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Taymaz-Nikerel H, Lara AR. Vitreoscilla Haemoglobin: A Tool to Reduce Overflow Metabolism. Microorganisms 2021; 10:microorganisms10010043. [PMID: 35056491 PMCID: PMC8779101 DOI: 10.3390/microorganisms10010043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022] Open
Abstract
Overflow metabolism is a phenomenon extended in nature, ranging from microbial to cancer cells. Accumulation of overflow metabolites pose a challenge for large-scale bioprocesses. Yet, the causes of overflow metabolism are not fully clarified. In this work, the underlying mechanisms, reasons and consequences of overflow metabolism in different organisms have been summarized. The reported effect of aerobic expression of Vitreoscilla haemoglobin (VHb) in different organisms are revised. The use of VHb to reduce overflow metabolism is proposed and studied through flux balance analysis in E. coli at a fixed maximum substrate and oxygen uptake rates. Simulations showed that the presence of VHb increases the growth rate, while decreasing acetate production, in line with the experimental measurements. Therefore, aerobic VHb expression is considered a potential tool to reduce overflow metabolism in cells.
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Affiliation(s)
- Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, İstanbul 34060, Turkey;
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
- Correspondence:
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2
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Bioleaching of Manganese Oxides at Different Oxidation States by Filamentous Fungus Aspergillus niger. J Fungi (Basel) 2021; 7:jof7100808. [PMID: 34682230 PMCID: PMC8540447 DOI: 10.3390/jof7100808] [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: 08/06/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
This work aimed to examine the bioleaching of manganese oxides at various oxidation states (MnO, MnO·Mn2O3, Mn2O3 and MnO2) by a strain of the filamentous fungus Aspergillus niger, a frequent soil representative. Our results showed that the fungus effectively disintegrated the crystal structure of selected mineral manganese phases. Thereby, during a 31-day static incubation of oxides in the presence of fungus, manganese was bioextracted into the culture medium and, in some cases, transformed into a new biogenic mineral. The latter resulted from the precipitation of extracted manganese with biogenic oxalate. The Mn(II,III)-oxide was the most susceptible to fungal biodeterioration, and up to 26% of the manganese content in oxide was extracted by the fungus into the medium. The detected variabilities in biogenic oxalate and gluconate accumulation in the medium are also discussed regarding the fungal sensitivity to manganese. These suggest an alternative pathway of manganese oxides’ biodeterioration via a reductive dissolution. There, the oxalate metabolites are consumed as the reductive agents. Our results highlight the significance of fungal activity in manganese mobilization and transformation. The soil fungi should be considered an important geoactive agent that affects the stability of natural geochemical barriers.
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Metabolic Changes by Wine Flor-Yeasts with Gluconic Acid as the Sole Carbon Source. Metabolites 2021; 11:metabo11030150. [PMID: 33800958 PMCID: PMC8001445 DOI: 10.3390/metabo11030150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 11/30/2022] Open
Abstract
Gluconic acid consumption under controlled conditions by a Saccharomyces cerevisiae flor yeast was studied in artificial media. Gluconic acid was the sole carbon source and the compounds derived from this metabolism were tracked by endo-metabolomic analysis using a Gas Chromatography-Mass Spectrometry (GC-MSD) coupled methodology. After 6 days, about 30% of gluconic acid (1.5 g/L) had been consumed and 34 endo-metabolites were identified. Metabolomic pathway analysis showed the TCA cycle, glyoxylate-dicarboxylate, glycine-serine-threonine, and glycerolipid metabolic pathway were significantly affected. These results contribute to the knowledge of intracellular metabolomic fluctuations in flor yeasts during gluconic acid uptake, opening possibilities for future experiments to improve their applications to control gluconic acid contents during the production of fermented beverages.
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Kager J, Tuveri A, Ulonska S, Kroll P, Herwig C. Experimental verification and comparison of model predictive, PID and model inversion control in a Penicillium chrysogenum fed-batch process. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Artmann DJ, Vrabl P, Gianordoli R, Burgstaller W. Challenging the charge balance hypothesis: reconsidering buffer effect and reuptake of previously excreted organic acids by Penicillium ochrochloron. FEMS Microbiol Lett 2020; 367:5780226. [PMID: 32129848 PMCID: PMC7150580 DOI: 10.1093/femsle/fnaa039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/03/2020] [Indexed: 01/15/2023] Open
Abstract
Penicillium ochrochloron was used in the past for the leaching of zinc from a zinc oxide containing filter dust via excreted organic acids. Organic acid excretion by P. ochrochloron was stimulated by the addition of an extracellular buffer (2-(N-Morpholino)ethanesulfonic acid, MES; or zinc oxide, ZnO: ZnO + 2 H+ → Zn2+ + H2O). It was tested if the buffer stimulated excretion of organic acid anions is due to the necessity of an anion efflux across the plasma membrane to maintain electroneutrality by balancing the excretion of protons by the H+-ATPase. This charge balance hypothesis was previously postulated for P. ochrochloron. Two strains of P. ochrochloron were studied, which differed in growth parameters and amount of excreted organic acids. From the results, it was concluded that charge balance at the plasma membrane is not the main reason for organic acid excretion in these two strains of P. ochrochloron. Furthermore, the phenomenon of reuptake of excreted organic acids in the presence of about 100 mM of glucose is confirmed. It is suggested that the equilibrium between extracellular and intracellular organic acid anions may be maintained passively by a facilitated diffusion transporter.
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Affiliation(s)
- D J Artmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - P Vrabl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - R Gianordoli
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
| | - W Burgstaller
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Österreich
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Vrabl P, Schinagl CW, Artmann DJ, Heiss B, Burgstaller W. Fungal Growth in Batch Culture - What We Could Benefit If We Start Looking Closer. Front Microbiol 2019; 10:2391. [PMID: 31681243 PMCID: PMC6805767 DOI: 10.3389/fmicb.2019.02391] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022] Open
Abstract
Since filamentous fungi rapidly adjust their metabolic properties to environmental changes, a rigorous standardization and characterization of cultivation conditions is necessary to obtain meaningful and reproducible results. In batch cultures, which are commonly characterized according to the classical growth curve in textbooks (i.e., lag, exponential, stationary, and declining phase), this is of special difficulty. Although various studies in literature report atypically shaped growth curves of filamentous fungi in batch culture, systematic investigations on this topic are scarce and deviations are barely mentioned in textbooks. Summarizing approximately a decade of observations of growth characteristics from bioreactor batch grown filamentous fungi - in particular two strains (CBS123.823 and CBS123.824) of Penicillium ochrochloron - we demonstrate with a series of highly standardized bioreactor batch culture experiments that the classical growth curve failed to describe growth dynamics of the studied fungi in this work. The nature of the first exhausted nutrient was of remarkable importance for the resulting shape of the growth curve. In all experiments, online respirometry proved to be a powerful tool to distinguish growth phases and revealed more physiological states than expected from the mere biomass curve. In this respect we discuss why "atypical" shaped growth curves often remain unrecognized and that they might be the rule rather than the exception. Acknowledging the importance of the correct presentation of this complex topic in textbooks, we also propose a modified growth curve scheme to sensitize students for potential alternative shaped growth curves.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
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State estimation for a penicillin fed-batch process combining particle filtering methods with online and time delayed offline measurements. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2017.11.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Stelzer IV, Kager J, Herwig C. Comparison of Particle Filter and Extended Kalman Filter Algorithms for Monitoring of Bioprocesses. COMPUTER AIDED CHEMICAL ENGINEERING 2017. [DOI: 10.1016/b978-0-444-63965-3.50249-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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10
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Grünberger A, Schöler K, Probst C, Kornfeld G, Hardiman T, Wiechert W, Kohlheyer D, Noack S. Real-time monitoring of fungal growth and morphogenesis at single-cell resolution. Eng Life Sci 2016; 17:86-92. [PMID: 32624732 DOI: 10.1002/elsc.201600083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/12/2016] [Accepted: 06/15/2016] [Indexed: 02/01/2023] Open
Abstract
Development times for efficient large-scale production, utilizing fungal species, are still very long. This is mainly due to the poor knowledge of many important variables related to fungal growth and morphogenesis. We specifically addressed this knowledge gap by combining a microfluidic cultivation device with time-lapse live cell imaging. This combination facilitates (i) studying population heterogeneity at single-cell resolution, (ii) monitoring of fungal morphogenesis in a high spatiotemporal manner under defined environmental conditions, and (iii) parallelization of experiments for statistical data analysis. Our analysis of Penicillium chrysogenum, the workhorse for antibiotic production worldwide, revealed significant heterogeneity in size, vitality and differentiation times between spore, mycelium and pellets when cultivated under industrially relevant conditions. For example, the swelling rate of single spores in complex medium ( μ = 0.077 ± 0.036 h - 1 ) and the formation rate of higher branched mycelia in defined glucose medium ( μ = 0.046 ± 0.031 h - 1 ) were estimated from broad time-dependent cell size distributions, which in turn were derived from computational image analysis of 257 and 49 time-lapse series, respectively. In order to speed up the development of new fungal production processes, a deeper understanding of these heterogeneities is required and the presented microfluidic single-cell approach provides a solid technical foundation for such quantitative studies.
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Affiliation(s)
- Alexander Grünberger
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
| | - Katja Schöler
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
| | - Christopher Probst
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
| | - Georg Kornfeld
- SU Development Anti-Infectives Sandoz GmbH Biochemiestrasse 10 Kundl Tyrol Austria
| | - Timo Hardiman
- SU Development Anti-Infectives Sandoz GmbH Biochemiestrasse 10 Kundl Tyrol Austria
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences IBG-1: Biotechnology Forschungszentrum Jülich Jülich Germany
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Golabgir A, Herwig C. Combining Mechanistic Modeling and Raman Spectroscopy for Real-Time Monitoring of Fed-Batch Penicillin Production. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201500101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Karpe AV, Beale DJ, Godhani NB, Morrison PD, Harding IH, Palombo EA. Untargeted Metabolic Profiling of Winery-Derived Biomass Waste Degradation by Penicillium chrysogenum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10696-704. [PMID: 26611372 DOI: 10.1021/acs.jafc.5b04834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Winery-derived biomass waste was degraded by Penicillium chrysogenum under solid state fermentation over 8 days in a (2)H2O-supplemented medium. Multivariate statistical analysis of the gas chromatography-mass spectrometry (GC-MS) data resulted in the identification of 94 significant metabolites, within 28 different metabolic pathways. The majority of biomass sugars were utilized by day 4 to yield products such as sugars, fatty acids, isoprenoids, and amino acids. The fungus was observed to metabolize xylose to xylitol, an intermediate of ethanol production. However, enzyme inhibition and autolysis were observed from day 6, indicating 5 days as the optimal time for fermentation. P. chrysogenum displayed metabolism of pentoses (to alcohols) and degraded tannins and lignins, properties that are lacking in other biomass-degrading ascomycetes. Rapid fermentation (3-5 days) may not only increase the pentose metabolizing efficiency but also increase the yield of medicinally important metabolites, such as syringate.
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Affiliation(s)
- Avinash V Karpe
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), P.O. Box 2583, Dutton Park, Queensland 4001, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), P.O. Box 2583, Dutton Park, Queensland 4001, Australia
| | - Nainesh B Godhani
- Department of Mechanical and Product Design Engineering, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Paul D Morrison
- Australian Centre for Research on Separation Science, School of Applied Sciences, RMIT University , P.O. Box 2547, Melbourne, Victoria 3000, Australia
| | - Ian H Harding
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
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13
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Farrán A, Cai C, Sandoval M, Xu Y, Liu J, Hernáiz MJ, Linhardt RJ. Green solvents in carbohydrate chemistry: from raw materials to fine chemicals. Chem Rev 2015; 115:6811-53. [PMID: 26121409 DOI: 10.1021/cr500719h] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angeles Farrán
- †Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, Paseo Senda del Rey 4, 28040 Madrid, Spain
| | - Chao Cai
- ‡Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Manuel Sandoval
- §Escuela de Química, Universidad Nacional of Costa Rica, Post Office Box 86, 3000 Heredia, Costa Rica
| | - Yongmei Xu
- ∥Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jian Liu
- ∥Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - María J Hernáiz
- ▽Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense de Madrid, Pz/Ramón y Cajal s/n, 28040 Madrid, Spain
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