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Vásquez Castro E, Memari G, Ata Ö, Mattanovich D. Carbon efficient production of chemicals with yeasts. Yeast 2023; 40:583-593. [PMID: 37997485 PMCID: PMC10946752 DOI: 10.1002/yea.3909] [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: 07/04/2023] [Revised: 10/16/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023] Open
Abstract
Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO2 , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.
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Affiliation(s)
- Evelyn Vásquez Castro
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Golnaz Memari
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Özge Ata
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
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2
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Baumschabl M, Ata Ö, Mitic BM, Lutz L, Gassler T, Troyer C, Hann S, Mattanovich D. Conversion of CO 2 into organic acids by engineered autotrophic yeast. Proc Natl Acad Sci U S A 2022; 119:e2211827119. [PMID: 36383601 PMCID: PMC9704707 DOI: 10.1073/pnas.2211827119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/13/2022] [Indexed: 10/23/2023] Open
Abstract
The increase of CO2 emissions due to human activity is one of the preeminent reasons for the present climate crisis. In addition, considering the increasing demand for renewable resources, the upcycling of CO2 as a feedstock gains an extensive importance to establish CO2-neutral or CO2-negative industrial processes independent of agricultural resources. Here we assess whether synthetic autotrophic Komagataella phaffii (Pichia pastoris) can be used as a platform for value-added chemicals using CO2 as a feedstock by integrating the heterologous genes for lactic and itaconic acid synthesis. 13C labeling experiments proved that the resulting strains are able to produce organic acids via the assimilation of CO2 as a sole carbon source. Further engineering attempts to prevent the lactic acid consumption increased the titers to 600 mg L-1, while balancing the expression of key genes and modifying screening conditions led to 2 g L-1 itaconic acid. Bioreactor cultivations suggest that a fine-tuning on CO2 uptake and oxygen demand of the cells is essential to reach a higher productivity. We believe that through further metabolic and process engineering, the resulting engineered strain can become a promising host for the production of value-added bulk chemicals by microbial assimilation of CO2, to support sustainability of industrial bioprocesses.
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Affiliation(s)
- Michael Baumschabl
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Özge Ata
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Bernd M. Mitic
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Lisa Lutz
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Thomas Gassler
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
- Present address: Institute of Microbiology, ETH Zurich, Zurich, 8093, Switzerland
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190, Austria
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3
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State of the Art on the Microbial Production of Industrially Relevant Organic Acids. Catalysts 2022. [DOI: 10.3390/catal12020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by many cells. They are the products, by-products or co-products of many primary metabolic processes of microbial cells. Thanks to the potential of microbial cell factories and to the development of industrial biotechnology, from the last decades of the previous century, the microbial-based production of these molecules has started to approach the market. This was possible because of a joint effort of microbial biotechnologists and biochemical and process engineers that boosted natural production up to the titer, yield and productivity needed to be industrially competitive. More recently, the possibility to utilize renewable residual biomasses as feedstock not only for biofuels, but also for organic acids production is further augmenting the sustainability of their production, in a logic of circular bioeconomy. In this review, we briefly present the latest updates regarding the production of some industrially relevant organic acids (citric fumaric, itaconic, lactic and succinic acid), discussing the challenges and possible future developments of successful production.
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4
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Genome Mining as New Challenge in Natural Products Discovery. Mar Drugs 2020; 18:md18040199. [PMID: 32283638 PMCID: PMC7230286 DOI: 10.3390/md18040199] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.
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Complementing the intrinsic repertoire of Ustilago maydis for degradation of the pectin backbone polygalacturonic acid. J Biotechnol 2020; 307:148-163. [DOI: 10.1016/j.jbiotec.2019.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
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Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS. Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. J Biotechnol 2019; 302:67-76. [PMID: 31254549 DOI: 10.1016/j.jbiotec.2019.06.303] [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: 01/10/2019] [Revised: 04/20/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022]
Abstract
Natural compounds and derivatives play an essential role in the pharmaceutical industry, however, the difficulty in resynthesizing natural products or isolate them from the native host, often limit their availability, elevate costs and slow down the pharmaceutical manufacturing process. In this context, application of synthetic biology could enable the efficient production of large amounts of drugs or drug precursors in heterologous microorganisms aiming to accelerate the entire manufacturing process. Considering this perspective, here we developed a pipeline to automatically search for metabolites available in the metabolic space that are structurally similar to worldwide approved drugs. This pipeline involved the in silico screening of metabolites from a metabolic pathway meta-database using both Tanimoto coefficients based on Daylight like fingerprints and Maximum Common Substructure algorithm. The method was successfully applied to identify metabolites sharing essential scaffolds with one or more drugs as potential candidates for metabolic engineering. Three of these metabolites (Festuclavine, Scopolamine, and Baccatin III) were identified as similar to many drugs like Cabergoline, Oxitropium, Paclitaxel and had their metabolic pathways computationally mapped for their production in Saccharomyces cerevisiae with our proprietary pathway design software. These compounds are examples of new opportunities for the application of synthetic biology in pharmaceutical production.
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Affiliation(s)
- Vanessa V C Sinatti
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil.
| | - Carlos Alberto X Gonçalves
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
| | - Aline S Romão-Dumaresq
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
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Metabolism of sucrose in a non-fermentative Escherichia coli under oxygen limitation. Appl Microbiol Biotechnol 2019; 103:6245-6256. [PMID: 31147757 PMCID: PMC6616217 DOI: 10.1007/s00253-019-09909-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/21/2023]
Abstract
Biotechnological industry strives to develop anaerobic bioprocesses fueled by abundant and cheap carbon sources, like sucrose. However, oxygen-limiting conditions often lead to by-product formation and reduced ATP yields. While by-product formation is typically decreased by gene deletion, the breakdown of oligosaccharides with inorganic phosphate instead of water could increment the ATP yield. To observe the effect of oxygen limitation during sucrose consumption, a non-fermentative Escherichia coli K-12 strain was transformed with genes enabling sucrose assimilation. It was observed that the combined deletion of the genes adhE, adhP, mhpF, ldhA, and pta abolished the anaerobic growth using sucrose. Therefore, the biomass-specific conversion rates were obtained using oxygen-limited continuous cultures. Strains performing the breakdown of the sucrose by hydrolysis (SUC-HYD) or phosphorolysis (SUC-PHOSP) were studied in such conditions. An experimentally validated in silico model, modified to account for plasmid and protein burdens, was employed to calculate carbon and electron consistent conversion rates. In both strains, the biomass yields were lower than expected and, strikingly, SUC-PHOSP showed a yield lower than SUC-HYD. Flux balance analyses indicated a significant increase in the non-growth-associated ATP expenses by comparison with the growth on glucose. The observed fructose-1,6-biphosphatase and phosphoglucomutase activities, as well as the concentrations of glycogen, suggest the operation of ATP futile cycles triggered by a combination of the oxygen limitation and the metabolites released during the sucrose breakdown.
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8
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John G, Nagarajan S, Vemula PK, Silverman JR, Pillai C. Natural monomers: A mine for functional and sustainable materials – Occurrence, chemical modification and polymerization. Prog Polym Sci 2019. [DOI: 10.1016/j.progpolymsci.2019.02.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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10
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Berterame NM, Bertagnoli S, Codazzi V, Porro D, Branduardi P. Temperature-induced lipocalin (TIL): a shield against stress-inducing environmental shocks in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:4056149. [PMID: 28830085 DOI: 10.1093/femsyr/fox056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 11/14/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a well-established workhorse, either for recombinant or natural products, thanks to its natural traits and easily editable metabolism. However, during a bio-based industrial process it meets multiple stresses generated by operative conditions such as non-optimal temperature, pH, oxygenation and product accumulation. The development of tolerant strains is therefore indispensable for the improvement of production, yield and productivity of fermentative processes. In this regard, plants as resilient organisms are a generous source for fishing genes and/or metabolites that can help the cell factory to counteract environmental constraints. Plants possess proteins named temperature-induced lipocalins, TIL, whose levels in the cells correlates with the tolerance to sudden temperature changes and with the scavenging of reactive oxygen species. In this work, the gene encoding for the Arabidopsis thaliana TIL protein was for the first time expressed in S. cerevisiae. The recombinant strain was compared and analysed against the parental counterpart under heat shock, freezing, exposure to organic acid and oxidative agents. In all the tested conditions, TIL expression conferred a higher tolerance to the stress imposed, making this strain a promising candidate for the development of robust cell factories able to overtake the major impairments of industrial processes.
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Affiliation(s)
- Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Stefano Bertagnoli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Vera Codazzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
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11
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Dhakal D, Sohng JK. Coalition of Biology and Chemistry for Ameliorating Antimicrobial Drug Discovery. Front Microbiol 2017; 8:734. [PMID: 28522993 PMCID: PMC5415603 DOI: 10.3389/fmicb.2017.00734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon UniversityAsan-si, South Korea
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12
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Abstract
The diversity and natural modularity of their biosynthetic pathways has turned natural products into attractive, but challenging, targets for synthetic biology approaches. Here, we discuss the current state of the field, highlighting recent advances and remaining bottlenecks. Global genomic assessments of natural product biosynthetic capacities across large parts of microbial diversity provide a first survey of the available natural parts libraries and identify evolutionary design rules for further engineering. Methods for compound and pathway detection and characterization are developed increasingly on the basis of synthetic biology tools, contributing to an accelerated translation of genomic information into usable building blocks for pathway assembly. A wide range of methods is also becoming available for accessing ever larger parts of chemical space by rational diversification of natural products, guided by rapid progress in our understanding of the underlying biochemistry and enzymatic mechanisms. Enhanced genome assembly and editing tools, adapted to the needs of natural products research, facilitate the realization of ambitious engineering strategies, ranging from combinatorial library generation to high-throughput optimization of product titers. Together, these tools and concepts contribute to the emergence of a new generation of revitalized natural product research.
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Affiliation(s)
- Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
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13
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Sauer M. Industrial production of acetone and butanol by fermentation-100 years later. FEMS Microbiol Lett 2016; 363:fnw134. [PMID: 27199350 PMCID: PMC4894279 DOI: 10.1093/femsle/fnw134] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 11/12/2022] Open
Abstract
Microbial production of acetone and butanol was one of the first large-scale industrial fermentation processes of global importance. During the first part of the 20th century, it was indeed the second largest fermentation process, superseded in importance only by the ethanol fermentation. After a rapid decline after the 1950s, acetone-butanol-ethanol (ABE) fermentation has recently gained renewed interest in the context of biorefinery approaches for the production of fuels and chemicals from renewable resources. The availability of new methods and knowledge opens many new doors for industrial microbiology, and a comprehensive view on this process is worthwhile due to the new interest. This thematic issue of FEMS Microbiology Letters, dedicated to the 100th anniversary of the first industrial exploitation of Chaim Weizmann's ABE fermentation process, covers the main aspects of old and new developments, thereby outlining a model development in biotechnology. All major aspects of industrial microbiology are exemplified by this single process. This includes new technologies, such as the latest developments in metabolic engineering, the exploitation of biodiversity and discoveries of new regulatory systems such as for microbial stress tolerance, as well as technological aspects, such as bio- and down-stream processing. Industrial production of acetone and butanol by fermentation—100 years later.
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Affiliation(s)
- Michael Sauer
- Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria CD-Laboratory for Biotechnology of Glycerol, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190 Vienna, Austria
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14
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Branduardi P, Porro D. n-butanol: challenges and solutions for shifting natural metabolic pathways into a viable microbial production. FEMS Microbiol Lett 2016; 363:fnw070. [DOI: 10.1093/femsle/fnw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2016] [Indexed: 12/13/2022] Open
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15
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Branduardi P. Synthetic Biology for Cellular Remodelling to Elicit Industrially Relevant Microbial Phenotypes. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Martani F, Marano F, Bertacchi S, Porro D, Branduardi P. The Saccharomyces cerevisiae poly(A) binding protein Pab1 as a target for eliciting stress tolerant phenotypes. Sci Rep 2015; 5:18318. [PMID: 26658950 PMCID: PMC4677312 DOI: 10.1038/srep18318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/16/2015] [Indexed: 11/29/2022] Open
Abstract
When exploited as cell factories, Saccharomyces cerevisiae cells are exposed to harsh environmental stresses impairing titer, yield and productivity of the fermentative processes. The development of robust strains therefore represents a pivotal challenge for the implementation of cost-effective bioprocesses. Altering master regulators of general cellular rewiring represents a possible strategy to evoke shaded potential that may accomplish the desirable features. The poly(A) binding protein Pab1, as stress granules component, was here selected as the target for obtaining widespread alterations in mRNA metabolism, resulting in stress tolerant phenotypes. Firstly, we demonstrated that the modulation of Pab1 levels improves robustness against different stressors. Secondly, the mutagenesis of PAB1 and the application of a specific screening protocol on acetic acid enriched medium allowed the isolation of the further ameliorated mutant pab1 A60-9. These findings pave the way for a novel approach to unlock industrially promising phenotypes through the modulation of a post-transcriptional regulatory element.
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Affiliation(s)
- Francesca Martani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Francesca Marano
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy.,SYSBIO - Centre of Systems Biology, Milano and Roma, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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18
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Cueto-Rojas HF, van Maris A, Wahl SA, Heijnen J. Thermodynamics-based design of microbial cell factories for anaerobic product formation. Trends Biotechnol 2015; 33:534-46. [DOI: 10.1016/j.tibtech.2015.06.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/20/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
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Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. BIOMED RESEARCH INTERNATIONAL 2015; 2015:769471. [PMID: 25874228 PMCID: PMC4385633 DOI: 10.1155/2015/769471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/30/2014] [Indexed: 11/18/2022]
Abstract
Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.
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Willrodt C, Karande R, Schmid A, Julsing MK. Guiding efficient microbial synthesis of non-natural chemicals by physicochemical properties of reactants. Curr Opin Biotechnol 2015; 35:52-62. [PMID: 25835779 DOI: 10.1016/j.copbio.2015.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 11/18/2022]
Abstract
The recent progress in sustainable chemistry and in synthetic biology increased the interest of chemical and pharmaceutical industries to implement microbial processes for chemical synthesis. However, most organisms used in biotechnological applications are not evolved by Nature for the production of hydrophobic, non-charged, volatile, or toxic compounds. In order to overcome this discrepancy, bioprocess design should consist of an integrated approach addressing pathway, cellular, reaction, and process engineering. Highlighting selected examples, we show that surprisingly often Nature provides conceptual solutions to enable chemical synthesis. Complemented by established methods from (bio)chemical and metabolic engineering, these concepts offer potential strategies yet to be explored and translated into innovative technical solutions enabling sustainable microbial production of non-natural chemicals.
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Affiliation(s)
- Christian Willrodt
- Department of Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.
| | - Mattijs K Julsing
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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21
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Synthetic biology advances for pharmaceutical production. Curr Opin Biotechnol 2015; 35:46-51. [PMID: 25744872 PMCID: PMC4617476 DOI: 10.1016/j.copbio.2015.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/12/2023]
Abstract
Synthetic biology is quickly moving from proof of concept to industrial application. Pharmaceuticals are a promising target for advanced genetic engineering. Genome sequence data indicate vast underexploited biosynthetic capacity. Synthetic biology can create libraries of novel chemicals enriched for bioactivity. Synthetic biology expands the range of available chassis organisms for industry.
Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.
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