1
|
Turanli B, Gulfidan G, Aydogan OO, Kula C, Selvaraj G, Arga KY. Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models. Mol Omics 2024; 20:234-247. [PMID: 38444371 DOI: 10.1039/d3mo00152k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and applications. Owing to the development of genome sequencing technologies and available biochemical data, it is possible to reconstruct GEMs for model and non-model microorganisms as well as for multicellular organisms such as humans and animal models. GEMs will evolve in parallel with the availability of biological data, new mathematical modeling techniques and the development of automated GEM reconstruction tools. The use of high-quality, context-specific GEMs, a subset of the original GEM in which inactive reactions are removed while maintaining metabolic functions in the extracted model, for model organisms along with machine learning (ML) techniques could increase their applications and effectiveness in translational research in the near future. Here, we briefly review the current state of GEMs, discuss the potential contributions of ML approaches for more efficient and frequent application of these models in translational research, and explore the extension of GEMs to integrative cellular models.
Collapse
Affiliation(s)
- Beste Turanli
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Gizem Gulfidan
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
| | - Ozge Onluturk Aydogan
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
| | - Ceyda Kula
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Gurudeeban Selvaraj
- Concordia University, Centre for Research in Molecular Modeling & Department of Chemistry and Biochemistry, Quebec, Canada
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospital, Department of Biomaterials, Bioinformatics Unit, Chennai, India
| | - Kazim Yalcin Arga
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
- Marmara University, Genetic and Metabolic Diseases Research and Investigation Center, Istanbul, Turkey
| |
Collapse
|
2
|
Halomonas spp., as chassis for low-cost production of chemicals. Appl Microbiol Biotechnol 2022; 106:6977-6992. [PMID: 36205763 DOI: 10.1007/s00253-022-12215-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Halomonas spp. are the well-studied platform organisms or chassis for next-generation industrial biotechnology (NGIB) due to their contamination-resistant nature combined with their fast growth property. Several Halomonas spp. have been studied regarding their genomic information and molecular engineering approaches. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), proteins including surfactants and enzymes, small molecular compounds including amino acids and derivates, as well as organic acids. This paper reviews all the progress reported in the last 10 years regarding this robust microbial cell factory. KEY POINTS: • Halomonas spp. are robust chassis for low-cost production of chemicals • Genomic information of some Halomonas spp. has been revealed • Molecular tools and approaches for Halomonas spp. have been developed • Halomonas spp. are becoming more and more important for biotechnology.
Collapse
|
3
|
Erkorkmaz BA, Kırtel O, Abaramak G, Nikerel E, Öner ET. UV and Chemically Induced Halomonas smyrnensis Mutants for Enhanced Levan Productivity. J Biotechnol 2022; 356:19-29. [PMID: 35914617 DOI: 10.1016/j.jbiotec.2022.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Halomonas smyrnensis AAD6T is a moderately halophilic bacterium proven to be a powerful biotechnological tool with its ability to accumulate valuable biopolymers such as levan and poly(3-hydroxybutyrate) (PHB). Levan is a fructose homopolymer with β-2,6 fructofuranosidic linkages on the polymer backbone, and its distinctive applications in various industries such as food, pharmaceutical, medical, and chemical have been well-defined. On the other hand, PHB is a promising raw material to produce biodegradable plastics. Although it was shown in our previous studies that H. smyrnensis AAD6T exhibits one of the highest conversion yields of sucrose to levan reported to date, novel strategies are required to overcome high costs of levan production. In this study, we aimed at increasing levan productivity of H. smyrnensis AAD6T cultures using random mutagenesis techniques combined (i.e., ethyl methanesulfate treatment and/or ultraviolet irradiation). After several consecutive treatments, mutant strains BAE2, BAE5 and BAE6 were selected as efficient levan producers, as BAE2 standing out as the most efficient one not only in sucrose utilization and levan production rates, but also in final PHB concentrations. The mutants' whole genome sequences were analysed to determine the mutations occurred. Several mutations in genes related to central carbon metabolism and osmoregulation were found. Our results suggest that random mutagenesis can be a facile and efficient strategy to enhance the performance of extremophiles in adverse conditions.
Collapse
Affiliation(s)
- Burak Adnan Erkorkmaz
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Onur Kırtel
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Gülbahar Abaramak
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, 34755 Istanbul, Turkey
| | - Ebru Toksoy Öner
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey.
| |
Collapse
|
4
|
Halomonas as a chassis. Essays Biochem 2021; 65:393-403. [PMID: 33885142 PMCID: PMC8314019 DOI: 10.1042/ebc20200159] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/04/2023]
Abstract
With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.
Collapse
|
5
|
Aydin B, Ozer T, Oner ET, Arga KY. The Genome-Based Metabolic Systems Engineering to Boost Levan Production in a Halophilic Bacterial Model. ACTA ACUST UNITED AC 2018; 22:198-209. [DOI: 10.1089/omi.2017.0216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Busra Aydin
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Tugba Ozer
- Department of Bioengineering, Marmara University, Istanbul, Turkey
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Ebru Toksoy Oner
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | | |
Collapse
|
6
|
Öner ET, Hernández L, Combie J. Review of Levan polysaccharide: From a century of past experiences to future prospects. Biotechnol Adv 2016; 34:827-844. [DOI: 10.1016/j.biotechadv.2016.05.002] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 01/24/2023]
|
7
|
Ates O. Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol 2015; 3:200. [PMID: 26734603 PMCID: PMC4683990 DOI: 10.3389/fbioe.2015.00200] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.
Collapse
Affiliation(s)
- Ozlem Ates
- Department of Medical Services and Techniques, Nisantasi University, Istanbul, Turkey
| |
Collapse
|
8
|
Diken E, Ozer T, Arikan M, Emrence Z, Oner ET, Ustek D, Arga KY. Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T. SPRINGERPLUS 2015; 4:393. [PMID: 26251777 PMCID: PMC4523562 DOI: 10.1186/s40064-015-1184-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/27/2015] [Indexed: 01/21/2023]
Abstract
Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological mechanisms, and the whole-genome organization of the bacterium. Industrially crucial genes, including the levansucrase, were detected and the genome-scale metabolic model of H. smyrnensis AAD6T was reconstructed. The bacterium was found to have many potential applications in biotechnology not only being a levan producer, but also because of its capacity to produce Pel exopolysaccharide, polyhydroxyalkanoates, and osmoprotectants. The genomic information presented here will not only provide additional information to enhance our understanding of the genetic and metabolic network of halophilic bacteria, but also accelerate the research on systematical design of engineering strategies for biotechnology applications.
Collapse
Affiliation(s)
- Elif Diken
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Tugba Ozer
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Muzaffer Arikan
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Zeliha Emrence
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Ebru Toksoy Oner
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Duran Ustek
- />Department of Medical Genetics, School of Medicine, REMER, Medipol University, 34810 Istanbul, Turkey
| | - Kazim Yalcin Arga
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| |
Collapse
|
9
|
Kazak Sarilmiser H, Ates O, Ozdemir G, Arga KY, Toksoy Oner E. Effective stimulating factors for microbial levan production by Halomonas smyrnensis AAD6T. J Biosci Bioeng 2015; 119:455-63. [DOI: 10.1016/j.jbiosc.2014.09.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 09/19/2014] [Accepted: 09/23/2014] [Indexed: 02/04/2023]
|
10
|
Isolation and Characterization of Levan from Moderate Halophilic Bacteria Bacillus licheniformis BK AG21. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.proche.2015.12.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Yin J, Chen JC, Wu Q, Chen GQ. Halophiles, coming stars for industrial biotechnology. Biotechnol Adv 2014; 33:1433-42. [PMID: 25447783 DOI: 10.1016/j.biotechadv.2014.10.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/10/2014] [Accepted: 10/19/2014] [Indexed: 10/24/2022]
Abstract
Industrial biotechnology aims to produce chemicals, materials and biofuels to ease the challenges of shortage on petroleum. However, due to the disadvantages of bioprocesses including energy consuming sterilization, high fresh water consumption, discontinuous fermentation to avoid microbial contamination, highly expensive stainless steel fermentation facilities and competing substrates for human consumption, industrial biotechnology is less competitive compared with chemical processes. Recently, halophiles have shown promises to overcome these shortcomings. Due to their unique halophilic properties, some halophiles are able to grow in high pH and high NaCl containing medium under higher temperature, allowing fermentation processes to run contamination free under unsterile conditions and continuous way. At the same time, genetic manipulation methods have been developed for halophiles. So far, halophiles have been used to produce bioplastics polyhydroxyalkanoates (PHA), ectoines, enzymes, and bio-surfactants. Increasing effects have been made to develop halophiles into a low cost platform for bioprocessing with advantages of low energy, less fresh water consumption, low fixed capital investment, and continuous production.
Collapse
Affiliation(s)
- Jin Yin
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
12
|
Costa RR, Neto AI, Calgeris I, Correia CR, Pinho ACM, Fonseca J, Öner ET, Mano JF. Adhesive nanostructured multilayer films using a bacterial exopolysaccharide for biomedical applications. J Mater Chem B 2013; 1:2367-2374. [DOI: 10.1039/c3tb20137f] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|