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Noirungsee N, Changkhong S, Phinyo K, Suwannajak C, Tanakul N, Inwongwan S. Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13231. [PMID: 38192220 PMCID: PMC10866088 DOI: 10.1111/1758-2229.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Metabolic modelling approaches have become the powerful tools in modern biology. These mathematical models are widely used to predict metabolic phenotypes of the organisms or communities of interest, and to identify metabolic targets in metabolic engineering. Apart from a broad range of industrial applications, the possibility of using metabolic modelling in the contexts of astrobiology are poorly explored. In this mini-review, we consolidated the concepts and related applications of applying metabolic modelling in studying organisms in space-related environments, specifically the extremophilic microbes. We recapitulated the current state of the art in metabolic modelling approaches and their advantages in the astrobiological context. Our review encompassed the applications of metabolic modelling in the theoretical investigation of the origin of life within prebiotic environments, as well as the compilation of existing uses of genome-scale metabolic models of extremophiles. Furthermore, we emphasize the current challenges associated with applying this technique in extreme environments, and conclude this review by discussing the potential implementation of metabolic models to explore theoretically optimal metabolic networks under various space conditions. Through this mini-review, our aim is to highlight the potential of metabolic modelling in advancing the study of astrobiology.
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Affiliation(s)
- Nuttapol Noirungsee
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
| | - Sakunthip Changkhong
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Department of Thoracic SurgeryUniversity Hospital ZurichZurichSwitzerland
| | - Kittiya Phinyo
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research group on Earth—Space Ecology (ESE), Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Office of Research AdministrationChiang Mai UniversityChiang MaiThailand
| | | | - Nahathai Tanakul
- National Astronomical Research Institute of ThailandChiang MaiThailand
| | - Sahutchai Inwongwan
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
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2
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Bannikova S, Khlebodarova T, Vasilieva A, Mescheryakova I, Bryanskaya A, Shedko E, Popik V, Goryachkovskaya T, Peltek S. Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation. Int J Mol Sci 2022; 23:ijms232315216. [PMID: 36499542 PMCID: PMC9735757 DOI: 10.3390/ijms232315216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Studying the effects of terahertz (THz) radiation on the proteome of temperature-sensitive organisms is limited by a number of significant technical difficulties, one of which is maintaining an optimal temperature range to avoid thermal shock as much as possible. In the case of extremophilic species with an increased temperature tolerance, it is easier to isolate the effects of THz radiation directly. We studied the proteomic response to terahertz radiation of the thermophilic Geobacillus icigianus, persisting under wide temperature fluctuations with a 60 °C optimum. The experiments were performed with a terahertz free-electron laser (FEL) from the Siberian Center for Synchrotron and Terahertz Radiation, designed and employed by the Institute of Nuclear Physics of the SB of the RAS. A G. icigianus culture in LB medium was THz-irradiated for 15 min with 0.23 W/cm2 and 130 μm, using a specially designed cuvette. The life cycle of this bacterium proceeds under conditions of wide temperature and osmotic fluctuations, which makes its enzyme systems stress-resistant. The expression of several proteins was shown to change immediately after fifteen minutes of irradiation and after ten minutes of incubation at the end of exposure. The metabolic systems of electron transport, regulation of transcription and translation, cell growth and chemotaxis, synthesis of peptidoglycan, riboflavin, NADH, FAD and pyridoxal phosphate cofactors, Krebs cycle, ATP synthesis, chaperone and protease activity, and DNA repair, including methylated DNA, take part in the fast response to THz radiation. When the response developed after incubation, the systems of the cell's anti-stress defense, chemotaxis, and, partially, cell growth were restored, but the respiration and energy metabolism, biosynthesis of riboflavin, cofactors, peptidoglycan, and translation system components remained affected and the amino acid metabolism system was involved.
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Affiliation(s)
- Svetlana Bannikova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Correspondence:
| | - Tamara Khlebodarova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Asya Vasilieva
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Irina Mescheryakova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Alla Bryanskaya
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Elizaveta Shedko
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Vasily Popik
- Budker Institute of Nuclear Physics, Siberian Branch Russian Academy of Sciences (SB RAS), 11 Acad. Lavrentieva Pr., 630090 Novosibirsk, Russia
| | - Tatiana Goryachkovskaya
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Sergey Peltek
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
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3
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Genome-scale reconstruction and metabolic modelling of the fast-growing thermophile Geobacillus sp. LC300. Metab Eng Commun 2022; 15:e00212. [DOI: 10.1016/j.mec.2022.e00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
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Kolpakov F, Akberdin I, Kiselev I, Kolmykov S, Kondrakhin Y, Kulyashov M, Kutumova E, Pintus S, Ryabova A, Sharipov R, Yevshin I, Zhatchenko S, Kel A. BioUML-towards a universal research platform. Nucleic Acids Res 2022; 50:W124-W131. [PMID: 35536253 PMCID: PMC9252820 DOI: 10.1093/nar/gkac286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/04/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022] Open
Abstract
BioUML (https://www.biouml.org)—is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrated with git repositories where users can store their models and other data. We have also expanded the capabilities of BioUML for data analysis and visualization of biomedical data: (i) any programs and Jupyter kernels can be plugged into the BioUML platform using Docker technology; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks): scripts can be executed on the BioUML web pages, and BioUML functions can be called from scripts; (iv) using plug-in architecture, specialized viewers and editors can be added. For example, powerful genome browsers as well as viewers for molecular 3D structure are integrated in this way; (v) BioUML supports data analyses using workflows (own format, Galaxy, CWL, BPMN, nextFlow). Using these capabilities, we have initiated a new branch of the BioUML development—u-science—a universal scientific platform that can be configured for specific research requirements.
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Affiliation(s)
- Fedor Kolpakov
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation.,Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090, Russian Federation
| | - Ilya Akberdin
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Ilya Kiselev
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation.,Budker Institute of Nuclear Physics SB RAS, Novosibirsk 630090, Russian Federation
| | - Semyon Kolmykov
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation
| | - Yury Kondrakhin
- Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation
| | | | - Elena Kutumova
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Federal Research Center for Information and Computational Technologies, Novosibirsk 630090, Russian Federation
| | - Sergey Pintus
- Sirius University of Science and Technology, Sochi 354340, Russian Federation
| | - Anna Ryabova
- Sirius University of Science and Technology, Sochi 354340, Russian Federation
| | - Ruslan Sharipov
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Ivan Yevshin
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation
| | - Sergey Zhatchenko
- Sirius University of Science and Technology, Sochi 354340, Russian Federation.,Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation
| | - Alexander Kel
- Biosoft.ru, LLC, Novosibirsk 630058, Russian Federation.,geneXplain GmbH, Wolfenbüttel 38302, Germany
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Panikov NS. Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges. Microorganisms 2021; 9:2352. [PMID: 34835477 PMCID: PMC8621822 DOI: 10.3390/microorganisms9112352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022] Open
Abstract
This review is a part of the SI 'Genome-Scale Modeling of Microorganisms in the Real World'. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc. Constraint-based metabolic reconstructions were successfully started two decades ago as FBA, followed by more advanced models, but this review starts from the earlier nongenomic predecessors to show that some GEMs inherited the outdated biokinetic frameworks compromising their performances. The most essential deficiencies are: (i) an inadequate account of environmental conditions, such as various degrees of nutrients limitation and other factors shaping phenotypes; (ii) a failure to simulate the adaptive changes of MMCC (MacroMolecular Cell Composition) in response to the fluctuating environment; (iii) the misinterpretation of the SGR (Specific Growth Rate) as either a fixed constant parameter of the model or independent factor affecting the conditional expression of macromolecules; (iv) neglecting stress resistance as an important objective function; and (v) inefficient experimental verification of GEM against simple growth (constant MMCC and SGR) data. Finally, we propose several ways to improve GEMs, such as replacing the outdated Monod equation with the SCM (Synthetic Chemostat Model) that establishes the quantitative relationships between primary and secondary metabolism, growth rate and stress resistance, process kinetics, and cell composition.
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Affiliation(s)
- Nicolai S Panikov
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA
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6
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Mol V, Bennett M, Sánchez BJ, Lisowska BK, Herrgård MJ, Nielsen AT, Leak DJ, Sonnenschein N. Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metab Eng 2021; 65:123-134. [PMID: 33753231 DOI: 10.1016/j.ymben.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022]
Abstract
Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.
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Affiliation(s)
- Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martyn Bennett
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Benjamín J Sánchez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Beata K Lisowska
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; BioInnovation Institute, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - David J Leak
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom.
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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Orlov YL, Ignatov AN, Galieva ER, Dobrovolskaya OB. Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school. BMC Microbiol 2020; 20:348. [PMID: 33228539 PMCID: PMC7686665 DOI: 10.1186/s12866-020-02038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119146, Moscow, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia. .,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
| | - Alexander N Ignatov
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,PhytoEngineering R&D Centre, 141880, Moscow Region, Moscow, Russia
| | | | - Oxana B Dobrovolskaya
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
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