1
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Sokolova N, Peng B, Haslinger K. Design and engineering of artificial biosynthetic pathways-where do we stand and where do we go? FEBS Lett 2023; 597:2897-2907. [PMID: 37777818 DOI: 10.1002/1873-3468.14745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini-review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.
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Affiliation(s)
- Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Bo Peng
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
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2
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Ji J, Zhang D, Ye J, Zheng Y, Cui J, Sun X. MycotoxinDB: A Data-Driven Platform for Investigating Masked Forms of Mycotoxins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37145977 DOI: 10.1021/acs.jafc.3c01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Mycotoxins are likely to be converted into masked forms when subjected to plant metabolism or food processing. These masked forms of mycotoxins together with their prototypes may cause mixture toxicity effects, causing adverse effects on animal welfare and productivity. The structure elucidation of masked mycotoxins is the most challenging task in mycotoxin research due to the limitations of traditional analysis methods. To assist in the rapid identification of masked mycotoxins, we developed a data-driven online prediction tool, MycotoxinDB, based on reaction rules. Using MycotoxinDB, we identified seven masked DONs from wheat samples. Given its widespread applications, we expect that MycotoxinDB will become an indispensable tool in future mycotoxin research. MycotoxinDB is freely available at: http://www.mycotoxin-db.com/.
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Affiliation(s)
- Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- College of Food Science and Pharmacy, Xinjiang Agricultural University, No. 311 Nongda Dong Road, Ürümqi, 830052 Xinjiang Uygur Autonomous Region, P. R. China
| | - Dachuan Zhang
- Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich, Zurich 8093, Switzerland
| | - Jin Ye
- Academy of National Food and Strategic Reserves Administration, No. 11 Baiwanzhuang Str, Xicheng District, Beijing 100037, P. R. China
| | - Yi Zheng
- Jiangsu Agri-animal Husbandry Vocational College, Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Taizhou, Jiangsu 225300, P. R. China
| | - Jing Cui
- Wuxi Food Safety Inspection and Test Center, No. 1 Building, Life Science Park, Xinwu District, Jiangsu, P. R. China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
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3
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Xu Z, Mahadevan R. Efficient Enumeration of Branched Novel Biochemical Pathways Using a Probabilistic Technique. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c02211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiqing Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
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4
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ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds. Metab Eng 2022; 72:259-274. [DOI: 10.1016/j.ymben.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/15/2022] [Accepted: 03/26/2022] [Indexed: 12/16/2022]
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5
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Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. Nat Commun 2022; 13:1560. [PMID: 35322036 PMCID: PMC8943196 DOI: 10.1038/s41467-022-29238-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Metabolic “dark matter” describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. In this work, we use 489 generalized enzymatic reaction rules to map both known and unknown metabolic processes around a biochemical database of 1.5 million biological compounds. We predict over 5 million reactions and integrate nearly 2 million naturally and synthetically-derived compounds into the global network of biochemical knowledge, named ATLASx. ATLASx is available to researchers as a powerful online platform that supports the prediction and analysis of biochemical pathways and evaluates the biochemical vicinity of molecule classes (https://lcsb-databases.epfl.ch/Atlas2). “Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. Here the authors present ATLASx, a repository of known and predicted enzymatic reaction, connecting millions of compounds to help synthetic biologists and metabolic engineers to design and explore metabolic pathways.”
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6
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Vila-Santa A, Mendes FC, Ferreira FC, Prather KLJ, Mira NP. Implementation of Synthetic Pathways to Foster Microbe-Based Production of Non-Naturally Occurring Carboxylic Acids and Derivatives. J Fungi (Basel) 2021; 7:jof7121020. [PMID: 34947002 PMCID: PMC8706239 DOI: 10.3390/jof7121020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/15/2021] [Accepted: 11/20/2021] [Indexed: 11/20/2022] Open
Abstract
Microbially produced carboxylic acids (CAs) are considered key players in the implementation of more sustainable industrial processes due to their potential to replace a set of oil-derived commodity chemicals. Most CAs are intermediates of microbial central carbon metabolism, and therefore, a biochemical production pathway is described and can be transferred to a host of choice to enable/improve production at an industrial scale. However, for some CAs, the implementation of this approach is difficult, either because they do not occur naturally (as is the case for levulinic acid) or because the described production pathway cannot be easily ported (as it is the case for adipic, muconic or glucaric acids). Synthetic biology has been reshaping the range of molecules that can be produced by microbial cells by setting new-to-nature pathways that leverage on enzyme arrangements not observed in vivo, often in association with the use of substrates that are not enzymes’ natural ones. In this review, we provide an overview of how the establishment of synthetic pathways, assisted by computational tools for metabolic retrobiosynthesis, has been applied to the field of CA production. The translation of these efforts in bridging the gap between the synthesis of CAs and of their more interesting derivatives, often themselves non-naturally occurring molecules, is also reviewed using as case studies the production of methacrylic, methylmethacrylic and poly-lactic acids.
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Affiliation(s)
- Ana Vila-Santa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Fernão C. Mendes
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Frederico C. Ferreira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Kristala L. J. Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Nuno P. Mira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Department of Bioengineering, University of Lisbon, 1049-001 Lisbon, Portugal; (A.V.-S.); (F.C.M.); (F.C.F.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Correspondence:
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Heid E, Goldman S, Sankaranarayanan K, Coley CW, Flamm C, Green WH. EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. J Chem Inf Model 2021; 61:4949-4961. [PMID: 34587449 PMCID: PMC8549070 DOI: 10.1021/acs.jcim.1c00921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 11/29/2022]
Abstract
Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply, and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here, we present EHreact, a purely data-driven open-source software tool, to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.
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Affiliation(s)
- Esther Heid
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Samuel Goldman
- Computational
and Systems Biology, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Karthik Sankaranarayanan
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Connor W. Coley
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Christoph Flamm
- Department
of Theoretical Chemistry, University of
Vienna, 1090 Vienna, Austria
| | - William H. Green
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
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8
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Jiang J, Liu LP, Hassoun S. Learning graph representations of biochemical networks and its application to enzymatic link prediction. Bioinformatics 2021; 37:793-799. [PMID: 33051674 PMCID: PMC8097755 DOI: 10.1093/bioinformatics/btaa881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/01/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
Motivation The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity. Results We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization. Availability and implementation The code and datasets are available through https://github.com/HassounLab/ELP.
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Affiliation(s)
- Julie Jiang
- Department of Computer Science, Tufts University, Medford 02155, USA
| | - Li-Ping Liu
- Department of Computer Science, Tufts University, Medford 02155, USA
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford 02155, USA.,Department of Chemical and Biological Engineering, Tufts University, Medford 02155, USA
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9
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Vila-Santa A, Islam MA, Ferreira FC, Prather KLJ, Mira NP. Prospecting Biochemical Pathways to Implement Microbe-Based Production of the New-to-Nature Platform Chemical Levulinic Acid. ACS Synth Biol 2021; 10:724-736. [PMID: 33764057 DOI: 10.1021/acssynbio.0c00518] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Levulinic acid is a versatile platform molecule with potential to be used as an intermediate in the synthesis of many value-added products used across different industries, from cosmetics to fuels. Thus far, microbial biosynthetic pathways having levulinic acid as a product or an intermediate are not known, which restrains the development and optimization of a microbe-based process envisaging the sustainable bioproduction of this chemical. One of the doors opened by synthetic biology in the design of microbial systems is the implementation of new-to-nature pathways, that is, the assembly of combinations of enzymes not observed in vivo, where the enzymes can use not only their native substrates but also non-native ones, creating synthetic steps that enable the production of novel compounds. Resorting to a combined approach involving complementary computational tools and extensive manual curation, in this work, we provide a thorough prospect of candidate biosynthetic pathways that can be assembled for the production of levulinic acid in Escherichia coli or Saccharomyces cerevisiae. Out of the hundreds of combinations screened, five pathways were selected as best candidates on the basis of the availability of substrates and of candidate enzymes to catalyze the synthetic steps (that is, those steps that involve conversions not previously described). Genome-scale metabolic modeling was used to assess the performance of these pathways in the two selected hosts and to anticipate possible bottlenecks. Not only does the herein described approach offer a platform for the future implementation of the microbial production of levulinic acid but also it provides an organized research strategy that can be used as a framework for the implementation of other new-to-nature biosynthetic pathways for the production of value-added chemicals, thus fostering the emerging field of synthetic industrial microbiotechnology.
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Affiliation(s)
- Ana Vila-Santa
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - M. Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Leicestershire, LE11 3TU Loughborough, United Kingdom
| | - Frederico C. Ferreira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Kristala L. J. Prather
- Department of Chemical Engineering and Center for Integrative Synthetic Biology (CISB), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nuno P. Mira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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10
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Hafner J, Payne J, MohammadiPeyhani H, Hatzimanikatis V, Smolke C. A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. Nat Commun 2021; 12:1760. [PMID: 33741955 PMCID: PMC7979880 DOI: 10.1038/s41467-021-22022-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valuable starting point to explore and produce novel PNP derivatives. Here, we introduce a computational workflow to systematically screen the biochemical vicinity of a biosynthetic pathway for pharmaceutical compounds that could be produced by derivatizing pathway intermediates. We apply our workflow to the biosynthetic pathway of noscapine, a benzylisoquinoline alkaloid (BIA) with a long history of medicinal use. Our workflow identifies pathways and enzyme candidates for the production of (S)-tetrahydropalmatine, a known analgesic and anxiolytic, and three additional derivatives. We then construct pathways for these compounds in yeast, resulting in platforms for de novo biosynthesis of BIA derivatives and demonstrating the value of cheminformatic tools to predict reactions, pathways, and enzymes in synthetic biology and metabolic engineering.
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Affiliation(s)
- Jasmin Hafner
- Laboratory of Computational Systems Biotechnology, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - James Payne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Homa MohammadiPeyhani
- Laboratory of Computational Systems Biotechnology, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| | - Christina Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Ding S, Tian Y, Cai P, Zhang D, Cheng X, Sun D, Yuan L, Chen J, Tu W, Wei DQ, Hu QN. novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. Nucleic Acids Res 2020; 48:W477-W487. [PMID: 32313937 PMCID: PMC7319456 DOI: 10.1093/nar/gkaa230] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/16/2020] [Accepted: 03/28/2020] [Indexed: 12/14/2022] Open
Abstract
To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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Affiliation(s)
- 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, Shanghai 200031, People's Republic of China
| | - Yu Tian
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
| | - Pengli Cai
- 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, Shanghai 200031, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People's Republic of China
| | - Dachuan Zhang
- 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, Shanghai 200031, People's Republic of China
| | - Xingxiang Cheng
- 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, Shanghai 200031, People's Republic of China
| | - Dandan Sun
- 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, Shanghai 200031, People's Republic of China
| | - Le Yuan
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden
| | - Junni Chen
- Wuhan LifeSynther Science and Technology Co. Limited, Wuhan 430070, People's Republic of China
| | - Weizhong Tu
- Wuhan LifeSynther Science and Technology Co. Limited, Wuhan 430070, People's Republic of China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism (Shanghai Jiao Tong University), Shanghai 200240, 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, Shanghai 200031, People's Republic of China
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12
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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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13
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Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Exploring Chemical Biosynthetic Design Space with Transform-MinER. ACS Synth Biol 2019; 8:2494-2506. [PMID: 31647630 DOI: 10.1021/acssynbio.9b00105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user toward promising start points for enzyme design projects or directed evolution experiments. Two types of search are possible: Molecule Search allows a user to submit a source substrate enabling Transform-MinER to search for enzyme reactions acting on similar substrates, whereas Path Search additionally allows a user to submit a target molecule enabling Transform-MinER to search for a path of enzyme reactions acting on similar substrates to link source and target. Transform-MinER searches for potential reaction centers in the source substrate and uses chemoinformatic fingerprints to identify those that are situated in molecular environments similar to native counterparts, prioritizing steps that move closer to the target using reactions most similar to native in its exploration of search space. The ligand-based methodology behind Transform-MinER is presented, and its performance is validated yielding 90% success rates: first, on a data set of native pathways from the KEGG database, and second, on a data set of de novo enzyme reactions.
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Affiliation(s)
- Jonathan D. Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Antonio J. M. Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Neera Borkakoti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Janet M. Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
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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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15
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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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Sivakumar TV, Bhaduri A, Duvvuru Muni RR, Park JH, Kim TY. SimCAL: a flexible tool to compute biochemical reaction similarity. BMC Bioinformatics 2018; 19:254. [PMID: 29969981 PMCID: PMC6029250 DOI: 10.1186/s12859-018-2248-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 06/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Computation of reaction similarity is a pre-requisite for several bioinformatics applications including enzyme identification for specific biochemical reactions, enzyme classification and mining for specific inhibitors. Reaction similarity is often assessed at either two levels: (i) comparison across all the constituent substrates and products of a reaction, reaction level similarity, (ii) comparison at the transformation center with various degrees of neighborhood, transformation level similarity. Existing reaction similarity computation tools are designed for specific applications and use different features and similarity measures. A single system integrating these diverse features enables comparison of the impact of different molecular properties on similarity score computation. Results To address these requirements, we present SimCAL, an integrated system to calculate reaction similarity with novel features and capability to perform comparative assessment. SimCAL provides reaction similarity computation at both whole reaction level and transformation level. Novel physicochemical features such as stereochemistry, mass, volume and charge are included in computing reaction fingerprint. Users can choose from four different fingerprint types and nine molecular similarity measures. Further, a comparative assessment of these features is also enabled. The performance of SimCAL is assessed on 3,688,122 reaction pairs with Enzyme Commission (EC) number from MetaCyc and achieved an area under the curve (AUC) of > 0.9. In addition, SimCAL results showed strong correlation with state-of-the-art EC-BLAST and molecular signature based reaction similarity methods. Conclusions SimCAL is developed in java and is available as a standalone tool, with intuitive, user-friendly graphical interface and also as a console application. With its customizable feature selection and similarity calculations, it is expected to cater a wide audience interested in studying and analyzing biochemical reactions and metabolic networks. Electronic supplementary material The online version of this article (10.1186/s12859-018-2248-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anirban Bhaduri
- Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore, 560037, India
| | | | - Jin Hwan Park
- Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do, 443803, South Korea
| | - Tae Yong Kim
- Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do, 443803, South Korea.
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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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Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform 2017; 9:33. [PMID: 29086040 PMCID: PMC5461230 DOI: 10.1186/s13321-017-0220-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/16/2017] [Indexed: 12/15/2022] Open
Abstract
Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. Conclusions This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.CDK 2.0 provides new features and improved performance ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6200 MD, Maastricht, The Netherlands.
| | | | - Jonathan Alvarsson
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden
| | - Arvid Berg
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden
| | - Lars Carlsson
- AstraZeneca, Innovative Medicines & Early Development, Quantitative Biology, Möndal, Sweden
| | | | - Stefan Kuhn
- Department of Informatics, University of Leicester, Leicester, UK
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden
| | | | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany
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