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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison. Biomimetics (Basel) 2022; 7:biomimetics7010027. [PMID: 35225919 PMCID: PMC8883897 DOI: 10.3390/biomimetics7010027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Metabolic pathways provide key information for achieving a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy, and other similar areas. The main analysis tool used to study these pathways is based on pathway comparison, using graph data structures. Metabolic pathway comparison has been defined as a computationally complex task. In a previous work, two new algorithms were introduced to treat the problem of metabolic pathway pairwise comparison. Here we provide an extended analysis with more data and a deeper analysis of metabolic pathway comparison as listed in the discussion and results section.
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Behler J, Vijay D, Hess WR, Akhtar MK. CRISPR-Based Technologies for Metabolic Engineering in Cyanobacteria. Trends Biotechnol 2018; 36:996-1010. [DOI: 10.1016/j.tibtech.2018.05.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022]
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Xu Z, Sun J, Wu Q, Zhu D. Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks. Sci Rep 2017; 7:17334. [PMID: 29229946 PMCID: PMC5725421 DOI: 10.1038/s41598-017-17552-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 11/28/2017] [Indexed: 11/09/2022] Open
Abstract
Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.
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Affiliation(s)
- Zixiang Xu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key laboratory of systems microbial biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Jibin Sun
- Key laboratory of systems microbial biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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Beurton-Aimar M, Nguyen TVN, Colombié S. Metabolic network reconstruction and their topological analysis. Methods Mol Biol 2014; 1090:19-38. [PMID: 24222407 DOI: 10.1007/978-1-62703-688-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This chapter focuses on the way to build a metabolic network and how to analyze its structure. The first part of this chapter describes the methods of the network model reconstruction from biochemical data found in specialized databases and/or literature. The second part deals with metabolic pathway analysis as a useful tool for better understanding the complex architecture of intracellular metabolism. The graph analysis and the stoichiometric network analysis are important approaches for understanding the network topology and consequently the function of metabolic networks. Among the methods presented, the Elementary Flux Modes analysis will be more detailed. Finally, we illustrate in this chapter an example of network reconstruction from heterotrophic plant cells metabolism and its topological analysis leading to a huge number of Elementary Flux Modes.
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Kumar V, Ashok S, Park S. Recent advances in biological production of 3-hydroxypropionic acid. Biotechnol Adv 2013; 31:945-61. [DOI: 10.1016/j.biotechadv.2013.02.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/13/2013] [Accepted: 02/24/2013] [Indexed: 11/16/2022]
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8
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Binns M, Theodoropoulos C. An integrated knowledge-based approach for modelling biochemical reaction networks. Comput Chem Eng 2011. [DOI: 10.1016/j.compchemeng.2011.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Database searching for structural identification of metabolites in complex biofluids for mass spectrometry-based metabonomics. Bioanalysis 2011; 1:1627-43. [PMID: 21083108 DOI: 10.4155/bio.09.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MS and HPLC are commonly used for compound characterization and obtaining structural information; in the field of metabonomics, these two analytical techniques are often combined to characterize unknown endogenous or exogenous metabolites present in complex biological samples. Since the structures of a majority of these metabolites are not actually identified, the result of most metabonomic studies is a list of m/z values and retention times. However, without knowing actual structures, the biological significance of these 'features' cannot be determined. The process of identifying the structures of unknown compounds can be time intensive, costly and frequently requires the use of multiple orthogonal analytical techniques - this laborious procedure seems insurmountable for the long lists of unknowns that must be identified for each study. In addition, the limited sample volume and the extremely low concentration of most endogenous analytes frequently make purification and identification by other instrumentation nearly impossible. This review is intended to explore the problems and progress with current tools that are available for MS-based structure identification for both endogenous and exogenous metabolites.
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Mavrovouniotis ML, Stephanopoulos G, Stephanopoulos G. Computer-aided synthesis of biochemical pathways. Biotechnol Bioeng 2010; 36:1119-32. [PMID: 18595053 DOI: 10.1002/bit.260361107] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The synthesis of biochemical pathways satisfying stoichiometric constraints is discussed. Stoichiometric constraints arise primarily from designating compounds as required or allowed reactants, and required or allowed products of the pathways; they also arise from similar restrictions on intermediate metabolites and bioreactions participating in the pathways. An algorithm for the complete and correct solution of the problem is presented; the algorithm satisfies each constraint by recursively transforming a base-set of pathways. The algorithm is applied to the problem of lysine synthesis from glucose and ammonia. In addition to the established synthesis routes, the algorithm constructs several alternative pathways that bypass key enzymes, such as malate dehydrogenase and pyruvate dehydrogenase. Apart from the construction of pathways with desired characteristics, the systematic synthesis of pathways can also uncover fundamental constraints in a particular problem, by demonstrating that no pathways exist to meet certain sets of specifications. In the case of lysine, the algorithm shows that oxaloacetate is a necessary intermediate in all pathways leading to lysine from glucose, and that the yield of lysine over glucose cannot exceed 67% in the absence of enzymatic recovery of carbon dioxide.
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Affiliation(s)
- M L Mavrovouniotis
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Trinh CT, Wlaschin A, Srienc F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 2008; 81:813-26. [PMID: 19015845 DOI: 10.1007/s00253-008-1770-1] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 10/23/2008] [Accepted: 10/25/2008] [Indexed: 12/19/2022]
Abstract
Elementary mode analysis is a useful metabolic pathway analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering.
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Affiliation(s)
- Cong T Trinh
- Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Ave SE, Minneapolis, MN 55455, USA
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12
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Planes FJ, Beasley JE. A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Brief Bioinform 2008; 9:422-36. [DOI: 10.1093/bib/bbn018] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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HAPPEL JOHN, SELLERS PETERH. ENZYME MECHANISM AND KINETICS*. CHEM ENG COMMUN 2007. [DOI: 10.1080/00986449608936577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- JOHN HAPPEL
- a Department of Chemical Engineering , Materials Science and Mining, Columbia University , New York , NY , 10027
| | - PETER H. SELLERS
- b The Rockefeller University , 1230 York Avenue, New York , NY , 1002
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RUGGERI† BERNARDO, SASSI GUIDO. ON THE MODELLING APPROACHES OF BIOMASS BEHAVIOUR IN BIOREACTOR. CHEM ENG COMMUN 2007. [DOI: 10.1080/00986449308936148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- BERNARDO RUGGERI†
- a Dip. Scienza dei Materiali ed Ingegneria Chimica , Politecnico di Torino, c.so Duca degli Abruzzi 24, Torino, 10122, Italy
| | - GUIDO SASSI
- a Dip. Scienza dei Materiali ed Ingegneria Chimica , Politecnico di Torino, c.so Duca degli Abruzzi 24, Torino, 10122, Italy
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15
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Schuster S, von Kamp A, Pachkov M. Understanding the roadmap of metabolism by pathway analysis. Methods Mol Biol 2007; 358:199-226. [PMID: 17035688 DOI: 10.1007/978-1-59745-244-1_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The theoretical investigation of the structure of metabolic systems has recently attracted increasing interest. In this chapter, the basic concepts of metabolic pathway analysis are described and various applications are outlined. In particular, the concepts of nullspace and elementary flux modes are explained. The presentation is illustrated by a simple example from tyrosine metabolism and a system describing lysine production in Corynebacterium glutamicum. The latter system gives rise to 37 elementary modes, 36 of which produce lysine with different molar yields. The examples illustrate that metabolic pathway analysis is a useful tool for better understanding the complex architecture of intracellular metabolism, for determining the pathways on which the molar conversion yield of a substrate-product pair under study is maximal, and for assigning functions to orphan genes (functional genomics). Moreover, problems emerging in the modeling of large networks are discussed. An outlook on current trends in the field concludes the chapter.
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Affiliation(s)
- Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller University of Jena, Germany
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Abstract
A metabolic pathway is a coherent set of enzyme catalysed biochemical reactions by which a living organism transforms an initial (source) compound into a final (target) compound. Some of the different metabolic pathways adopted within organisms have been experimentally determined. In this paper, we show that a number of experimentally determined metabolic pathways can be recovered by a mathematical optimization model.
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Affiliation(s)
- John E Beasley
- Mathematical Sciences, Brunel University Uxbridge, UB8 3PH, UK.
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17
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Holiastos K, Manousiouthakis V. Automatic synthesis of thermodynamically feasible reaction clusters. AIChE J 2006. [DOI: 10.1002/aic.690440117] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Lee DY, Fan LT, Park S, Lee SY, Shafie S, Bertók B, Friedler F. Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab Eng 2005; 7:182-200. [PMID: 15885617 DOI: 10.1016/j.ymben.2005.02.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 12/07/2004] [Accepted: 02/08/2005] [Indexed: 11/27/2022]
Abstract
Cell robustness and complexity have been recognized as unique features of biological systems. Such robustness and complexity of metabolic-reaction systems can be explored by discovering, or identifying, the multiple flux distributions (MFD) and redundant pathways that lead to a given external state; however, this is exceedingly cumbersome to accomplish. It is, therefore, highly desirable to establish an effective computational method for their identification, which, in turn, gives rise to a novel insight into the cellular function. An effective approach is proposed for complementarily identifying MFD in metabolic flux analysis and multiple metabolic pathways (MMP) in structural pathway analysis. This approach judiciously integrates flux balance analysis (FBA) based on linear programming and the graph-theoretic method for determining reaction pathways. A single metabolic pathway, with the concomitant flux distribution and the overall reaction manifesting itself as the desired phenotype under some environmental conditions, is determined by FBA from the initial candidate sequence of metabolic reactions. Subsequently, the graph-theoretic method recovers all feasible MMP and the corresponding MFD. The approach's efficacy is demonstrated by applying it to the in silico Escherichia coli model under various culture conditions. The resultant MMP and MFD attaining a unique external state reveal the surprising adaptability and robustness of the intricate cellular network as a key to cell survival against environmental or genetic changes. These results indicate that the proposed approach would be useful in facilitating drug discovery.
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Affiliation(s)
- Dong-Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea
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19
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Ho RLX. Biosystems modelling for in silico target validation: challenges to implementation. ACTA ACUST UNITED AC 2005. [DOI: 10.1517/14728222.4.6.699] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2005; 14:2367-76. [PMID: 15520298 PMCID: PMC525696 DOI: 10.1101/gr.2872004] [Citation(s) in RCA: 375] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction of targeted compounds. These compounds may range from electrons or hydrogen in biofuel cell and environmental applications to complex drug precursor molecules. A comprehensive database of biotransformations, referred to as the Universal database (with >5700 reactions), is compiled and regularly updated by downloading and curating reactions from multiple biopathway database sources. Combinatorial optimization is then used to elucidate the set(s) of non-native functionalities, extracted from this Universal database, to add to the examined production host for enabling the desired product formation. Subsequently, competing functionalities that divert flux away from the targeted product are identified and removed to ensure higher product yields coupled with growth. This work represents an advancement over earlier efforts by establishing an integrated computational framework capable of constructing stoichiometrically balanced pathways, imposing maximum product yield requirements, pinpointing the optimal substrate(s), and evaluating different microbial hosts. The range and utility of OptStrain are demonstrated by addressing two very different product molecules. The hydrogen case study pinpoints reaction elimination strategies for improving hydrogen yields using two different substrates for three separate production hosts. In contrast, the vanillin study primarily showcases which non-native pathways need to be added into Escherichia coli. In summary, OptStrain provides a useful tool to aid microbial strain design and, more importantly, it establishes an integrated framework to accommodate future modeling developments.
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Affiliation(s)
- Priti Pharkya
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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21
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Li C, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V, Broadbelt LJ. Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 2004. [DOI: 10.1016/j.ces.2004.09.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Clarke B, Fawcett G, Mittenthal JE. Netscan: a procedure for generating reaction networks by size. J Theor Biol 2004; 230:591-602. [PMID: 15363678 DOI: 10.1016/j.jtbi.2004.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2003] [Revised: 02/24/2004] [Accepted: 03/29/2004] [Indexed: 11/17/2022]
Abstract
In this paper, we describe an algorithm which can be used to generate the collection of networks, in order of increasing size, that are compatible with a list of chemical reactions and that satisfy a constraint. Our algorithm has been encoded and the software, called Netscan, can be freely downloaded from ftp://ftp.stat.ubc.ca/pub/riffraff/Netscanfiles, along with a manual, for general scientific use. Our algorithm may require pre-processing to ensure that the quantities it acts on are physically relevant and because it outputs sets of reactions, which we call canonical networks, that must be elaborated into full networks.
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Affiliation(s)
- Bertrand Clarke
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
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23
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Bulter T, Bernstein JR, Liao JC. A perspective of metabolic engineering strategies: moving up the systems hierarchy. Biotechnol Bioeng 2004; 84:815-21. [PMID: 14708122 DOI: 10.1002/bit.10845] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic engineering has been established as an important field in biotechnology. It involves the analysis, design, and alteration of the stoichiometric network using sophisticated mathematical and molecular biology techniques. It allows for improvement of pathway kinetics by removing flux bottlenecks, balancing precursors, and recycling cofactors used to increase product formation. The next step in the systems hierarchy is the constructive manipulation of regulatory networks. As our understanding of regulation continues to expand rapidly, engineering of intracellular regulation will become an integral aspect of metabolic engineering.
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Affiliation(s)
- Thomas Bulter
- Department of Chemical Engineering, University of California, 405 Hilgard Avenue, Los Angeles, California 90095-1592, USA
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24
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Oliveira JS, Bailey CG, Jones-Oliveira JB, Dixon DA, Gull DW, Chandler ML. A computational model for the identification of biochemical pathways in the krebs cycle. J Comput Biol 2003; 10:57-82. [PMID: 12676051 DOI: 10.1089/106652703763255679] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have applied an algorithmic methodology which provably decomposes any complex network into a complete family of principal subcircuits to study the minimal circuits that describe the Krebs cycle. Every operational behavior that the network is capable of exhibiting can be represented by some combination of these principal subcircuits and this computational decomposition is linearly efficient. We have developed a computational model that can be applied to biochemical reaction systems which accurately renders pathways of such reactions via directed hypergraphs (Petri nets). We have applied the model to the citric acid cycle (Krebs cycle). The Krebs cycle, which oxidizes the acetyl group of acetyl CoA to CO(2) and reduces NAD and FAD to NADH and FADH(2), is a complex interacting set of nine subreaction networks. The Krebs cycle was selected because of its familiarity to the biological community and because it exhibits enough complexity to be interesting in order to introduce this novel analytic approach. This study validates the algorithmic methodology for the identification of significant biochemical signaling subcircuits, based solely upon the mathematical model and not upon prior biological knowledge. The utility of the algebraic-combinatorial model for identifying the complete set of biochemical subcircuits as a data set is demonstrated for this important metabolic process.
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Affiliation(s)
- Joseph S Oliveira
- Radiological & Chemical Sciences Group, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Abstract
MOTIVATION Automated methods for biochemical pathway inference are becoming increasingly important for understanding biological processes in living and synthetic systems. With the availability of data on complete genomes and increasing information about enzyme-catalyzed biochemistry it is becoming feasible to approach this problem computationally. In this paper we present PathMiner, a system for automatic metabolic pathway inference. PathMiner predicts metabolic routes by reasoning over transformations using chemical and biological information. RESULTS We build a biochemical state-space using data from known enzyme-catalyzed transformations in Ligand, including, 2917 unique transformations between 3890 different compounds. To predict metabolic pathways we explore this state-space by developing an informed search algorithm. For this purpose we develop a chemically motivated heuristic to guide the search. Since the algorithm does not depend on predefined pathways, it can efficiently identify plausible routes using known biochemical transformations.
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Affiliation(s)
- D C McShan
- School of Medicine, University of Colorado, 4200 East Ninth Avenue, C-245 Denver, Colorado 80262, USA
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Abstract
Metabolic pathways are a central paradigm in biology. Historically, they have been defined on the basis of their step-by-step discovery. However, the genome-scale metabolic networks now being reconstructed from annotation of genome sequences demand new network-based definitions of pathways to facilitate analysis of their capabilities and functions, such as metabolic versatility and robustness, and optimal growth rates. This demand has led to the development of a new mathematically based analysis of complex, metabolic networks that enumerates all their unique pathways that take into account all requirements for cofactors and byproducts. Applications include the design of engineered biological systems, the generation of testable hypotheses regarding network structure and function, and the elucidation of properties that can not be described by simple descriptions of individual components (such as product yield, network robustness, correlated reactions and predictions of minimal media). Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems.
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Affiliation(s)
- Jason A Papin
- Department of Bioengineering, University of California, San Diego, La Jolla 92093-0412, USA
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27
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A review on metabolic pathway analysis with emphasis on isotope labeling approach. BIOTECHNOL BIOPROC E 2002. [DOI: 10.1007/bf02932832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Abstract
In metabolic pathway analysis, it should be considered that many enzymes operate with low specificity (e.g. nucleoside diphosphokinase, uridine kinase, transketolase, aldolase), so that various substrates and products can be converted. Here, we analyze the effect of enzymes with low substrate specificity on the elementary flux modes (pathways). We also study the benefits of two different approaches to describing multifunctional enzymes. The usual description is in terms of (overall) enzymatic reactions. At a more detailed level, the reaction steps (half-reactions, hemi-reactions) of the formation and conversion of enzyme-substrate complexes are considered. Multifunctional enzymes operate according to various mechanisms. This is illustrated here by the reaction schemes for the different enzyme mechanisms of bifunctional enzymes. For enzymes with two or more functions, it is important to consider only linearly independent functions, because otherwise cyclic elementary modes would occur which do not perform any net transformation. However, the choice of linearly independent functions is not a priori unique. We give a method for making this choice unique by considering the extreme pathways of the hemi-reactions system. A formal application of the algorithm for computing elementary flux modes (pathways) yields the result that the number of such modes sometimes depend on the level of description if some reactions are reversible and the products of the multifunctional enzymes are external metabolites or some multifunctional enzymes partly share the same metabolites. However, this problem can be solved by appropriate interpretation of the definition of elementary modes and the correct choice of independent functions of multifunctional enzymes. The analysis is illustrated by a biochemical example taken from nucleotide metabolism, comparing the two ways of description for nucleoside diphosphokinase and adenylate kinase, and by several smaller examples.
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Affiliation(s)
- Stefan Schuster
- Max Delbrück Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Str 10, 13092, Berlin, Germany.
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Abstract
Mathematical modeling is one of the key methodologies of metabolic engineering. Based on a given metabolic model different computational tools for the simulation, data evaluation, systems analysis, prediction, design and optimization of metabolic systems have been developed. The currently used metabolic modeling approaches can be subdivided into structural models, stoichiometric models, carbon flux models, stationary and nonstationary mechanistic models and models with gene regulation. However, the power of a model strongly depends on its basic modeling assumptions, the simplifications made and the data sources used. Model validation turns out to be particularly difficult for metabolic systems. The different modeling approaches are critically reviewed with respect to their potential and benefits for the metabolic engineering cycle. Several tools that have emerged from the different modeling approaches including structural pathway synthesis, stoichiometric pathway analysis, metabolic flux analysis, metabolic control analysis, optimization of regulatory architectures and the evaluation of rapid sampling experiments are discussed.
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Affiliation(s)
- Wolfgang Wiechert
- Department of Simulation and Computer Science, Institute of Mechanical and Control Engineering, University of Siegen, Paul-Bonatz-Str. 9-11, D-57068 Siegen, Germany.
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Schilling CH, Edwards JS, Letscher D, Palsson BØ. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng 2001. [DOI: 10.1002/1097-0290(2000)71:4<286::aid-bit1018>3.0.co;2-r] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Li HY, Ho PY. Subnetwork Analysis for the Determination of Multiple Steady States in Complex Reaction Networks. Ind Eng Chem Res 2000. [DOI: 10.1021/ie990620c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsing-Ya Li
- Department of Chemical Engineering, National Lien Ho Institute of Technology, Miaoli, Taiwan 36012, Republic of China
| | - Pang-Yen Ho
- Department of Chemical Engineering, National Lien Ho Institute of Technology, Miaoli, Taiwan 36012, Republic of China
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32
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Databank transfer-of-information, shortcut and exact estimators used in the wastewater biological treatment process identification. Comput Chem Eng 2000. [DOI: 10.1016/s0098-1354(00)00447-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Schilling CH, Letscher D, Palsson BO. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 2000; 203:229-48. [PMID: 10716907 DOI: 10.1006/jtbi.2000.1073] [Citation(s) in RCA: 374] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cellular metabolism is most often described and interpreted in terms of the biochemical reactions that make up the metabolic network. Genomics is providing near complete information regarding the genes/gene products participating in cellular metabolism for a growing number of organisms. As the true functional units of metabolic systems are its pathways, the time has arrived to define metabolic pathways in the context of whole-cell metabolism for the analysis of the structural design and capabilities of the metabolic network. In this study, we present the theoretical foundations for the identification of the unique set of systemically independent biochemical pathways, termed extreme pathways, based on system stochiometry and limited thermodynamics. These pathways represent the edges of the steady-state flux cone derived from convex analysis, and they can be used to represent any flux distribution achievable by the metabolic network. An algorithm is presented to determine the set of extreme pathways for a system of any complexity and a classification scheme is introduced for the characterization of these pathways. The property of systemic independence is discussed along with its implications for issues related to metabolic regulation and the evolution of cellular metabolic networks. The underlying pathway structure that is determined from the set of extreme pathways now provides us with the ability to analyse, interpret, and perhaps predict metabolic function from a pathway-based perspective in addition to the traditional reaction-based perspective. The algorithm and classification scheme developed can be used to describe the pathway structure in annotated genomes to explore the capabilities of an organism.
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Affiliation(s)
- C H Schilling
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
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Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. Predicting function: from genes to genomes and back. J Mol Biol 1998; 283:707-25. [PMID: 9790834 DOI: 10.1006/jmbi.1998.2144] [Citation(s) in RCA: 262] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Predicting function from sequence using computational tools is a highly complicated procedure that is generally done for each gene individually. This review focuses on the added value that is provided by completely sequenced genomes in function prediction. Various levels of sequence annotation and function prediction are discussed, ranging from genomic sequence to that of complex cellular processes. Protein function is currently best described in the context of molecular interactions. In the near future it will be possible to predict protein function in the context of higher order processes such as the regulation of gene expression, metabolic pathways and signalling cascades. The analysis of such higher levels of function description uses, besides the information from completely sequenced genomes, also the additional information from proteomics and expression data. The final goal will be to elucidate the mapping between genotype and phenotype.
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Affiliation(s)
- P Bork
- European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, PF 10.2209, Germany.
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Abstract
This article gives an overview of recent developments in the modelling of the structure, control and optimality of metabolic networks. In particular, methods of algebraically analysing the topology of such networks are presented. By these methods, conservation relations and elementary modes of functioning (biochemical routes) can be detected. The principles of metabolic control analysis are outlined. Various recent extensions of this theory are presented, such as an analysis in terms of time dependent variables and modular analysis. Evolutionary optimisation principles are applied to explain the catalytic efficiency of single enzymes as well as the structural design of metabolic pathways. Special results concern the optimal distribution of ATP consuming and ATP producing reactions in glycolysis.
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Affiliation(s)
- R Heinrich
- Institute of Biology, Section of Theoretical Biophysics, Humboldt University Berlin, Germany. reinhart=
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36
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Shi H, Shimizu K. An integrated metabolic pathway analysis based on metabolic signal flow diagram and cellular energetics for Saccharomyces cerevisiae. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)80992-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.
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Affiliation(s)
- P D Karp
- Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
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38
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Modified Integral Procedure (MIP) as a reliable short-cut method in mechanistic based ODE kinetic model estimation : Non-isothermal and (semi-)batch process cases. Comput Chem Eng 1995. [DOI: 10.1016/0098-1354(95)87118-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Metabolic pathway analysis of recombinant Saccharomyces cerevisiae with a galactose-inducible promoter based on a signal flow modeling approach. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0922-338x(96)87729-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Abstract
Metabolic engineering is defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. Cellular engineering, a more inclusive term, is defined as the purposeful modification of cell properties using the same techniques. Examples of cellular and metabolic engineering are divided into five categories: 1. Improved production of chemicals already produced by the host organism; 2. Extended substrate range for growth and product formation; 3. Addition of new catabolic activities for degradation of toxic chemicals; 4. Production of chemicals new to the host organism; and 5. Modification of cell properties. Over 100 examples of cellular and metabolic engineering are summarized. Several molecular biological, analytical chemistry, and mathematical and computational tools of relevance to cellular and metabolic engineering are reviewed. The importance of host selection and gene selection is emphasized. Finally, some future directions and emerging areas are presented.
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Affiliation(s)
- D C Cameron
- Department of Chemical Engineering, University of Wisconsin-Madison 53706-1691
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41
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Maria G. Expert system for ode chemical kinetic model identification by using a transfer of information numerical strategy. Comput Chem Eng 1993. [DOI: 10.1016/0098-1354(93)80263-m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Locher G, Sonnleitner B, Fiechter A. On-line measurement in biotechnology: Exploitation, objectives and benefits. J Biotechnol 1992; 25:55-73. [PMID: 1368463 DOI: 10.1016/0168-1656(92)90109-m] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sound data biologically relevant are prerequisites when developing high-performance bioprocesses. Understanding of physiological regulation as well as sophisticated control strategies are highly dependent on the observability of the culture, i.e. the generation and exploitation of suited signals even under complex environmental measurement conditions. Against this background, the increasing number of analytical systems is very supportive and, accordingly, an appropriate handling of sensors and measured data is of decisive importance. This article reports on practical experience with routines for maintenance, service and calibration of hardware sensors which improve the quality of measurements significantly. Verification and validation of signals is outlined in order to make the value of data exploitation tools obvious. A method for the characterization of information is introduced by practical examples of Saccharomyces cerevisiae cultures when explaining the specific properties of extracting biological information from raw data. Finally, examples for advantageous exploitation of on-line data are given.
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Affiliation(s)
- G Locher
- Institute of Biotechnology, ETH Zürich Hönggerberg, Switzerland
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Mavrovouniotis M, Stephanopoulos G, Stephanopoulos G. Synthesis of biochemical production routes. Comput Chem Eng 1992. [DOI: 10.1016/0098-1354(92)80071-g] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Abstract
An ability to predict the metabolic fate of a drug is important to drug design. Programs for predicting drug metabolites are becoming available, as are databases that will facilitate the development of such programs. Objective analysis of the performance of these programs will require statistical methods. The development of appropriate statistical methods must address a fundamental data representation problem that arises from the fact that the basic metabolic information uses chemical graph representations rather than the usual vector representations that typify statistical methodology. This study addresses the representation problem by using concepts arising from molecular similarity analysis. The statistical methods that are developed are illustrated by evaluating the performance of MetabolExpert in predicting the metabolic fate of benzodiazepines.
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Affiliation(s)
- M Johnson
- Upjohn Research Laboratories, Kalamazoo, Michigan 49001
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47
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Affiliation(s)
- G A Montague
- Department of Chemical and Process Engineering, University of Newcastle, Newcastle-upon-Tyne, England
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