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Emelianova M, Gainullina A, Poperechnyi N, Loboda A, Artyomov M, Sergushichev A. Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks. Nucleic Acids Res 2022; 50:W690-W696. [PMID: 35639928 PMCID: PMC9252739 DOI: 10.1093/nar/gkac427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
Multiple high-throughput omics techniques provide different angles on systematically quantifying and studying metabolic regulation of cellular processes. However, an unbiased analysis of such data and, in particular, integration of multiple types of data remains a challenge. Previously, for this purpose we developed GAM web-service for integrative metabolic network analysis. Here we describe an updated pipeline GATOM and the corresponding web-service Shiny GATOM, which takes as input transcriptional and/or metabolomic data and finds a metabolic subnetwork most regulated between the two conditions of interest. GATOM features a new metabolic network topology based on atom transition, which significantly improves interpretability of the analysis results. To address computational challenges arising with the new network topology, we introduce a new variant of the maximum weight connected subgraph problem and provide a corresponding exact solver. To make the used networks up-to-date we upgraded the KEGG-based network construction pipeline and developed one based on the Rhea database, which allows analysis of lipidomics data. Finally, we simplified local installation, providing R package mwcsr for solving relevant graph optimization problems and R package gatom, which implements the GATOM pipeline. The web-service is available at https://ctlab.itmo.ru/shiny/gatom and https://artyomovlab.wustl.edu/shiny/gatom.
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Affiliation(s)
- Mariia Emelianova
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia
| | - Anastasiia Gainullina
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Nikolay Poperechnyi
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia
| | - Alexander Loboda
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia
| | - Maxim Artyomov
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia
| | - Alexey Sergushichev
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia 197101, Russia.,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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2
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Gao Y, Yuan Q, Mao Z, Liu H, Ma H. Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis. BMC Microbiol 2021; 21:292. [PMID: 34696732 PMCID: PMC8543872 DOI: 10.1186/s12866-021-02357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background Graph-based analysis (GBA) of genome-scale metabolic networks has revealed system-level structures such as the bow-tie connectivity that describes the overall mass flow in a network. However, many pathways obtained by GBA are biologically impossible, making it difficult to study how the global structures affect the biological functions of a network. New method that can calculate the biologically relevant pathways is desirable for structural analysis of metabolic networks. Results Here, we present a new method to determine the bow-tie connectivity structure by calculating possible pathways between any pairs of metabolites in the metabolic network using a flux balance analysis (FBA) approach to ensure that the obtained pathways are biologically relevant. We tested this method with 15 selected high-quality genome-scale metabolic models from BiGG database. The results confirmed the key roles of central metabolites in network connectivity, locating in the core part of the bow-tie structure, the giant strongly connected component (GSC). However, the sizes of GSCs revealed by GBA are significantly larger than those by FBA approach. A great number of metabolites in the GSC from GBA actually cannot be produced from or converted to other metabolites through a mass balanced pathway and thus should not be in GSC but in other subsets of the bow-tie structure. In contrast, the bow-tie structural classification of metabolites obtained by FBA is more biologically relevant and suitable for the study of the structure-function relationships of genome scale metabolic networks. Conclusions The FBA based pathway calculation improve the biologically relevant classification of metabolites in the bow-tie connectivity structure of the metabolic network, taking us one step further toward understanding how such system-level structures impact the biological functions of an organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02357-1.
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Affiliation(s)
- Yajie Gao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Qianqian Yuan
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhitao Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hao Liu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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3
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Zhu F, Peña M, Bennett GN. Metabolic engineering of Escherichia coli for quinolinic acid production by assembling L-aspartate oxidase and quinolinate synthase as an enzyme complex. Metab Eng 2021; 67:164-172. [PMID: 34192552 PMCID: PMC10024596 DOI: 10.1016/j.ymben.2021.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/23/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Quinolinic acid (QA) is a key intermediate of nicotinic acid (Niacin) which is an essential human nutrient and widely used in food and pharmaceutical industries. In this study, a quinolinic acid producer was constructed by employing comprehensive engineering strategies. Firstly, the quinolinic acid production was improved by deactivation of NadC (to block the consumption pathway), NadR (to eliminate the repression of L-aspartate oxidase and quinolinate synthase), and PtsG (to slow the glucose utilization rate and achieve a more balanced metabolism, and also to increase the availability of the precursor phosphoenolpyruvate). Further modifications to enhance quinolinic acid production were investigated by increasing the oxaloacetate pool through overproduction of phosphoenolpyruvate carboxylase and deactivation of acetate-producing pathway enzymes. Moreover, quinolinic acid production was accelerated by assembling NadB and NadA as an enzyme complex with the help of peptide-peptide interaction peptides RIAD and RIDD, which resulted in up to 3.7 g/L quinolinic acid being produced from 40 g/L glucose in shake-flask cultures. A quinolinic acid producer was constructed in this study, and these results lay a foundation for further engineering of microbial cell factories to efficiently produce quinolinic acid and subsequently convert this product to nicotinic acid for industrial applications.
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Affiliation(s)
- Fayin Zhu
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Matthew Peña
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - George N Bennett
- Department of BioSciences, Rice University, Houston, TX, 77005, USA; Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA.
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4
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Hafner J, Hatzimanikatis V. Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. Bioinformatics 2021; 37:3560-3568. [PMID: 34003971 PMCID: PMC8545321 DOI: 10.1093/bioinformatics/btab368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022] Open
Abstract
Motivation Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in biosynthetic pathway design is the extraction of novel metabolic pathways from big networks that integrate known biological, as well as novel, predicted biotransformations. However, the efficient analysis and the navigation of big biochemical networks remain a challenge. Results Here, we propose the construction of searchable graph representations of metabolic networks. Each reaction is decomposed into pairs of reactants and products, and each pair is assigned a weight, which is calculated from the number of conserved atoms between the reactant and the product molecule. We test our method on a biochemical network that spans 6546 known enzymatic reactions to show how our approach elegantly extracts biologically relevant metabolic pathways from biochemical networks, and how the proposed network structure enables the application of efficient graph search algorithms that improve navigation and pathway identification in big metabolic networks. The weighted reactant–product pairs of an example network and the corresponding graph search algorithm are available online. The proposed method extracts metabolic pathways fast and reliably from big biochemical networks, which is inherently important for all applications involving the engineering of metabolic networks. Availability and implementation https://github.com/EPFL-LCSB/nicepath. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jasmin Hafner
- Laboratory of Computational Systems Biotechnology (LCSB), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences (SB), Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences (SB), Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
- To whom correspondence should be addressed.
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5
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Huang Y, Xie Y, Zhong C, Zhou F. Finding branched pathways in metabolic network via atom group tracking. PLoS Comput Biol 2021; 17:e1008676. [PMID: 33529200 PMCID: PMC7880430 DOI: 10.1371/journal.pcbi.1008676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/12/2021] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Finding non-standard or new metabolic pathways has important applications in metabolic engineering, synthetic biology and the analysis and reconstruction of metabolic networks. Branched metabolic pathways dominate in metabolic networks and depict a more comprehensive picture of metabolism compared to linear pathways. Although progress has been developed to find branched metabolic pathways, few efforts have been made in identifying branched metabolic pathways via atom group tracking. In this paper, we present a pathfinding method called BPFinder for finding branched metabolic pathways by atom group tracking, which aims to guide the synthetic design of metabolic pathways. BPFinder enumerates linear metabolic pathways by tracking the movements of atom groups in metabolic network and merges the linear atom group conserving pathways into branched pathways. Two merging rules based on the structure of conserved atom groups are proposed to accurately merge the branched compounds of linear pathways to identify branched pathways. Furthermore, the integrated information of compound similarity, thermodynamic feasibility and conserved atom groups is also used to rank the pathfinding results for feasible branched pathways. Experimental results show that BPFinder is more capable of recovering known branched metabolic pathways as compared to other existing methods, and is able to return biologically relevant branched pathways and discover alternative branched pathways of biochemical interest. The online server of BPFinder is available at http://114.215.129.245:8080/atomic/. The program, source code and data can be downloaded from https://github.com/hyr0771/BPFinder. Computational search of branched metabolic pathways is a fundamental problem in metabolic engineering and metabolic network analysis, which provides a systematic way of understanding the metabolism and discovering alternative pathways for synthesis of useful biomolecules. We propose BPFinder, a novel computational approach to identify branched metabolic pathways via atom group tracking. Different from other pathfinding methods using atom tracking, BPFinder tracks the movement of atom groups in metabolic network to find linear atom group conserving pathways, and merge the found linear pathways by the selected branched compounds to generate branched pathways. Based on the structure of conserved atom groups in branched compounds, we design two merging rules for branched compounds: overlapping rule and non-overlapping rule. The user can flexibly adopt these rules to accurately find the branched pathways that contain overlapping/non-overlapping conserved atom groups. BPFinder also enables the user to combine the information of compound similarity, Gibbs free energy of reactions, and conserved atom groups to sort resulting pathways. Compared with other existing methods, BPFinder can more accurately recover the known branched pathways. The alternative branched pathways returned by BPFinder reveal that the user can flexibly utilize our proposed merging rules to discover biochemically meaningful pathways of interest.
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Affiliation(s)
- Yiran Huang
- School of Computer and Electronics and Information, Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, China
- * E-mail:
| | - Yusi Xie
- School of Computer and Electronics and Information, Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, China
| | - Cheng Zhong
- School of Computer and Electronics and Information, Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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6
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Mack SG, Sriram G. NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks. Metab Eng Commun 2021; 12:e00154. [PMID: 33489751 PMCID: PMC7807149 DOI: 10.1016/j.mec.2020.e00154] [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: 08/31/2020] [Revised: 11/11/2020] [Accepted: 11/21/2020] [Indexed: 01/04/2023] Open
Abstract
Genome-scale stoichiometric models (GSMs) have been widely utilized to predict and understand cellular metabolism. GSMs and the flux predictions resulting from them have proven indispensable to fields ranging from metabolic engineering to human disease. Nonetheless, it is challenging to parse these flux predictions due to the inherent size and complexity of the GSMs. Several previous approaches have reduced this complexity by identifying key pathways contained within the genome-scale flux predictions. However, a reduction method that overlays carbon atom transitions on stoichiometry and flux predictions is lacking. To fill this gap, we developed NetFlow, an algorithm that leverages genome-scale carbon mapping to extract and quantitatively distinguish biologically relevant metabolic pathways from a given genome-scale flux prediction. NetFlow extends prior approaches by utilizing both full carbon mapping and context-specific flux predictions. Thus, NetFlow is uniquely able to quantitatively distinguish between biologically relevant pathways of carbon flow within the given flux map. NetFlow simulates 13C isotope labeling experiments to calculate the extent of carbon exchange, or carbon yield, between every metabolite in the given GSM. Based on the carbon yield, the carbon flow to or from any metabolite or between any pair of metabolites of interest can be isolated and readily visualized. The resulting pathways are much easier to interpret, which enables an in-depth mechanistic understanding of the metabolic phenotype of interest. Here, we first demonstrate NetFlow with a simple network. We then depict the utility of NetFlow on a model of central carbon metabolism in E. coli. Specifically, we isolated the production pathway for succinate synthesis in this model and the metabolic mechanism driving the predicted increase in succinate yield in a double knockout of E. coli. Finally, we describe the application of NetFlow to a GSM of lycopene-producing E. coli, which enabled the rapid identification of the mechanisms behind the measured increases in lycopene production following single, double, and triple knockouts.
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Affiliation(s)
- Sean G Mack
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
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7
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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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8
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Atom Identifiers Generated by a Neighborhood-Specific Graph Coloring Method Enable Compound Harmonization across Metabolic Databases. Metabolites 2020; 10:metabo10090368. [PMID: 32933023 PMCID: PMC7570338 DOI: 10.3390/metabo10090368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. However, useful metabolic models can be difficult to derive due to the lack of relatively complete atom-resolved metabolic networks for a variety of organisms, including human. Here, we developed a neighborhood-specific graph coloring method that creates unique identifiers for each atom in a compound facilitating construction of an atom-resolved metabolic network. What is more, this method is guaranteed to generate the same identifier for symmetric atoms, enabling automatic identification of possible additional mappings caused by molecular symmetry. Furthermore, a compound coloring identifier derived from the corresponding atom coloring identifiers can be used for compound harmonization across various metabolic network databases, which is an essential first step in network integration. With the compound coloring identifiers, 8865 correspondences between KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc compounds are detected, with 5451 of them confirmed by other identifiers provided by the two databases. In addition, we found that the Enzyme Commission numbers (EC) of reactions can be used to validate possible correspondence pairs, with 1848 unconfirmed pairs validated by commonality in reaction ECs. Moreover, we were able to detect various issues and errors with compound representation in KEGG and MetaCyc databases by compound coloring identifiers, demonstrating the usefulness of this methodology for database curation.
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9
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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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10
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Litsa EE, Peña MI, Moll M, Giannakopoulos G, Bennett GN, Kavraki LE. Machine Learning Guided Atom Mapping of Metabolic Reactions. J Chem Inf Model 2018; 59:1121-1135. [DOI: 10.1021/acs.jcim.8b00434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eleni E. Litsa
- Department of Computer Science, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Matthew I. Peña
- Department of BioSciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Mark Moll
- Department of Computer Science, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - George Giannakopoulos
- SKEL Lab, Institute of Informatics and Telecommunications, NCSR Demokritos, Agia Paraskevi 15310, Greece
| | - George N. Bennett
- Department of BioSciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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11
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Metabolic pathways synthesis based on ant colony optimization. Sci Rep 2018; 8:16398. [PMID: 30401873 PMCID: PMC6219534 DOI: 10.1038/s41598-018-34454-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 10/17/2018] [Indexed: 02/02/2023] Open
Abstract
One of the current challenges in bioinformatics is to discover new ways to transform a set of compounds into specific products. The usual approach is finding the reactions to synthesize a particular product, from a given substrate, by means of classical searching algorithms. However, they have three main limitations: difficulty in handling large amounts of reactions and compounds; absence of a step that verifies the availability of substrates; and inability to find branched pathways. We present here a novel bio-inspired algorithm for synthesizing linear and branched metabolic pathways. It allows relating several compounds simultaneously, ensuring the availability of substrates for every reaction in the solution. Comparisons with classical searching algorithms and other recent metaheuristic approaches show clear advantages of this proposal, fully recovering well-known pathways. Furthermore, solutions found can be analyzed in a simple way through graphical representations on the web.
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12
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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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13
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Abd Algfoor Z, Shahrizal Sunar M, Abdullah A, Kolivand H. Identification of metabolic pathways using pathfinding approaches: a systematic review. Brief Funct Genomics 2017; 16:87-98. [PMID: 26969656 DOI: 10.1093/bfgp/elw002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches.
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Affiliation(s)
- Zeyad Abd Algfoor
- MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Mohd Shahrizal Sunar
- MaGIC-X (Media and Games Innovation Centre of Excellence), UTM-IRDA Digital Media Centre, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Afnizanfaizal Abdullah
- Boston University School of Medicine, Boston Medical Center, Boston, MA, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Program, Duke Kunshan University, Jiangsu, China
| | - Hoshang Kolivand
- Department of Computer Science, Liverpool John Moores University, Liverpool, UK
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14
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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: 75] [Impact Index Per Article: 10.7] [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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15
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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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16
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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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17
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Hadadi N, Hafner J, Soh KC, Hatzimanikatis V. Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/21/2016] [Accepted: 11/28/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Noushin Hadadi
- Laboratory of Computational Systems Biotechnology (LCSB); Swiss Federal Institute of Technology (EPFL); Lausanne Switzerland
| | - Jasmin Hafner
- Laboratory of Computational Systems Biotechnology (LCSB); Swiss Federal Institute of Technology (EPFL); Lausanne Switzerland
| | - Keng Cher Soh
- Laboratory of Computational Systems Biotechnology (LCSB); Swiss Federal Institute of Technology (EPFL); Lausanne Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB); Swiss Federal Institute of Technology (EPFL); Lausanne Switzerland
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18
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Huang Y, Zhong C, Lin HX, Wang J. A Method for Finding Metabolic Pathways Using Atomic Group Tracking. PLoS One 2017; 12:e0168725. [PMID: 28068354 PMCID: PMC5221824 DOI: 10.1371/journal.pone.0168725] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/05/2016] [Indexed: 12/13/2022] Open
Abstract
A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways between two given compounds. In AGPathFinder, we find alternative pathways by tracking the movement of atomic groups through metabolic networks and use combined information of reaction thermodynamics and compound similarity to guide the search towards more feasible pathways and better performance. The experimental results show that atomic group tracking enables our method to find pathways without the need of defining the atoms to be tracked, avoid hub metabolites, and obtain biochemically meaningful pathways. Our results also demonstrate that atomic group tracking, when incorporated with combined information of reaction thermodynamics and compound similarity, improves the quality of the found pathways. In most cases, the average compound inclusion accuracy and reaction inclusion accuracy for the top resulting pathways of our method are around 0.90 and 0.70, respectively, which are better than those of the existing methods. Additionally, AGPathFinder provides the information of thermodynamic feasibility and compound similarity for the resulting pathways.
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Affiliation(s)
- Yiran Huang
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
- School of Computer, Electronics and Information, Guangxi University, Nanning, China
- * E-mail: (YH); (CZ)
| | - Cheng Zhong
- School of Computer, Electronics and Information, Guangxi University, Nanning, China
- * E-mail: (YH); (CZ)
| | - Hai Xiang Lin
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Jianyi Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
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19
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Yamanishi Y, Tabei Y, Kotera M. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. Bioinformatics 2015; 31:i161-70. [PMID: 26072478 PMCID: PMC4765868 DOI: 10.1093/bioinformatics/btv224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. RESULTS In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-filling framework. We proposed a novel chemical graph alignment algorithm, which we called PACHA (Pairwise Chemical Aligner), to detect the regioisomer-sensitive connectivities between the aligned substructures of two compounds. Unlike other existing graph alignment methods, PACHA can efficiently detect only one common subgraph between two compounds. Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers and PIERO (Enzymatic Reaction Ontology for Partial Information) terms to substrate-product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate-product pairs.
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Affiliation(s)
- Yoshihiro Yamanishi
- Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8581, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8581, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yasuo Tabei
- Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8581, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Kotera
- Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8582, Institute for Advanced Study, Kyushu University, Higashi-ku, Fukuoka, Fukuoka 812-8581, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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20
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Gerard MF, Stegmayer G, Milone DH. EvoMS: An evolutionary tool to find de novo metabolic pathways. Biosystems 2015; 134:43-7. [PMID: 26092635 DOI: 10.1016/j.biosystems.2015.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/19/2022]
Abstract
The evolutionary metabolic synthesizer (EvoMS) is an evolutionary tool capable of finding novel metabolic pathways linking several compounds through feasible reactions. It allows system biologists to explore different alternatives for relating specific metabolites, offering the possibility of indicating the initial compound or allowing the algorithm to automatically select it. Searching process can be followed graphically through several plots of the evolutionary process. Metabolic pathways found are displayed in a web browser as directed graphs. In all cases, solutions are networks of reactions that produce linear or branched metabolic pathways which are feasible from the specified set of available compounds. Source code of EvoMS is available at http://sourceforge.net/projects/sourcesinc/files/evoms/. Subsets of reactions are provided, as well as four examples for searching metabolic pathways among several compounds. Available as a web service at http://fich.unl.edu.ar/sinc/web-demo/evoms/.
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Affiliation(s)
- Matias F Gerard
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina.
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21
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Liu F, Vilaça P, Rocha I, Rocha M. Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015; 118:134-146. [PMID: 25580014 DOI: 10.1016/j.cmpb.2014.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/31/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
Metabolic Engineering (ME) aims to design microbial cell factories towards the production of valuable compounds. In this endeavor, one important task relates to the search for the most suitable heterologous pathway(s) to add to the selected host. Different algorithms have been developed in the past towards this goal, following distinct approaches spanning constraint-based modeling, graph-based methods and knowledge-based systems based on chemical rules. While some of these methods search for pathways optimizing specific objective functions, here the focus will be on methods that address the enumeration of pathways that are able to convert a set of source compounds into desired targets and their posterior evaluation according to different criteria. Two pathway enumeration algorithms based on (hyper)graph-based representations are selected as the most promising ones and are analyzed in more detail: the Solution Structure Generation and the Find Path algorithms. Their capabilities and limitations are evaluated when designing novel heterologous pathways, by applying these methods on three case studies of synthetic ME related to the production of non-native compounds in E. coli and S. cerevisiae: 1-butanol, curcumin and vanillin. Some targeted improvements are implemented, extending both methods to address limitations identified that impair their scalability, improving their ability to extract potential pathways over large-scale databases. In all case-studies, the algorithms were able to find already described pathways for the production of the target compounds, but also alternative pathways that can represent novel ME solutions after further evaluation.
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Affiliation(s)
- F Liu
- Centre for Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - P Vilaça
- Centre for Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; SilicoLife Lda., Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - I Rocha
- Centre for Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - M Rocha
- Centre for Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
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22
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Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 2014; 25:140-58. [DOI: 10.1016/j.ymben.2014.07.009] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022]
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23
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24
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Arora PK, Bae H. Integration of bioinformatics to biodegradation. Biol Proced Online 2014; 16:8. [PMID: 24808763 PMCID: PMC4012781 DOI: 10.1186/1480-9222-16-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/19/2014] [Indexed: 12/22/2022] Open
Abstract
Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.
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Affiliation(s)
- Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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25
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Latendresse M, Krummenacker M, Karp PD. Optimal metabolic route search based on atom mappings. Bioinformatics 2014; 30:2043-50. [DOI: 10.1093/bioinformatics/btu150] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Yadav VG. Combining Metabolic Pathway Design and Retrosynthetic Planning for the Design of a Novel Semisynthetic Manufacturing Scheme for Paclitaxel. Org Process Res Dev 2014. [DOI: 10.1021/op4003505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vikramaditya G. Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Abstract
MOTIVATION Pathway analysis tools are a powerful strategy to analyze 'omics' data in the field of systems biology. From a metabolic perspective, several pathway definitions can be found in the literature, each one appropriate for a particular study. Recently, a novel pathway concept termed carbon flux paths (CFPs) was introduced and benchmarked against existing approaches, showing a clear advantage for finding linear pathways from a given source to target metabolite. CFPs are simple paths in a metabolite-metabolite graph that satisfy typical constraints in stoichiometric models: mass balancing and thermodynamics (irreversibility). In addition, CFPs guarantee carbon exchange in each of their intermediate steps, but not between the source and the target metabolites and consequently false positive solutions may arise. These pathways often lack biological interest, particularly when studying biosynthetic or degradation routes of a metabolite. To overcome this issue, we amend the formulation in CFP, so as to account for atomic fate information. This approach is termed atomic CFP (aCFP). RESULTS By means of a side-by-side comparison in a medium scale metabolic network in Escherichia Coli, we show that aCFP provides more biologically relevant pathways than CFP, because canonical pathways are more easily recovered, which reflects the benefits of removing false positives. In addition, we demonstrate that aCFP can be successfully applied to genome-scale metabolic networks. As the quality of genome-scale atomic reconstruction is improved, methods such as the one presented here will undoubtedly be of value to interpret 'omics' data.
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Affiliation(s)
- Jon Pey
- CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain and Mathematical Sciences, Brunel University, Kingston Lane, UB8 3PH, Uxbridge, UK
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28
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Lee SY, Sohn SB, Kim YB, Shin JH, Kim JE, Kim TY. Computational Methods for Strain Design. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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29
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Jouhten P. Metabolic modelling in the development of cell factories by synthetic biology. Comput Struct Biotechnol J 2012; 3:e201210009. [PMID: 24688669 PMCID: PMC3962133 DOI: 10.5936/csbj.201210009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/05/2012] [Accepted: 11/07/2012] [Indexed: 11/22/2022] Open
Abstract
Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.
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Affiliation(s)
- Paula Jouhten
- VTT Technical Research Centre of Finland, Tietotie 2, 02044 VTT, Espoo, Finland
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30
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31
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Zhou W, Nakhleh L. Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. J Chem Inf Model 2012; 52:2684-96. [DOI: 10.1021/ci300259u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wanding Zhou
- Department of Bioengineering and ‡Department of Computer
Science, Rice University,
Houston, Texas 77005, United States
| | - Luay Nakhleh
- Department of Bioengineering and ‡Department of Computer
Science, Rice University,
Houston, Texas 77005, United States
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32
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Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O. MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics 2012; 13:99. [PMID: 22591066 PMCID: PMC3495401 DOI: 10.1186/1471-2105-13-99] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 04/25/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome- reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites. RESULTS We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development. CONCLUSIONS MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu.
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Abstract
As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology.
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Tonon T, Eveillard D, Prigent S, Bourdon J, Potin P, Boyen C, Siegel A. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:883-92. [PMID: 22136637 DOI: 10.1089/omi.2011.0089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.
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Affiliation(s)
- Thierry Tonon
- UPMC Univ Paris 6 , UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.
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35
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Heath AP, Bennett GN, Kavraki LE. An algorithm for efficient identification of branched metabolic pathways. J Comput Biol 2011; 18:1575-97. [PMID: 21999288 DOI: 10.1089/cmb.2011.0165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This article presents a new graph-based algorithm for identifying branched metabolic pathways in multi-genome scale metabolic data. The term branched is used to refer to metabolic pathways between compounds that consist of multiple pathways that interact biochemically. A branched pathway may produce a target compound through a combination of linear pathways that split compounds into smaller ones, work in parallel with many compounds, and join compounds into larger ones. While branched metabolic pathways predominate in metabolic networks, most previous work has focused on identifying linear metabolic pathways. The ability to automatically identify branched pathways is important in applications that require a deeper understanding of metabolism, such as metabolic engineering and drug target identification. The algorithm presented in this article utilizes explicit atom tracking to identify linear metabolic pathways and then merges them together into branched metabolic pathways. We provide results on several well-characterized metabolic pathways that demonstrate that the new merging approach can efficiently find biologically relevant branched metabolic pathways.
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Affiliation(s)
- Allison P Heath
- Department of Computer Science, Rice University, Houston, TX 77005, USA
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Stelzer M, Sun J, Kamphans T, Fekete SP, Zeng AP. An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. Integr Biol (Camb) 2011; 3:1071-86. [DOI: 10.1039/c1ib00008j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Michael Stelzer
- Former address: Systems Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Langer Kamp 19B, 38106 Braunschweig, Germany
| | - Jibin Sun
- Former address: Systems Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqidao 32 Tianjin Airport Economic Area, Tianjin 300308, China
| | - Tom Kamphans
- Department for Computer Science, Algorithms Group Braunschweig University of Technology, Mühlenpfordtstr. 23, 38106 Braunschweig, Germany
| | - Sándor P. Fekete
- Department for Computer Science, Algorithms Group Braunschweig University of Technology, Mühlenpfordtstr. 23, 38106 Braunschweig, Germany
| | - An-Ping Zeng
- Former address: Systems Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, 21073 Hamburg, Germany
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Carbonell P, Planson AG, Fichera D, Faulon JL. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC SYSTEMS BIOLOGY 2011; 5:122. [PMID: 21819595 PMCID: PMC3163555 DOI: 10.1186/1752-0509-5-122] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/05/2011] [Indexed: 01/10/2023]
Abstract
BACKGROUND Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach to the production of therapeutics with the goal of developing an in situ drug delivery device in host cells. Retrosynthesis, a concept originally proposed for synthetic chemistry, iteratively applies reversed chemical transformations (reversed enzyme-catalyzed reactions in the metabolic space) starting from a target product to reach precursors that are endogenous to the chassis. So far, a wider adoption of retrosynthesis into the manufacturing pipeline has been hindered by the complexity of enumerating all feasible biosynthetic pathways for a given compound. RESULTS In our method, we efficiently address the complexity problem by coding substrates, products and reactions into molecular signatures. Metabolic maps are represented using hypergraphs and the complexity is controlled by varying the specificity of the molecular signature. Furthermore, our method enables candidate pathways to be ranked to determine which ones are best to engineer. The proposed ranking function can integrate data from different sources such as host compatibility for inserted genes, the estimation of steady-state fluxes from the genome-wide reconstruction of the organism's metabolism, or the estimation of metabolite toxicity from experimental assays. We use several machine-learning tools in order to estimate enzyme activity and reaction efficiency at each step of the identified pathways. Examples of production in bacteria and yeast for two antibiotics and for one antitumor agent, as well as for several essential metabolites are outlined. CONCLUSIONS We present here a unified framework that integrates diverse techniques involved in the design of heterologous biosynthetic pathways through a retrosynthetic approach in the reaction signature space. Our engineering methodology enables the flexible design of industrial microorganisms for the efficient on-demand production of chemical compounds with therapeutic applications.
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Affiliation(s)
- Pablo Carbonell
- Institute of Systems and Synthetic Biology, University of Evry, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, Evry Cedex, France
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Planson AG, Carbonell P, Grigoras I, Faulon JL. Engineering antibiotic production and overcoming bacterial resistance. Biotechnol J 2011; 6:812-25. [PMID: 21661120 DOI: 10.1002/biot.201100085] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/21/2023]
Abstract
Progress in DNA technology, analytical methods and computational tools is leading to new developments in synthetic biology and metabolic engineering, enabling new ways to produce molecules of industrial and therapeutic interest. Here, we review recent progress in both antibiotic production and strategies to counteract bacterial resistance to antibiotics. Advances in sequencing and cloning are increasingly enabling the characterization of antibiotic biosynthesis pathways, and new systematic methods for de novo biosynthetic pathway prediction are allowing the exploration of the metabolic chemical space beyond metabolic engineering. Moreover, we survey the computer-assisted design of modular assembly lines in polyketide synthases and non-ribosomal peptide synthases for the development of tailor-made antibiotics. Nowadays, production of novel antibiotic can be tranferred into any chosen chassis by optimizing a host factory through specific strain modifications. These advances in metabolic engineering and synthetic biology are leading to novel strategies for engineering antimicrobial agents with desired specificities.
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Affiliation(s)
- Anne-Gaëlle Planson
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Esonne, 5 rue Henri Desbruères, Evry, France
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Faust K, Croes D, van Helden J. Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 2011; 105:109-21. [PMID: 21645586 DOI: 10.1016/j.biosystems.2011.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/23/2011] [Accepted: 05/05/2011] [Indexed: 01/06/2023]
Abstract
The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields groups of functionally related genes. In order to determine their biological function, associated gene groups are often projected onto known pathways or tested for enrichment of known functions. However, these approaches are not flexible enough to deal with variations or novel pathways. During the last decade, we developed and refined an approach that predicts metabolic pathways from a global metabolic network encompassing all known reactions and their substrates/products, by extracting a subgraph connecting at best a set of seed nodes (compounds, reactions, enzymes or enzyme-coding genes). In this review, we summarize this work, while discussing the problems and pitfalls but also the advantages and applications of network-based metabolic pathway prediction.
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Affiliation(s)
- Karoline Faust
- Research Group of Bioinformatics and (Eco-)Systems Biology (BSB), VIB - Vrije Universiteit Brussel, Pleinlaan, Belgium
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Pey J, Prada J, Beasley JE, Planes FJ. Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol 2011; 12:R49. [PMID: 21619601 PMCID: PMC3219972 DOI: 10.1186/gb-2011-12-5-r49] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/14/2011] [Accepted: 05/27/2011] [Indexed: 01/30/2023] Open
Abstract
Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks.
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Affiliation(s)
- Jon Pey
- CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain
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Engineering in complex systems. Curr Opin Biotechnol 2010; 21:586-91. [DOI: 10.1016/j.copbio.2010.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 07/12/2010] [Accepted: 07/13/2010] [Indexed: 01/30/2023]
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