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Takenaka M, Kamasaka K, Daryong K, Tsuchikane K, Miyazawa S, Fujihana S, Hori Y, Vavricka CJ, Hosoyama A, Kawasaki H, Shirai T, Araki M, Nakagawa A, Minami H, Kondo A, Hasunuma T. Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis. Microb Cell Fact 2024; 23:178. [PMID: 38879464 PMCID: PMC11179272 DOI: 10.1186/s12934-024-02453-7] [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: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compounds and those inferred from the chemical structures of established reactions, we can uncover previously undiscovered enzymatic processes. The application of the novel alternative pathways enables us to improve microbial bioproduction by bypassing or reinforcing metabolic bottlenecks. Benzylisoquinoline alkaloids (BIAs) are a diverse group of plant-derived compounds with important pharmaceutical properties. BIA biosynthesis has developed into a prime example of metabolic engineering and microbial bioproduction. The early bottleneck of BIA production in Escherichia coli consists of 3,4-dihydroxyphenylacetaldehyde (DHPAA) production and conversion to tetrahydropapaveroline (THP). Previous studies have selected monoamine oxidase (MAO) and DHPAA synthase (DHPAAS) to produce DHPAA from dopamine and oxygen; however, both of these enzymes produce toxic hydrogen peroxide as a byproduct. RESULTS In the current study, in silico pathway design is applied to relieve the bottleneck of DHPAA production in the synthetic BIA pathway. Specifically, the cytochrome P450 enzyme, tyrosine N-monooxygenase (CYP79), is identified to bypass the established MAO- and DHPAAS-mediated pathways in an alternative arylacetaldoxime route to DHPAA with a peroxide-independent mechanism. The application of this pathway is proposed to result in less formation of toxic byproducts, leading to improved production of reticuline (up to 60 mg/L at the flask scale) when compared with that from the conventional MAO pathway. CONCLUSIONS This study showed improved reticuline production using the bypass pathway predicted by the M-path computational platform. Reticuline production in E. coli exceeded that of the conventional MAO-mediated pathway. The study provides a clear example of the integration of pathway mining and enzyme design in creating artificial metabolic pathways and suggests further potential applications of this strategy in metabolic engineering.
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Affiliation(s)
- Musashi Takenaka
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouhei Kamasaka
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kim Daryong
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Keiko Tsuchikane
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Seiha Miyazawa
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Saeko Fujihana
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Yoshimi Hori
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Christopher J Vavricka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Akira Hosoyama
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Hiroko Kawasaki
- National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 1510066, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Michihiro Araki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606- 8501, Japan
- National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shimmachi, Suita, Osaka, 564-8565, Japan
| | - Akira Nakagawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi city, Ishikawa, Japan
| | - Hiromichi Minami
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi city, Ishikawa, Japan
| | - Akihiko Kondo
- Bacchus Bio innovation Co. Ltd, 6-3-7-505 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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Balzerani F, Blasco T, Pérez-Burillo S, Valcarcel LV, Hassoun S, Planes FJ. Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota. NPJ Syst Biol Appl 2024; 10:56. [PMID: 38802371 PMCID: PMC11130242 DOI: 10.1038/s41540-024-00381-1] [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: 05/15/2023] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Despite significant advances in reconstructing genome-scale metabolic networks, the understanding of cellular metabolism remains incomplete for many organisms. A promising approach for elucidating cellular metabolism is analysing the full scope of enzyme promiscuity, which exploits the capacity of enzymes to bind to non-annotated substrates and generate novel reactions. To guide time-consuming costly experimentation, different computational methods have been proposed for exploring enzyme promiscuity. One relevant algorithm is PROXIMAL, which strongly relies on KEGG to define generic reaction rules and link specific molecular substructures with associated chemical transformations. Here, we present a completely new pipeline, PROXIMAL2, which overcomes the dependency on KEGG data. In addition, PROXIMAL2 introduces two relevant improvements with respect to the former version: i) correct treatment of multi-step reactions and ii) tracking of electric charges in the transformations. We compare PROXIMAL and PROXIMAL2 in recovering annotated products from substrates in KEGG reactions, finding a highly significant improvement in the level of accuracy. We then applied PROXIMAL2 to predict degradation reactions of phenolic compounds in the human gut microbiota. The results were compared to RetroPath RL, a different and relevant enzyme promiscuity method. We found a significant overlap between these two methods but also complementary results, which open new research directions into this relevant question in nutrition.
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Affiliation(s)
- Francesco Balzerani
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Telmo Blasco
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Sergio Pérez-Burillo
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Luis V Valcarcel
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
- University of Navarra, Biomedical Engineering Center, Campus Universitario, 31009, Pamplona, Navarra, Spain
- University of Navarra, Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, 31080, Pamplona, Spain
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA, 02155, USA.
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA.
| | - Francisco J Planes
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain.
- University of Navarra, Biomedical Engineering Center, Campus Universitario, 31009, Pamplona, Navarra, Spain.
- University of Navarra, Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, 31080, Pamplona, Spain.
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Upadhyay V, Boorla VS, Maranas CD. Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network. Metab Eng 2023; 78:171-182. [PMID: 37301359 DOI: 10.1016/j.ymben.2023.06.001] [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: 12/15/2022] [Revised: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Retro-biosynthetic approaches have made significant advances in predicting synthesis routes of target biofuel, bio-renewable or bio-active molecules. The use of only cataloged enzymatic activities limits the discovery of new production routes. Recent retro-biosynthetic algorithms increasingly use novel conversions that require altering the substrate or cofactor specificities of existing enzymes while connecting pathways leading to a target metabolite. However, identifying and re-engineering enzymes for desired novel conversions are currently the bottlenecks in implementing such designed pathways. Herein, we present EnzRank, a convolutional neural network (CNN) based approach, to rank-order existing enzymes in terms of their suitability to undergo successful protein engineering through directed evolution or de novo design towards a desired specific substrate activity. We train the CNN model on 11,800 known active enzyme-substrate pairs from the BRENDA database as positive samples and data generated by scrambling these pairs as negative samples using substrate dissimilarity between an enzyme's native substrate and all other molecules present in the dataset using Tanimoto similarity score. EnzRank achieves an average recovery rate of 80.72% and 73.08% for positive and negative pairs on test data after using a 10-fold holdout method for training and cross-validation. We further developed a web-based user interface (available at https://huggingface.co/spaces/vuu10/EnzRank) to predict enzyme-substrate activity using SMILES strings of substrates and enzyme sequence as input to allow convenient and easy-to-use access to EnzRank. In summary, this effort can aid de novo pathway design tools to prioritize starting enzyme re-engineering candidates for novel reactions as well as in predicting the potential secondary activity of enzymes in cell metabolism.
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Affiliation(s)
- Vikas Upadhyay
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nat Commun 2022; 13:5082. [PMID: 36038542 PMCID: PMC9424320 DOI: 10.1038/s41467-022-32661-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/11/2022] [Indexed: 11/27/2022] Open
Abstract
Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows.
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6
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Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods. NPJ Syst Biol Appl 2022; 8:24. [PMID: 35831427 PMCID: PMC9279433 DOI: 10.1038/s41540-022-00234-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/20/2022] [Indexed: 11/08/2022] Open
Abstract
The relevance of phenolic compounds in the human diet has increased in recent years, particularly due to their role as natural antioxidants and chemopreventive agents in different diseases. In the human body, phenolic compounds are mainly metabolized by the gut microbiota; however, their metabolism is not well represented in public databases and existing reconstructions. In a previous work, using different sources of knowledge, bioinformatic and modelling tools, we developed AGREDA, an extended metabolic network more amenable to analyze the interaction of the human gut microbiota with diet. Despite the substantial improvement achieved by AGREDA, it was not sufficient to represent the diverse metabolic space of phenolic compounds. In this article, we make use of an enzyme promiscuity approach to complete further the metabolism of phenolic compounds in the human gut microbiota. In particular, we apply RetroPath RL, a previously developed approach based on Monte Carlo Tree Search strategy reinforcement learning, in order to predict the degradation pathways of compounds present in Phenol-Explorer, the largest database of phenolic compounds in the literature. Reactions predicted by RetroPath RL were integrated with AGREDA, leading to a more complete version of the human gut microbiota metabolic network. We assess the impact of our improvements in the metabolic processing of various foods, finding previously undetected connections with output microbial metabolites. By means of untargeted metabolomics data, we present in vitro experimental validation for output microbial metabolites released in the fermentation of lentils with feces of children representing different clinical conditions.
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7
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Kovács SC, Szappanos B, Tengölics R, Notebaart RA, Papp B. Underground metabolism as a rich reservoir for pathway engineering. Bioinformatics 2022; 38:3070-3077. [PMID: 35441658 PMCID: PMC9154287 DOI: 10.1093/bioinformatics/btac282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
Motivation Bioproduction of value-added compounds is frequently achieved by utilizing enzymes from other species. However, expression of such heterologous enzymes can be detrimental due to unexpected interactions within the host cell. Recently, an alternative strategy emerged, which relies on recruiting side activities of host enzymes to establish new biosynthetic pathways. Although such low-level ‘underground’ enzyme activities are prevalent, it remains poorly explored whether they may serve as an important reservoir for pathway engineering. Results Here, we use genome-scale modeling to estimate the theoretical potential of underground reactions for engineering novel biosynthetic pathways in Escherichia coli. We found that biochemical reactions contributed by underground enzyme activities often enhance the in silico production of compounds with industrial importance, including several cases where underground activities are indispensable for production. Most of these new capabilities can be achieved by the addition of one or two underground reactions to the native network, suggesting that only a few side activities need to be enhanced during implementation. Remarkably, we find that the contribution of underground reactions to the production of value-added compounds is comparable to that of heterologous reactions, underscoring their biotechnological potential. Taken together, our genome-wide study demonstrates that exploiting underground enzyme activities could be a promising addition to the toolbox of industrial strain development. Availability and implementation The data and scripts underlying this article are available on GitHub at https://github.com/pappb/Kovacs-et-al-Underground-metabolism. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Szabolcs Cselgő Kovács
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Balázs Szappanos
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.,Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Tengölics
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Richard A Notebaart
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
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8
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Tang S, Liao D, Li X, Lin Y, Han S, Zheng S. Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation. ACS Synth Biol 2021; 10:2417-2433. [PMID: 34529398 DOI: 10.1021/acssynbio.1c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The modification of intracellular metabolic pathways by metabolic engineering has generated many engineered strains with relatively high yields of various target products in the past few decades. However, the unpredictable accumulation of toxic products, the cell membrane barrier, and competition between the carbon flux of cell growth and product synthesis have severely retarded progress toward the industrial-scale production of many essential chemicals. On the basis of an in-depth understanding of intracellular metabolic pathways, scientists intend to explore more sustainable methods and construct a cell-free biosynthesis system in vitro. In this review, the synthesis and application of pyruvate as a platform compound is used as an example to introduce cell-free biosynthesis systems. We systematically summarize a proposed methodology workflow of cell-free biosynthesis systems, including pathway design, enzyme mining, enzyme modification, multienzyme assembly, and pathway optimization. Some new methods, such as machine learning, are also mentioned in this review.
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Affiliation(s)
- Shiming Tang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Daocheng Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Xuewen Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
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Nakazawa S, Imaichi O, Kogure T, Kubota T, Toyoda K, Suda M, Inui M, Ito K, Shirai T, Araki M. History-Driven Genetic Modification Design Technique Using a Domain-Specific Lexical Model for the Acceleration of DBTL Cycles for Microbial Cell Factories. ACS Synth Biol 2021; 10:2308-2317. [PMID: 34351735 DOI: 10.1021/acssynbio.1c00234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of microbes for conducting bioprocessing via synthetic biology involves design-build-test-learn (DBTL) cycles. To aid the designing step, we developed a computational technique that suggests next genetic modifications on the basis of relatedness to the user's design history of genetic modifications accumulated through former DBTL cycles conducted by the user. This technique, which comprehensively retrieves well-known designs related to the history, involves searching text for previous literature and then mining genes that frequently co-occur in the literature with those modified genes. We further developed a domain-specific lexical model that weights literature that is more related to the domain of metabolic engineering to emphasize genes modified for bioprocessing. Our technique made a suggestion by using a history of creating a Corynebacterium glutamicum strain producing shikimic acid that had 18 genetic modifications. Inspired by the suggestion, eight genes were considered by biologists for further modification, and modifying four of these genes proved experimentally efficient in increasing the production of shikimic acid. These results indicated that our proposed technique successfully utilized the former cycles to suggest relevant designs that biologists considered worth testing. Comprehensive retrieval of well-tested designs will help less-experienced researchers overcome the entry barrier as well as inspire experienced researchers to formulate design concepts that have been overlooked or suspended. This technique will aid DBTL cycles by feeding histories back to the next genetic design, thereby complementing the designing step.
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Affiliation(s)
- Shiori Nakazawa
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Osamu Imaichi
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Takahisa Kogure
- Research Institute of Innovative Technology for Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto 619-0292, Japan
| | - Takeshi Kubota
- Research Institute of Innovative Technology for Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto 619-0292, Japan
| | - Koichi Toyoda
- Research Institute of Innovative Technology for Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto 619-0292, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto 619-0292, Japan
| | - Kiyoto Ito
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Tomokazu Shirai
- Riken, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 240-0035, Japan
| | - Michihiro Araki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8638, Japan
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11
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Visani GM, Hughes MC, Hassoun S. Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification. Bioinformatics 2021; 37:btab054. [PMID: 33515234 PMCID: PMC8337005 DOI: 10.1093/bioinformatics/btab054] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/30/2020] [Accepted: 01/22/2021] [Indexed: 11/25/2022] Open
Abstract
MOTIVATION As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, as defined via the Enzyme Commission (EC) numbers, are likely to interact with a given query molecule. Our data consists of enzyme-substrate interactions from the BRENDA database. Some interactions are attributed to natural selection and involve the enzyme's natural substrates. The majority of the interactions however involve non-natural substrates, thus reflecting promiscuous enzymatic activities. RESULTS We frame this "enzyme promiscuity prediction" problem as a multi-label classification task. We maximally utilize inhibitor and unlabelled data to train prediction models that can take advantage of known hierarchical relationships between enzyme classes. We report that a hierarchical multi-label neural network, EPP-HMCNF, is the best model for solving this problem, outperforming k-nearest neighbours similarity-based and other machine learning models. We show that inhibitor information during training consistently improves predictive power, particularly for EPP-HMCNF. We also show that all promiscuity prediction models perform worse under a realistic data split when compared to a random data split, and when evaluating performance on non-natural substrates compared to natural substrates. AVAILABILITY AND IMPLEMENTATION We provide Python code for EPP-HMCNF and other models in a repository termed EPP (Enzyme Promiscuity Prediction) at https://github.com/hassounlab/EPP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gian Marco Visani
- Department of Computer Science, Tufts University, Medford, MA 02155, USA
| | - Michael C Hughes
- Department of Computer Science, Tufts University, Medford, MA 02155, USA
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA 02155, USA
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, USA
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Motwalli O, Uludag M, Mijakovic I, Alazmi M, Bajic VB, Gojobori T, Gao X, Essack M. PATH cre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes. ACS Synth Biol 2020; 9:3217-3227. [PMID: 33198455 DOI: 10.1021/acssynbio.0c00058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Developing computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand, the preferred host organisms may not have the native metabolic reactions needed to produce the compound of interest; thus, the computational tool needs to identify the metabolic reactions that will most efficiently produce the desired product. In this regard, we developed the generic tool PATHcre8 to facilitate an optimized search for heterologous biosynthetic pathway routes. PATHcre8 finds and ranks biosynthesis routes in a large number of organisms, including Cyanobacteria. The tool ranks the pathways based on feature scores that reflect reaction thermodynamics, the potentially toxic products in the pathway (compound toxicity), intermediate products in the pathway consumed by competing reactions (product consumption), and host-specific information such as enzyme copy number. A comparison with several other similar tools shows that PATHcre8 is more efficient in ranking functional pathways. To illustrate the effectiveness of PATHcre8, we further provide case studies focused on isoprene production and the biodegradation of cocaine. PATHcre8 is free for academic and nonprofit users and can be accessed at https://www.cbrc.kaust.edu.sa/pathcre8/.
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Affiliation(s)
- Olaa Motwalli
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Saudi Electronic University (SEU), College of Computing and Informatics, Madinah 41538-53307, Kingdom of Saudi Arabia
| | - Mahmut Uludag
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Meshari Alazmi
- Department of Information and Computer Science, College of Computer Science and Engineering, University of Ha’il, P.O. Box 2440, Ha’il 81411, Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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13
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Otero-Muras I, Carbonell P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metab Eng 2020; 63:61-80. [PMID: 33316374 DOI: 10.1016/j.ymben.2020.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/19/2022]
Abstract
Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.
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Affiliation(s)
- Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo, 36208, Spain.
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (ai2), Universitat Politècnica de València, 46022, Spain.
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14
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Gerard MF, Comelli RN. PhDSeeker: Pheromone-Directed Seeker for metabolic pathways. Biosystems 2020; 198:104259. [PMID: 32976925 DOI: 10.1016/j.biosystems.2020.104259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022]
Abstract
Manually finding relationship networks among compounds can be a hard and time-consuming task. However, this process is fundamental when looking for a metabolic pathway that explains how multiple compounds are related, to identify relevant pathways in organisms, filling gaps on metabolic networks, or when new mechanisms for the synthesis of important compounds are sought. Here, we present PhDSeeker, a new tool for the automatic search of metabolic pathways. This tool is able to relate simultaneously several compounds. Furthermore, its flexibility allows it to be easily configured for addressing a wide range of situations. Solutions found are provided not only in plain text but also as interactive representations that can be analyzed in a web browser. Source code is available at https://github.com/sinc-lab/phdseeker. A web service is also available at https://sinc.unl.edu.ar/web-demo/phds/. Several fully documented study cases, including their settings and solutions files, are also provided as Supplementary Material.
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Affiliation(s)
- Matias F Gerard
- Research Institute for Signals, Systems and Computational Intelligence (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina.
| | - Raúl N Comelli
- Departamento de Medio Ambiente, Fac. de Ingeniería y Ciencias Hídricas (FICH), Univ. Nacional del Litoral (UNL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Universitaria CC 242 Paraje El Pozo, 3000, Santa Fe, Argentina.
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15
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Chen F, Yuan L, Ding S, Tian Y, Hu QN. Data-driven rational biosynthesis design: from molecules to cell factories. Brief Bioinform 2020; 21:1238-1248. [PMID: 31243440 DOI: 10.1093/bib/bbz065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/28/2019] [Accepted: 05/08/2019] [Indexed: 11/12/2022] Open
Abstract
A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially be useful to construct target-oriented chassis organisms. Engineering the complicated metabolic systems of chassis organisms to biosynthesize target molecules from inexpensive biomass is the main goal of cell factory design. The process of data-driven cell factory design could be divided into several parts: (1) target molecule selection; (2) metabolic reaction and pathway design; (3) prediction of novel enzymes based on protein domain and structure transformation of biosynthetic reactions; (4) construction of large-scale DNA for metabolic pathways; and (5) DNA assembly methods and visualization tools. The construction of a one-stop cell factory system could achieve automated design from the molecule level to the chassis level. In this article, we outline data-driven rational biosynthesis design steps and provide an overview of related tools in individual steps.
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Affiliation(s)
- Fu Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Le Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shaozhen Ding
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Yu Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qian-Nan Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
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16
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Schneider P, Klamt S. Characterizing and ranking computed metabolic engineering strategies. Bioinformatics 2020; 35:3063-3072. [PMID: 30649194 PMCID: PMC6735923 DOI: 10.1093/bioinformatics/bty1065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/28/2018] [Accepted: 01/07/2019] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION The computer-aided design of metabolic intervention strategies has become a key component of an integrated metabolic engineering approach and a broad range of methods and algorithms has been developed for this task. Many of these algorithms enforce coupling of growth with product synthesis and may return thousands of possible intervention strategies from which the most suitable strategy must then be selected. RESULTS This work focuses on how to evaluate and rank, in a meaningful way, a given pool of computed metabolic engineering strategies for growth-coupled product synthesis. Apart from straightforward criteria, such as a preferably small number of necessary interventions, a reasonable growth rate and a high product yield, we present several new criteria useful to pick the most suitable intervention strategy. Among others, we investigate the robustness of the intervention strategies by searching for metabolites that may disrupt growth coupling when accumulated or secreted and by checking whether the interventions interrupt pathways at their origin (preferable) or at downstream steps. We also assess thermodynamic properties of the pathway(s) favored by the intervention strategy. Furthermore, strategies that have a significant overlap with alternative solutions are ranked higher because they provide flexibility in implementation. We also introduce the notion of equivalence classes for grouping intervention strategies with identical solution spaces. Our ranking procedure involves in total ten criteria and we demonstrate its applicability by assessing knockout-based intervention strategies computed in a genome-scale model of E.coli for the growth-coupled synthesis of l-methionine and of the heterologous product 1,4-butanediol. AVAILABILITY AND IMPLEMENTATION The MATLAB scripts that were used to characterize and rank the example intervention strategies are available at http://www2.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Philipp Schneider
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
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17
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Duigou T, du Lac M, Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Res 2020; 47:D1229-D1235. [PMID: 30321422 PMCID: PMC6323975 DOI: 10.1093/nar/gky940] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/09/2018] [Indexed: 01/03/2023] Open
Abstract
RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity. Here, we provide for the first time a complete set containing >400 000 stereochemistry-aware reaction rules extracted from public databases and expressed in the community-standard SMARTS (SMIRKS) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such numerous representations of reactions expand natural chemical diversity by predicting de novo reactions of promiscuous enzymes.
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Affiliation(s)
- Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Melchior du Lac
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pablo Carbonell
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.,CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, Évry 91000, France
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18
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Riaz MR, Preston GM, Mithani A. MAPPS: A Web-Based Tool for Metabolic Pathway Prediction and Network Analysis in the Postgenomic Era. ACS Synth Biol 2020; 9:1069-1082. [PMID: 32347714 DOI: 10.1021/acssynbio.9b00397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Comparative and evolutionary analyses of metabolic networks have a wide range of applications, ranging from research into metabolic evolution through to practical applications in drug development, synthetic biology, and biodegradation. We present MAPPS: Metabolic network Analysis and Pathway Prediction Server (https://mapps.lums.edu.pk), a web-based tool to study functions and evolution of metabolic networks using traditional and 'omics data sets. MAPPS provides diverse functionalities including an interactive interface, graphical visualization of results, pathway prediction and network comparison, identification of potential drug targets, in silico metabolic engineering, host-microbe interactions, and ancestral network building. Importantly, MAPPS also allows users to upload custom data, thus enabling metabolic analyses on draft and custom genomes, and has an 'omics pipeline to filter pathway results, making it relevant in today's postgenomic era.
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Affiliation(s)
- Muhammad Rizwan Riaz
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
| | - Gail M. Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Aziz Mithani
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
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19
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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20
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Abstract
Metabolic engineering aims to produce chemicals of interest from living organisms, to advance toward greener chemistry. Despite efforts, the research and development process is still long and costly, and efficient computational design tools are required to explore the chemical biosynthetic space. Here, we propose to explore the bioretrosynthesis space using an artificial intelligence based approach relying on the Monte Carlo Tree Search reinforcement learning method, guided by chemical similarity. We implement this method in RetroPath RL, an open-source and modular command line tool. We validate it on a golden data set of 20 manually curated experimental pathways as well as on a larger data set of 152 successful metabolic engineering projects. Moreover, we provide a novel feature that suggests potential media supplements to complement the enzymatic synthesis plan.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
- SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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21
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Kim SM, Peña MI, Moll M, Bennett GN, Kavraki LE. Improving the organization and interactivity of metabolic pathfinding with precomputed pathways. BMC Bioinformatics 2020; 21:13. [PMID: 31924164 PMCID: PMC6954563 DOI: 10.1186/s12859-019-3328-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022] Open
Abstract
Background The rapid growth of available knowledge on metabolic processes across thousands of species continues to expand the possibilities of producing chemicals by combining pathways found in different species. Several computational search algorithms have been developed for automating the identification of possible heterologous pathways; however, these searches may return thousands of pathway results. Although the large number of results are in part due to the large number of possible compounds and reactions, a subset of core reaction modules is repeatedly observed in pathway results across multiple searches, suggesting that some subpaths between common compounds were more consistently explored than others.To reduce the resources spent on searching the same metabolic space, a new meta-algorithm for metabolic pathfinding, Hub Pathway search with Atom Tracking (HPAT), was developed to take advantage of a precomputed network of subpath modules. To investigate the efficacy of this method, we created a table describing a network of common hub metabolites and how they are biochemically connected and only offloaded searches to and from this hub network onto an interactive webserver capable of visualizing the resulting pathways. Results A test set of nineteen known pathways taken from literature and metabolic databases were used to evaluate if HPAT was capable of identifying known pathways. HPAT found the exact pathway for eleven of the nineteen test cases using a diverse set of precomputed subpaths, whereas a comparable pathfinding search algorithm that does not use precomputed subpaths found only seven of the nineteen test cases. The capability of HPAT to find novel pathways was demonstrated by its ability to identify novel 3-hydroxypropanoate (3-HP) synthesis pathways. As for pathway visualization, the new interactive pathway filters enable a reduction of the number of displayed pathways from hundreds down to less than ten pathways in several test cases, illustrating their utility in reducing the amount of presented information while retaining pathways of interest. Conclusions This work presents the first step in incorporating a precomputed subpath network into metabolic pathfinding and demonstrates how this leads to a concise, interactive visualization of pathway results. The modular nature of metabolic pathways is exploited to facilitate efficient discovery of alternate pathways.
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Affiliation(s)
- Sarah M Kim
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Matthew I Peña
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Mark Moll
- Department of Computer Science, Rice University, Houston, Texas, USA.
| | | | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, Texas, USA
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22
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Amano K, Matsumoto T, Tanaka K, Funatsu K, Kotera M. Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. BMC Bioinformatics 2019; 20:728. [PMID: 31870296 PMCID: PMC6929434 DOI: 10.1186/s12859-019-3183-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through the synthetic biology approach. A number of studies have aimed to predict biosynthetic pathways from their chemical structures in a retrosynthesis manner; however, sometimes the calculation finishes without reaching the starting material from the target molecule. In order to address this problem, the method to find suitable starting materials is required. RESULTS In this study, we developed a predictive workflow named the Metabolic Disassembler that automatically disassembles the target molecule structure into relevant biosynthetic units (BUs), which are the substructures that correspond to the starting materials in the biosynthesis pathway. This workflow uses a biosynthetic unit library (BUL), which contains starting materials, key intermediates, and their derivatives. We obtained the starting materials from the KEGG PATHWAY database, and 765 BUs were registered in the BUL. We then examined the proposed workflow to optimize the combination of the BUs. To evaluate the performance of the proposed Metabolic Disassembler workflow, we used 943 molecules that are included in the secondary metabolism maps of KEGG PATHWAY. About 95.8% of them (903 molecules) were correctly disassembled by our proposed workflow. For comparison, we also implemented a genetic algorithm-based workflow, and found that the accuracy was only about 52.0%. In addition, for 90.7% of molecules, our workflow finished the calculation within one minute. CONCLUSIONS The Metabolic Disassembler enabled the effective disassembly of natural products in terms of both correctness and computational time. It also outputs automatically highlighted color-coded substructures corresponding to the BUs to help users understand the calculation results. The users do not have to specify starting molecules in advance, and can input any target molecule, even if it is not in databases. Our workflow will be very useful for understanding and predicting the biosynthesis of natural products.
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Affiliation(s)
- Kohei Amano
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tsubasa Matsumoto
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kenichi Tanaka
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kimito Funatsu
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masaaki Kotera
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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23
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Systems biology based metabolic engineering for non-natural chemicals. Biotechnol Adv 2019; 37:107379. [DOI: 10.1016/j.biotechadv.2019.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/23/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022]
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24
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Gilbert J, Pearcy N, Norman R, Millat T, Winzer K, King J, Hodgman C, Minton N, Twycross J. Gsmodutils: a python based framework for test-driven genome scale metabolic model development. Bioinformatics 2019; 35:3397-3403. [PMID: 30759197 PMCID: PMC6748746 DOI: 10.1093/bioinformatics/btz088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/29/2019] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include thousands of reactions and metabolites, with many crucial pathways that only become activated in specific simulation settings. However, despite their widespread use, power and the availability of tools to aid with the construction and analysis of large scale models, little methodology is suggested for their continued management. For example, when genome annotations are updated or new understanding regarding behaviour is discovered, models often need to be altered to reflect this. This is quickly becoming an issue for industrial systems and synthetic biotechnology applications, which require good quality reusable models integral to the design, build, test and learn cycle. RESULTS As part of an ongoing effort to improve genome scale metabolic analysis, we have developed a test-driven development methodology for the continuous integration of validation data from different sources. Contributing to the open source technology based around COBRApy, we have developed the gsmodutils modelling framework placing an emphasis on test-driven design of models through defined test cases. Crucially, different conditions are configurable allowing users to examine how different designs or curation impact a wide range of system behaviours, minimizing error between model versions. AVAILABILITY AND IMPLEMENTATION The software framework described within this paper is open source and freely available from http://github.com/SBRCNottingham/gsmodutils. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- James Gilbert
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Nicole Pearcy
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Rupert Norman
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, UK
| | - Thomas Millat
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Klaus Winzer
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - John King
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Charlie Hodgman
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, UK
| | - Nigel Minton
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Jamie Twycross
- School of Computer Science, University of Nottingham, Nottingham, UK
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25
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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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Alazmi M, Kuwahara H, Soufan O, Ding L, Gao X. Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinformatics 2019; 35:2634-2643. [PMID: 30590445 PMCID: PMC6662295 DOI: 10.1093/bioinformatics/bty1035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/26/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. RESULTS Here, we introduce a machine learning method with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. Since a manual selection of 2D structure-based features can be a tedious and time-consuming task, requiring expert knowledge about the structure-activity relationship of chemical compounds, the systematic feature selection step in our method offers a convenient means to identify relevant 2D fingerprint-based features. By comparing our method with state-of-the-art linear regression-based methods for the standard Gibbs free energy prediction, we demonstrated that its prediction accuracy and prediction coverage are most favorable. Our results show direct evidence that a number of 2D fingerprints collectively provide useful information about the Gibbs free energy of biochemical reactions and that our systematic feature selection procedure provides a convenient way to identify them. AVAILABILITY AND IMPLEMENTATION Our software is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Meshari Alazmi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Othman Soufan
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Lizhong Ding
- Inception Institute of Artificial Intelligence (IIAI), Abu Dhabi, UAE
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
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Presnell KV, Alper HS. Systems Metabolic Engineering Meets Machine Learning: A New Era for Data-Driven Metabolic Engineering. Biotechnol J 2019; 14:e1800416. [PMID: 30927499 DOI: 10.1002/biot.201800416] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/20/2019] [Indexed: 12/30/2022]
Abstract
The recent increase in high-throughput capacity of 'omics datasets combined with advances and interest in machine learning (ML) have created great opportunities for systems metabolic engineering. In this regard, data-driven modeling methods have become increasingly valuable to metabolic strain design. In this review, the nature of 'omics is discussed and a broad introduction to the ML algorithms combining these datasets into predictive models of metabolism and metabolic rewiring is provided. Next, this review highlights recent work in the literature that utilizes such data-driven methods to inform various metabolic engineering efforts for different classes of application including product maximization, understanding and profiling phenotypes, de novo metabolic pathway design, and creation of robust system-scale models for biotechnology. Overall, this review aims to highlight the potential and promise of using ML algorithms with metabolic engineering and systems biology related datasets.
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Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24 St., Austin, TX, 78712, USA
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28
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Lin GM, Warden-Rothman R, Voigt CA. Retrosynthetic design of metabolic pathways to chemicals not found in nature. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites. Proc Natl Acad Sci U S A 2019; 116:7298-7307. [PMID: 30910961 PMCID: PMC6462048 DOI: 10.1073/pnas.1818877116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in synthetic biochemistry have resulted in a wealth of novel hypothetical enzymatic reactions that are not matched to protein-encoding genes, deeming them “orphan.” A large number of known metabolic enzymes are also orphan, leaving important gaps in metabolic network maps. Proposing genes for the catalysis of orphan reactions is critical for applications ranging from biotechnology to medicine. In this work, the computational method BridgIT identified potential enzymes of orphan reactions and nearly all theoretically possible biochemical transformations, providing candidate genes to catalyze these reactions to the research community. The BridgIT online tool will allow researchers to fill the knowledge gaps in metabolic networks and will act as a starting point for designing novel enzymes to catalyze nonnatural transformations. Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, limiting protein engineering applications. Associating orphan and novel reactions with known biochemistry and suggesting enzymes to catalyze them is a daunting problem. We propose the method BridgIT to identify candidate genes and catalyzing proteins for these reactions. This method introduces information about the enzyme binding pocket into reaction-similarity comparisons. BridgIT assesses the similarity of two reactions, one orphan and one well-characterized nonorphan reaction, using their substrate reactive sites, their surrounding structures, and the structures of the generated products to suggest enzymes that catalyze the most-similar nonorphan reactions as candidates for also catalyzing the orphan ones. We performed two large-scale validation studies to test BridgIT predictions against experimental biochemical evidence. For the 234 orphan reactions from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 2011 (a comprehensive enzymatic-reaction database) that became nonorphan in KEGG 2018, BridgIT predicted the exact or a highly related enzyme for 211 of them. Moreover, for 334 of 379 novel reactions in 2014 that were later cataloged in KEGG 2018, BridgIT predicted the exact or highly similar enzymes. BridgIT requires knowledge about only four connecting bonds around the atoms of the reactive sites to correctly annotate proteins for 93% of analyzed enzymatic reactions. Increasing to seven connecting bonds allowed for the accurate identification of a sequence for nearly all known enzymatic reactions.
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Küken A, Nikoloski Z. Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. PLANT PHYSIOLOGY 2019; 179:894-906. [PMID: 30647083 PMCID: PMC6393797 DOI: 10.1104/pp.18.01273] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/09/2019] [Indexed: 05/05/2023]
Abstract
Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.
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Affiliation(s)
- Anika Küken
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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31
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Tokic M, Hadadi N, Ataman M, Neves D, Ebert BE, Blank LM, Miskovic L, Hatzimanikatis V. Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors. ACS Synth Biol 2018; 7:1858-1873. [PMID: 30021444 DOI: 10.1021/acssynbio.8b00049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia toward sustainable production of the second generation of biofuels, with methyl ethyl ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1325 identified compounds connecting to MEK with one reaction step, we selected 3-oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2-methylbutanenitrile for further study. We reconstructed 3 679 610 novel biosynthetic pathways toward these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18 622 were found to be the most biologically feasible ones on the basis of thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.
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Affiliation(s)
- Milenko Tokic
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Noushin Hadadi
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Meric Ataman
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Dário Neves
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Birgitta E. Ebert
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Ljubisa Miskovic
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
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Jeffryes JG, Seaver SMD, Faria JP, Henry CS. A pathway for every product? Tools to discover and design plant metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:61-70. [PMID: 29907310 DOI: 10.1016/j.plantsci.2018.03.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. Here we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.
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Affiliation(s)
- James G Jeffryes
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Samuel M D Seaver
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - José P Faria
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Christopher S Henry
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States.
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33
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Garcia-Ruiz E, HamediRad M, Zhao H. Pathway Design, Engineering, and Optimization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:77-116. [PMID: 27629378 DOI: 10.1007/10_2016_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.
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Affiliation(s)
- Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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34
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Exploring the combinatorial space of complete pathways to chemicals. Biochem Soc Trans 2018; 46:513-522. [DOI: 10.1042/bst20170272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol.
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35
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Advances in analytical tools for high throughput strain engineering. Curr Opin Biotechnol 2018; 54:33-40. [PMID: 29448095 DOI: 10.1016/j.copbio.2018.01.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 01/09/2023]
Abstract
The emergence of inexpensive, base-perfect genome editing is revolutionising biology. Modern industrial biotechnology exploits the advances in genome editing in combination with automation, analytics and data integration to build high-throughput automated strain engineering pipelines also known as biofoundries. Biofoundries replace the slow and inconsistent artisanal processes used to build microbial cell factories with an automated design-build-test cycle, considerably reducing the time needed to deliver commercially viable strains. Testing and hence learning remains relatively shallow, but recent advances in analytical chemistry promise to increase the depth of characterization possible. Analytics combined with models of cellular physiology in automated systems biology pipelines should enable deeper learning and hence a steeper pitch of the learning cycle. This review explores the progress, advances and remaining bottlenecks of analytical tools for high throughput strain engineering.
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36
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Underground metabolism: network-level perspective and biotechnological potential. Curr Opin Biotechnol 2018; 49:108-114. [DOI: 10.1016/j.copbio.2017.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022]
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Kumar A, Wang L, Ng CY, Maranas CD. Pathway design using de novo steps through uncharted biochemical spaces. Nat Commun 2018; 9:184. [PMID: 29330441 PMCID: PMC5766603 DOI: 10.1038/s41467-017-02362-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously considering any combination of the aforementioned design criteria. First, we track and codify as rules all reaction centers using a prime factorization-based encoding technique (rePrime). Reaction rules and known biotransformations are then simultaneously used by the pathway design algorithm (novoStoic) to trace both metabolites and molecular moieties through balanced bio-conversion strategies. We demonstrate the use of novoStoic in bypassing steps in existing pathways through putative transformations, assembling complex pathways blending both known and putative steps toward pharmaceuticals, and postulating ways to biodegrade xenobiotics.
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Affiliation(s)
- Akhil Kumar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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Carbonell P, Koch M, Duigou T, Faulon JL. Enzyme Discovery: Enzyme Selection and Pathway Design. Methods Enzymol 2018; 608:3-27. [PMID: 30173766 DOI: 10.1016/bs.mie.2018.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this protocol, we describe in silico design methods that can assist in the engineering of production pathways that are based on enzymatic transformations. The described protocols are the basis for automated processes to be integrated into an iterative Design-Build-Test-Learn cycle in synthetic biology for chemical production. Selecting the right enzyme sequence for a desired biocatalytic activity from the extensive catalogue of sequences available in databases is challenging and can dramatically influence the success of bioproducing chemical compounds. A method for enzyme selection is presented that helps identifying candidate enzyme sequences through a scoring approach that considers not only sequence homology but also reaction similarity. Selecting a viable biochemical pathway for compound production requires screening large sets of reactions in a process involving combinatorial complexity. A method for pathway design using retrosynthesis is presented. The protocol allows the discovery of alternative chemical pathways leading to the final product by using reaction rules of selectable degree of specificity. The protocols can be reversed through clustering discovery and product identification processes. The integration of these protocols into a general pipeline provides a toolbox for enhanced automated synthetic biology design and metabolic engineering.
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Affiliation(s)
- Pablo Carbonell
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom; Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France; School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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39
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Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metab Eng 2018; 45:158-170. [DOI: 10.1016/j.ymben.2017.12.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/03/2017] [Accepted: 12/05/2017] [Indexed: 12/01/2022]
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Asplund-Samuelsson J, Janasch M, Hudson EP. Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential. Metab Eng 2017; 45:223-236. [PMID: 29278749 DOI: 10.1016/j.ymben.2017.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 01/09/2023]
Abstract
Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, P-Box 1031, 171 21 Solna, Sweden.
| | - Markus Janasch
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, P-Box 1031, 171 21 Solna, Sweden.
| | - Elton P Hudson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, P-Box 1031, 171 21 Solna, Sweden.
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Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J Cheminform 2017; 9:64. [PMID: 29260340 PMCID: PMC5736515 DOI: 10.1186/s13321-017-0252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/08/2017] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. RESULTS Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. CONCLUSION We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Pablo Carbonell
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. .,CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000, Évry, France.
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Abstract
Determining the fraction of the chemical space that can be processed in vivo by using natural and synthetic biology devices is crucial for the development of advanced synthetic biology applications. The extended metabolic space is a coding system based on molecular signatures that enables the derivation of reaction rules for metabolic reactions and the enumeration of all possible substrates and products corresponding to the rules. The extended metabolic space expands capabilities for controlling the production, processing, sensing, and the release of specific molecules in chassis organisms.
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Wang L, Dash S, Ng CY, Maranas CD. A review of computational tools for design and reconstruction of metabolic pathways. Synth Syst Biotechnol 2017; 2:243-252. [PMID: 29552648 PMCID: PMC5851934 DOI: 10.1016/j.synbio.2017.11.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022] Open
Abstract
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.
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Affiliation(s)
- Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Satyakam Dash
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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Pertusi DA, Moura ME, Jeffryes JG, Prabhu S, Walters Biggs B, Tyo KEJ. Predicting novel substrates for enzymes with minimal experimental effort with active learning. Metab Eng 2017; 44:171-181. [PMID: 29030274 DOI: 10.1016/j.ymben.2017.09.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/20/2017] [Accepted: 09/18/2017] [Indexed: 01/26/2023]
Abstract
Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. To demonstrate this, we used existing studies and tested compounds for four different enzymes, developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of ~80% using ~33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. The application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways.
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Affiliation(s)
- Dante A Pertusi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Matthew E Moura
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - James G Jeffryes
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, United States
| | - Siddhant Prabhu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Bradley Walters Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States.
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Kim SM, Peña MI, Moll M, Bennett GN, Kavraki LE. A review of parameters and heuristics for guiding metabolic pathfinding. J Cheminform 2017; 9:51. [PMID: 29086092 PMCID: PMC5602787 DOI: 10.1186/s13321-017-0239-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/07/2017] [Indexed: 12/04/2022] Open
Abstract
Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells introduces the possibility of significantly reducing the total time and resources required for their production, and in turn, allows these valuable compounds to become cheaper and more readily available. Most biosynthesis pathways used in metabolic engineering applications have been discovered manually, requiring a tedious search of existing literature and metabolic databases. However, the recent rapid development of available metabolic information has enabled the development of automated approaches for identifying novel pathways. Computer-assisted pathfinding has the potential to save biochemists time in the initial discovery steps of metabolic engineering. In this paper, we review the parameters and heuristics used to guide the search in recent pathfinding algorithms. These parameters and heuristics capture information on the metabolic network structure, compound structures, reaction features, and organism-specificity of pathways. No one metabolic pathfinding algorithm or search parameter stands out as the best to use broadly for solving the pathfinding problem, as each method and parameter has its own strengths and shortcomings. As assisted pathfinding approaches continue to become more sophisticated, the development of better methods for visualizing pathway results and integrating these results into existing metabolic engineering practices is also important for encouraging wider use of these pathfinding methods.
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Affiliation(s)
- Sarah M Kim
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Matthew I Peña
- Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Mark Moll
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - George N Bennett
- Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA.
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47
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Hufsky F, Böcker S. Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data. MASS SPECTROMETRY REVIEWS 2017; 36:624-633. [PMID: 26763615 DOI: 10.1002/mas.21489] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Mass spectrometry (MS) is a key technology for the analysis of small molecules. For the identification and structural elucidation of novel molecules, new approaches beyond straightforward spectral comparison are required. In this review, we will cover computational methods that help with the identification of small molecules by analyzing fragmentation MS data. We focus on the four main approaches to mine a database of metabolite structures, that is rule-based fragmentation spectrum prediction, combinatorial fragmentation, competitive fragmentation modeling, and molecular fingerprint prediction. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:624-633, 2017.
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Affiliation(s)
- Franziska Hufsky
- Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, Jena, 07743, Germany
- Bioinformatik für Hochdurchsatzverfahren, Friedrich-Schiller-Universität Jena, Leutragraben 1, Jena, 07743, Germany
| | - Sebastian Böcker
- Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, Jena, 07743, Germany
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48
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Sankar A, Ranu S, Raman K. Predicting novel metabolic pathways through subgraph mining. Bioinformatics 2017; 33:3955-3963. [DOI: 10.1093/bioinformatics/btx481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/26/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Aravind Sankar
- Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - Sayan Ranu
- Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
- Initiative for Biological Systems Engineering (IBSE), Interdisciplinary Laboratory for Data Sciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - Karthik Raman
- Initiative for Biological Systems Engineering (IBSE), Interdisciplinary Laboratory for Data Sciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
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49
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Chao R, Mishra S, Si T, Zhao H. Engineering biological systems using automated biofoundries. Metab Eng 2017; 42:98-108. [PMID: 28602523 PMCID: PMC5544601 DOI: 10.1016/j.ymben.2017.06.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 05/22/2017] [Accepted: 06/05/2017] [Indexed: 11/19/2022]
Abstract
Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges.
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Affiliation(s)
- Ran Chao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Shekhar Mishra
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Tong Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Departments of Chemistry, Biochemistry, Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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50
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Islam MA, Hadadi N, Ataman M, Hatzimanikatis V, Stephanopoulos G. Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas. Metab Eng 2017; 41:173-181. [PMID: 28433737 DOI: 10.1016/j.ymben.2017.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/28/2016] [Accepted: 04/16/2017] [Indexed: 10/19/2022]
Abstract
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a greener and more sustainable alternative to the current production methods. Technologies of synthetic biology and metabolic engineering of microorganisms can be deployed for the expression of new biochemical pathways for MEG-synthesis from gases, provided that such promising alternative routes are first identified. We used the BNICE.ch algorithm to develop novel and previously unknown biological pathways to MEG from synthesis gas by leveraging the Wood-Ljungdahl pathway of carbon fixation of acetogenic bacteria. We developed a set of useful pathway pruning and analysis criteria to systematically assess thousands of pathways generated by BNICE.ch. Published genome-scale models of Moorella thermoacetica and Clostridium ljungdahlii were used to perform the pathway yield calculations and in-depth analyses of seven (7) newly developed biological MEG-producing pathways from gases, including CO2, CO, and H2. These analyses helped identify not only better candidate pathways, but also superior chassis organisms that can be used for metabolic engineering of the candidate pathways. The pathway generation, pruning, and detailed analysis procedures described in this study can also be used to develop biochemical pathways for other commodity chemicals from gaseous substrates.
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Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Noushin Hadadi
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Meric Ataman
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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