stem from. In this review, we place special emphasis on five well-known electroactive amino acids, namely cysteine, tyrosine, tryptophan, methionine and histidine. The recent research and achievements in this area and significant performance metrics of the proposed electrochemical sensors, including the limit of detection, sensitivity, stability, linear dynamic range(s) and applicability in real sample analysis, are summarized and presented in separate sections. More than 400 recent scientific studies were included in this review to portray a rich set of ideas and exemplify the capabilities of the electrochemical strategies to detect these essential biomolecules at trace and even ultra-trace levels. Finally, we discuss, in the last section, the remaining issues and the opportunities to push the boundaries of our knowledge in amino acid electrochemistry even further.
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Affiliation(s)
- Kaveh Moulaee
- Department of Engineering, University of Messina, C.Da Di Dio, I-98166 Messina, Italy;
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran 16846-13114, Iran
| | - Giovanni Neri
- Department of Engineering, University of Messina, C.Da Di Dio, I-98166 Messina, Italy;
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7
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Streamlining the Analysis of Dynamic 13C-Labeling Patterns for the Metabolic Engineering of Corynebacterium glutamicum as l-Histidine Production Host. Metabolites 2020; 10:metabo10110458. [PMID: 33198305 PMCID: PMC7696456 DOI: 10.3390/metabo10110458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/19/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
Today’s possibilities of genome editing easily create plentitudes of strain mutants that need to be experimentally qualified for configuring the next steps of strain engineering. The application of design-build-test-learn cycles requires the identification of distinct metabolic engineering targets as design inputs for subsequent optimization rounds. Here, we present the pool influx kinetics (PIK) approach that identifies promising metabolic engineering targets by pairwise comparison of up- and downstream 13C labeling dynamics with respect to a metabolite of interest. Showcasing the complex l-histidine production with engineered Corynebacterium glutamicuml-histidine-on-glucose yields could be improved to 8.6 ± 0.1 mol% by PIK analysis, starting from a base strain. Amplification of purA, purB, purH, and formyl recycling was identified as key targets only analyzing the signal transduction kinetics mirrored in the PIK values.
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8
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Hou Y, Liu X, Li S, Zhang X, Yu S, Zhao GR. Metabolic Engineering of Escherichia coli for de Novo Production of Betaxanthins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8370-8380. [PMID: 32627549 DOI: 10.1021/acs.jafc.0c02949] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Betalains are emerging natural pigments with high tinctorial strength and stability, physiological activities, and fluorescent properties for potential application in food, cosmetic, and pharmaceutical industries. Betalains including yellow betaxanthins and red betacyanins are mainly restricted in the Caryophyllales plants. To expand the availability of individual betaxanthins, here, we constructed an Escherichia coli BTA6 for de novo biosynthesis of betalamic acid. Using this strain as a monoculture platform, 14 yellow and 2 red betaxanthins were produced by feeding amino acids and amines. Furthermore, we constructed an l-histidine overproducing strain using chromosome engineering to deattenuate regulation and established a coculture system. After optimization of the initial inoculation ratios and fermentation conditions, the compatible and robust coculture system produced 287.69 mg/L of histidine-betaxanthin. This is the first report on de novo production of betaxanthins in engineered E. coli using glucose as a carbon source. Our work highlights the feasibility of microbial cell factories to produce individual betalains.
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Affiliation(s)
- Yanan Hou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Xue Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Shilin Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Xue Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Sili Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
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9
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Wu H, Tian D, Fan X, Fan W, Zhang Y, Jiang S, Wen C, Ma Q, Chen N, Xie X. Highly Efficient Production of l-Histidine from Glucose by Metabolically Engineered Escherichia coli. ACS Synth Biol 2020; 9:1813-1822. [PMID: 32470291 DOI: 10.1021/acssynbio.0c00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
l-Histidine is a functional amino acid with numerous therapeutic and ergogenic properties. It is one of the few amino acids that is not produced on a large scale by microbial fermentation due to the lack of an efficient microbial cell factory. In this study, we demonstrated the engineering of wild-type Escherichia coli to overproduce histidine from glucose. First, removal of transcription attenuation and histidine-mediated feedback inhibition resulted in 0.8 g/L histidine accumulation. Second, chromosome-based optimization of the expression levels of histidine biosynthesis genes led to a 4.75-fold increase in histidine titer. Third, strengthening phosphoribosyl pyrophosphate supply and rerouting the purine nucleotide biosynthetic pathway improved the histidine production to 8.2 g/L. Fourth, introduction of the NADH-dependent glutamate dehydrogenase from Bacillus subtilis and the lysine exporter from Corynebacterium glutamicum enabled the final strain HW6-3 to produce 11.8 g/L histidine. Finally, 66.5 g/L histidine was produced under fed-batch fermentation, with a yield of 0.23 g/g glucose and a productivity of 1.5 g/L/h. This is the highest titer and productivity of histidine ever reported from an engineered strain. Additionally, the metabolic strategies utilized here can be applied to engineering other microorganisms for the industrial production of histidine and related bioproducts.
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Affiliation(s)
- Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Daoguang Tian
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Xiaoguang Fan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Weiming Fan
- Zhejiang Zhenyuan Pharmaceutial Co., Ltd, Shaoxing, 312071, P. R. China
| | - Yue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Shuai Jiang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Chenhui Wen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
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10
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Expression and purification of the 5'-nucleotidase YitU from Bacillus species: its enzymatic properties and possible applications in biotechnology. Appl Microbiol Biotechnol 2020; 104:2957-2972. [PMID: 32040605 PMCID: PMC7062661 DOI: 10.1007/s00253-020-10428-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 11/05/2022]
Abstract
5’-Nucleotidases (EC 3.1.3.5) are enzymes that catalyze the hydrolytic dephosphorylation of 5′-ribonucleotides and 5′-deoxyribonucleotides to their corresponding nucleosides plus phosphate. In the present study, to search for new genes encoding 5′-nucleotidases specific for purine nucleotides in industrially important Bacillus species, “shotgun” cloning and the direct selection of recombinant clones grown in purine nucleosides at inhibitory concentrations were performed in the Escherichia coli GS72 strain, which is sensitive to these compounds. As a result, orthologous yitU genes from Bacillus subtilis and Bacillus amyloliquefaciens, whose products belong to the ubiquitous haloacid dehalogenase superfamily (HADSF), were selected and found to have a high sequence similarity of 87%. B. subtilis YitU was produced in E. coli as an N-terminal hexahistidine-tagged protein, purified and biochemically characterized as a soluble 5′-nucleotidase with broad substrate specificity with respect to various deoxyribo- and ribonucleoside monophosphates: dAMP, GMP, dGMP, CMP, AMP, XMP, IMP and 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranosyl 5′-monophosphate (AICAR-P). However, the preferred substrate for recombinant YitU was shown to be flavin mononucleotide (FMN). B. subtilis and B. amyloliquefaciens yitU overexpression increased riboflavin (RF) and 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) accumulation and can be applied to breed highly performing RF- and AICAR-producing strains.
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11
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Ziesack M, Gibson T, Oliver JKW, Shumaker AM, Hsu BB, Riglar DT, Giessen TW, DiBenedetto NV, Bry L, Way JC, Silver PA, Gerber GK. Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium. mSystems 2019; 4:e00352-19. [PMID: 31409662 PMCID: PMC6697442 DOI: 10.1128/msystems.00352-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/23/2019] [Indexed: 01/15/2023] Open
Abstract
In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.
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Affiliation(s)
- Marika Ziesack
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Travis Gibson
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John K W Oliver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew M Shumaker
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David T Riglar
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas V DiBenedetto
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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12
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Li L, Liao Y, Luo Y, Zhang G, Liao X, Zhang W, Zheng S, Han S, Lin Y, Liang S. Improved Efficiency of the Desulfurization of Oil Sulfur Compounds in Escherichia coli Using a Combination of Desensitization Engineering and DszC Overexpression. ACS Synth Biol 2019; 8:1441-1451. [PMID: 31132321 DOI: 10.1021/acssynbio.9b00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 4S pathway of biodesulfurization, which can specifically desulfurize aromatic S-heterocyclic compounds without destroying their combustion value, is a low-cost and environmentally friendly technology that is complementary to hydrodesulfurization. The four Dsz enzymes convert the model compound dibenzothiophene (DBT) into the sulfur-free compound 2-hydroxybiphenyl (HBP). Of these four enzymes, DszC, the first enzyme in the 4S pathway, is the most severely affected by the feedback inhibition caused by HBP. This study is the first attempt to directly modify DszC to decrease its inhibition by HBP, with the results showing that the modified protein is insensitive to HBP. On the basis of the principle that the final HBP product could show a blue color with Gibbs reagent, a high-throughput screening method for its rapid detection was established. The screening method and the combinatorial mutagenesis generated the mutant AKWC (A101K/W327C) of DszC. After the IC50 was calculated, the feedback inhibition of the AKWC mutant was observed to have been substantially reduced. Interestingly, the substrate inhibition of DszC had also been reduced as a result of directed evolution. Finally, the recombinant BL21(DE3)/BADC*+C* (C* represents AKWC) strain exhibited a specific conversion rate of 214.84 μmolHBP/gDCW/h, which was 13.8-fold greater than that of the wild-type strain. Desensitization engineering and the overexpression of the desensitized DszC protein resulted in the elimination of the feedback inhibition bottleneck in the 4S pathway, which is practical and effective progress toward the production of sulfur-free fuel oil. The results of this study demonstrate the utility of desensitization of feedback inhibition regulation in metabolic pathways by protein engineering.
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Affiliation(s)
- Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yibo Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yifan Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Guangming Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wei Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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13
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Schwentner A, Feith A, Münch E, Stiefelmaier J, Lauer I, Favilli L, Massner C, Öhrlein J, Grund B, Hüser A, Takors R, Blombach B. Modular systems metabolic engineering enables balancing of relevant pathways for l-histidine production with Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:65. [PMID: 30962820 PMCID: PMC6432763 DOI: 10.1186/s13068-019-1410-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/14/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND l-Histidine biosynthesis is embedded in an intertwined metabolic network which renders microbial overproduction of this amino acid challenging. This is reflected in the few available examples of histidine producers in literature. Since knowledge about the metabolic interplay is limited, we systematically perturbed the metabolism of Corynebacterium glutamicum to gain a holistic understanding in the metabolic limitations for l-histidine production. We, therefore, constructed C. glutamicum strains in a modularized metabolic engineering approach and analyzed them with LC/MS-QToF-based systems metabolic profiling (SMP) supported by flux balance analysis (FBA). RESULTS The engineered strains produced l-histidine, equimolar amounts of glycine, and possessed heavily decreased intracellular adenylate concentrations, despite a stable adenylate energy charge. FBA identified regeneration of ATP from 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) as crucial step for l-histidine production and SMP identified strong intracellular accumulation of inosine monophosphate (IMP) in the engineered strains. Energy engineering readjusted the intracellular IMP and ATP levels to wild-type niveau and reinforced the intrinsic low ATP regeneration capacity to maintain a balanced energy state of the cell. SMP further indicated limitations in the C1 supply which was overcome by expression of the glycine cleavage system from C. jeikeium. Finally, we rerouted the carbon flux towards the oxidative pentose phosphate pathway thereby further increasing product yield to 0.093 ± 0.003 mol l-histidine per mol glucose. CONCLUSION By applying the modularized metabolic engineering approach combined with SMP and FBA, we identified an intrinsically low ATP regeneration capacity, which prevents to maintain a balanced energy state of the cell in an l-histidine overproduction scenario and an insufficient supply of C1 units. To overcome these limitations, we provide a metabolic engineering strategy which constitutes a general approach to improve the production of ATP and/or C1 intensive products.
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Affiliation(s)
- Andreas Schwentner
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - André Feith
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Eugenia Münch
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Judith Stiefelmaier
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ira Lauer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lorenzo Favilli
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Christoph Massner
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | | | - Bastian Grund
- Evonik Creavis GmbH, Paul-Baumann-Straße 1, 45772 Marl, Germany
| | - Andrea Hüser
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
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14
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Yin X, Wu Orr M, Wang H, Hobbs EC, Shabalina SA, Storz G. The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels. Mol Microbiol 2018; 111:131-144. [PMID: 30276893 DOI: 10.1111/mmi.14143] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 01/04/2023]
Abstract
In response to low levels of magnesium (Mg2+ ), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pairs with the eptB mRNA thus affecting lipopolysaccharide modification. Surprisingly, we found overexpression of the MgtS protein also leads to induction of the PhoRB regulon. Studies to understand this activation showed that MgtS forms a complex with a second protein, PitA, a cation-phosphate symporter. Given that the additive effect of ∆mgtA and ∆mgtS mutations on intracellular Mg2+ concentrations seen previously is lost in the ∆pitA mutant, we suggest that MgtS binds to and prevents Mg2+ leakage through PitA under Mg2+ -limiting conditions. Consistent with a detrimental role of PitA in low Mg2+ , we also observe MgrR sRNA repression of PitA synthesis. Thus, PhoQP induces the expression of two convergent small genes in response to Mg2+ limitation whose products act to modulate PitA at different levels to increase intracellular Mg2+ .
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Affiliation(s)
- Xuefeng Yin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,Health Science Center, Peking University, Beijing, 100191, China
| | - Mona Wu Orr
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Hanbo Wang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Errett C Hobbs
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
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