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Upadhyay V, Boorla VS, Maranas CD. Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network. Metab Eng 2023; 78:171-182. [PMID: 37301359 DOI: 10.1016/j.ymben.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Retro-biosynthetic approaches have made significant advances in predicting synthesis routes of target biofuel, bio-renewable or bio-active molecules. The use of only cataloged enzymatic activities limits the discovery of new production routes. Recent retro-biosynthetic algorithms increasingly use novel conversions that require altering the substrate or cofactor specificities of existing enzymes while connecting pathways leading to a target metabolite. However, identifying and re-engineering enzymes for desired novel conversions are currently the bottlenecks in implementing such designed pathways. Herein, we present EnzRank, a convolutional neural network (CNN) based approach, to rank-order existing enzymes in terms of their suitability to undergo successful protein engineering through directed evolution or de novo design towards a desired specific substrate activity. We train the CNN model on 11,800 known active enzyme-substrate pairs from the BRENDA database as positive samples and data generated by scrambling these pairs as negative samples using substrate dissimilarity between an enzyme's native substrate and all other molecules present in the dataset using Tanimoto similarity score. EnzRank achieves an average recovery rate of 80.72% and 73.08% for positive and negative pairs on test data after using a 10-fold holdout method for training and cross-validation. We further developed a web-based user interface (available at https://huggingface.co/spaces/vuu10/EnzRank) to predict enzyme-substrate activity using SMILES strings of substrates and enzyme sequence as input to allow convenient and easy-to-use access to EnzRank. In summary, this effort can aid de novo pathway design tools to prioritize starting enzyme re-engineering candidates for novel reactions as well as in predicting the potential secondary activity of enzymes in cell metabolism.
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Affiliation(s)
- Vikas Upadhyay
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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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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Raj A, Kumar A. Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation. ENVIRONMENTAL RESEARCH 2022; 214:114011. [PMID: 35985484 DOI: 10.1016/j.envres.2022.114011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Chlorpyrifos (CP) is one of the Organophosphorus pesticides (OPs) primarily used in agriculture to safeguard crops from pests and diseases. The pervasive use of chlorpyrifos is hazardous to humans and the environment as it inhibits the receptor for acetylcholinesterase activity, leading to abnormalities linked to the central nervous system. Hence, there is an ardent need to develop an effective and sustainable approach to the on-site degradation of chlorpyrifos. The role of microbes in the remediation of pesticides is considered the most effective and eco-friendly approach, as they have strong degradative potential due to their gene and enzymes naturally adapted to these sites. Several reports have previously been published on exploring the role of microbes in the degradation of CP. However, detection of CP as an environmental contaminant is an essential prerequisite for developing an efficient microbial-mediated biodegradation method with less harmful intermediates. Most of the articles published to date discuss the fate and impact of CP in the environment along with its degradation mechanism but still fail to discuss the analytical portion. This review is focused on the latest developments in the field of bioremediation of CP along with its physicochemical properties, toxicity, fate, and conventional (UV-Visible spectrophotometer, FTIR, NMR, GC-MS, etc) and advanced detection methods (Biosensors and immunochromatography-based methods) from different environmental samples. Apart from it, this review explores the role of metagenomics, system biology, in-silico tools, and genetic engineering in facilitating the bioremediation of CP. One of the objectives of this review is to educate policymakers with scientific data that will enable the development of appropriate strategies to reduce pesticide exposure and the harmful health impacts on both Human and other environmental components. Moreover, this review provides up-to-date developments related to the sustainable remediation of CP.
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Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India.
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MohammadiPeyhani H, Chiappino-Pepe A, Haddadi K, Hafner J, Hadadi N, Hatzimanikatis V. NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. eLife 2021; 10:e65543. [PMID: 34340747 PMCID: PMC8331181 DOI: 10.7554/elife.65543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/07/2021] [Indexed: 12/30/2022] Open
Abstract
The discovery of a drug requires over a decade of intensive research and financial investments - and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied their enzymatic metabolic targets, fate, and toxicity. NICEdrug.ch includes a unique fingerprint that identifies reactive similarities between drug-drug and drug-metabolite pairs. We validated the application, scope, and performance of NICEdrug.ch over similar methods in the field on golden standard datasets describing drugs and metabolites sharing reactivity, drug toxicities, and drug targets. We use NICEdrug.ch to evaluate inhibition and toxicity by the anticancer drug 5-fluorouracil, and suggest avenues to alleviate its side effects. We propose shikimate 3-phosphate for targeting liver-stage malaria with minimal impact on the human host cell. Finally, NICEdrug.ch suggests over 1300 candidate drugs and food molecules to target COVID-19 and explains their inhibitory mechanism for further experimental screening. The NICEdrug.ch database is accessible online to systematically identify the reactivity of small molecules and druggable enzymes with practical applications in lead discovery and drug repurposing.
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Affiliation(s)
- Homa MohammadiPeyhani
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Kiandokht Haddadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Jasmin Hafner
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Noushin Hadadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
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Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE. Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence? ACS ES&T WATER 2021; 1:1541-1554. [PMID: 34278380 PMCID: PMC8276273 DOI: 10.1021/acsestwater.1c00025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 05/14/2023]
Abstract
Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is lacking for many emerging contaminants encountered at low concentrations and in complex mixtures across natural and engineered systems. Any advanced approaches aiming to reduce environmental exposure to such contaminants (e.g., novel engineered biological water treatment systems, design of readily degradable chemicals, or improved regulatory assessment strategies to determine contaminant persistence a priori) will depend on understanding the causal links among contaminant removal, the key driving agents of biotransformation at low concentrations (i.e., relevant microbes and their metabolic activities), and how their presence and activity depend on environmental conditions. In this Perspective, we present the current understanding and recent methodological advances that can help to identify such links, even in complex environmental microbiomes and for contaminants present at low concentrations in complex chemical mixtures. We discuss the ensuing insights into contaminant biotransformation across varying environments and conditions and ask how much closer we have come to designing improved approaches to reducing environmental exposure to contaminants.
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Affiliation(s)
- Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448 Bayreuth, Germany
| | - Michael S McLachlan
- Department of Environmental Science (ACES), Stockholm University, 106 91 Stockholm, Sweden
| | - Lawrence P Wackett
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany
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Dixon TA, Williams TC, Pretorius IS. Bioinformational trends in grape and wine biotechnology. Trends Biotechnol 2021; 40:124-135. [PMID: 34108075 DOI: 10.1016/j.tibtech.2021.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
The creative destruction caused by the coronavirus pandemic is yielding immense opportunity for collaborative innovation networks. The confluence of biosciences, information sciences, and the engineering of biology, is unveiling promising bioinformational futures for a vibrant and sustainable bioeconomy. Bioinformational engineering, underpinned by DNA reading, writing, and editing technologies, has become a beacon of opportunity in a world paralysed by uncertainty. This article draws on lessons from the current pandemic and previous agricultural blights, and explores bioinformational research directions aimed at future-proofing the grape and wine industry against biological shocks from global blights and climate change.
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Affiliation(s)
- Thomas A Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, NSW 2109, Australia
| | - Isak S Pretorius
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, NSW 2109, Australia; Chancellery, Macquarie University, Sydney, NSW 2109, Australia.
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10
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Wang G, Lopez L, Coile M, Chen Y, Torkelson JM, Broadbelt LJ. Identification of Known and Novel Monomers for Poly(hydroxyurethanes) from Biobased Materials. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c06351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Guanhua Wang
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lauren Lopez
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Matthew Coile
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Yixuan Chen
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - John M. Torkelson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Linda J. Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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11
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Porokhin V, Amin SA, Nicks TB, Gopinarayanan VE, Nair NU, Hassoun S. Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity. Metab Eng Commun 2021; 12:e00170. [PMID: 33850714 PMCID: PMC8039717 DOI: 10.1016/j.mec.2021.e00170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/22/2021] [Accepted: 03/01/2021] [Indexed: 11/30/2022] Open
Abstract
Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation of progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, and environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between biological parts, and the design of robust and modular biological systems remains elusive. Such interactions are difficult to predict when designing synthetic systems and may manifest during experimental testing as inefficiencies that need to be overcome. Transforming organisms such as Escherichia coli into microbial factories is achieved via several engineering strategies, used individually or in combination, with the goal of maximizing the production of chosen target compounds. One technique relies on suppressing or overexpressing selected genes; another involves introducing heterologous enzymes into a microbial host. These modifications steer mass flux towards the set of desired metabolites but may create unexpected interactions. In this work, we develop a computational method, termed Metabolic Disruption Workflow (MDFlow), for discovering interactions and network disruptions arising from enzyme promiscuity – the ability of enzymes to act on a wide range of molecules that are structurally similar to their native substrates. We apply MDFlow to two experimentally verified cases where strains with essential genes knocked out are rescued by interactions resulting from overexpression of one or more other genes. We demonstrate how enzyme promiscuity may aid cells in adapting to disruptions of essential metabolic functions. We then apply MDFlow to predict and evaluate a number of putative promiscuous reactions that can interfere with two heterologous pathways designed for 3-hydroxypropionic acid (3-HP) production. Using MDFlow, we can identify putative enzyme promiscuity and the subsequent formation of unintended and undesirable byproducts that are not only disruptive to the host metabolism but also to the intended end-objective of high biosynthetic productivity and yield. As we demonstrate, MDFlow provides an innovative workflow to systematically identify incompatibilities between the native metabolism of the host and its engineered modifications due to enzyme promiscuity. Engineering modifications to cellular hosts result in undesirable byproducts. Metabolic Disruption: changes in engineered host due to enzyme promiscuity. Metabolic Disruption Workflow (MDFlow) uncovers metabolic disruption. MDFlow corroborates previously experimentally verified promiscuous interactions. MDFlow compares disruption due to heterologous pathways targeting 3-HP production.
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Affiliation(s)
| | - Sara A Amin
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Trevor B Nicks
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA
| | | | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA, USA.,Department of Chemical and Biological Engineering, Tufts University, Medford, MA, USA
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12
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Stolerman LM, Ghosh P, Rangamani P. Stability Analysis of a Signaling Circuit with Dual Species of GTPase Switches. Bull Math Biol 2021; 83:34. [PMID: 33609194 PMCID: PMC8378325 DOI: 10.1007/s11538-021-00864-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, function, vesicular transport between organelles, and signal transduction. These hydrolase enzymes operate by toggling between an active ("ON") guanosine triphosphate (GTP)-bound state and an inactive ("OFF") guanosine diphosphate (GDP)-bound state; such a toggle is regulated by GEFs (guanine nucleotide exchange factors) and GAPs (GTPase activating proteins). Here we propose a model for a network motif between monomeric (m) and trimeric (t) GTPases assembled exclusively in eukaryotic cells of multicellular organisms. We develop a system of ordinary differential equations in which these two classes of GTPases are interlinked conditional to their ON/OFF states within a motif through coupling and feedback loops. We provide explicit formulae for the steady states of the system and perform classical local stability analysis to systematically investigate the role of the different connections between the GTPase switches. Interestingly, a coupling of the active mGTPase to the GEF of the tGTPase was sufficient to provide two locally stable states: one where both active/inactive forms of the mGTPase can be interpreted as having low concentrations and the other where both m- and tGTPase have high concentrations. Moreover, when a feedback loop from the GEF of the tGTPase to the GAP of the mGTPase was added to the coupled system, two other locally stable states emerged. In both states the tGTPase is inactivated and active tGTPase concentrations are low. Finally, the addition of a second feedback loop, from the active tGTPase to the GAP of the mGTPase, gives rise to a family of steady states that can be parametrized by a range of inactive tGTPase concentrations. Our findings reveal that the coupling of these two different GTPase motifs can dramatically change their steady-state behaviors and shed light on how such coupling may impact signaling mechanisms in eukaryotic cells.
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Affiliation(s)
- Lucas M Stolerman
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Moores Comprehensive Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
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Sleight TW, Khanna V, Gilbertson LM, Ng CA. Network Analysis for Prioritizing Biodegradation Metabolites of Polycyclic Aromatic Hydrocarbons. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10735-10744. [PMID: 32692172 DOI: 10.1021/acs.est.0c02217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a diverse group of environmental contaminants released during the combustion of organic materials and the production and utilization of fossil fuels. Once released, PAHs deposit in soil and water bodies where they are subjected to environmental transport and transformations. As they degrade, intermediate transformation products may play an important role in their environmental impact. However, studying the effects of these degradation products has proven challenging because of the complexity, transience, and low concentration of many intermediates. Herein, a novel integration of a pathway prediction system and network theory was developed and applied to a set of four PAHs to demonstrate a possible solution to this challenge. Network analysis techniques were employed to refine the thousands of potential outputs and elucidate compounds of interest. Using these tools, we determined correlations between PAH degradation network data and intermediate metabolite structures, gaining information about the chemical characteristics of compounds based on their placement within the degradation network. Upon applying our developed filtering algorithm, we are able to predict up to 48% of the most common transformation products identified in a comprehensive empirical literature review. Additionally, our integrated approach uncovers potential metabolites which connect those found by past empirical studies but are currently undetected, thereby filling in the gaps of information in PAH degradation pathways.
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Affiliation(s)
- Trevor W Sleight
- Department of Civil and Environmental Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Vikas Khanna
- Department of Civil and Environmental Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
- Secondary Appointment, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Leanne M Gilbertson
- Department of Civil and Environmental Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
- Secondary Appointment, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Carla A Ng
- Department of Civil and Environmental Engineering, University of Pittsburgh, Benedum Hall, 3700 O'Hara Street, Pittsburgh, Pennsylvania 15261, United States
- Secondary Appointment, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, Pennsylvania 15261, United States
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14
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Wackett LP, Robinson SL. The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Biochem J 2020; 477:2875-2891. [PMID: 32797216 PMCID: PMC7428800 DOI: 10.1042/bcj20190720] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted 'non-biodegradable,' only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.
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Affiliation(s)
- Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A
- Biotechnology Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A
- Program in Microbiology, Immunology and Cancer Biology, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A
| | - Serina L. Robinson
- Biotechnology Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A
- Program in Microbiology, Immunology and Cancer Biology, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A
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Hafner J, MohammadiPeyhani H, Sveshnikova A, Scheidegger A, Hatzimanikatis V. Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. ACS Synth Biol 2020; 9:1479-1482. [PMID: 32421310 PMCID: PMC7309321 DOI: 10.1021/acssynbio.0c00052] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since then. Here, we present an updated version of ATLAS created from KEGG 2018 using an increased set of generalized reaction rules. Furthermore, we improved the accuracy of the enzymes that are predicted for catalyzing novel reactions. ATLAS now contains ∼150 000 reactions, out of which 96% are novel. In this report, we present detailed statistics on the updated ATLAS and highlight the improvements with regard to the previous version. Most importantly, 107 reactions predicted in the original ATLAS are now known to KEGG, which validates the predictive power of our approach. The updated ATLAS is available at https://lcsb-databases.epfl.ch/atlas.
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Affiliation(s)
- Jasmin Hafner
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Homa MohammadiPeyhani
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Anastasia Sveshnikova
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Alan Scheidegger
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
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16
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Omics Approaches to Pesticide Biodegradation. Curr Microbiol 2020; 77:545-563. [DOI: 10.1007/s00284-020-01916-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/08/2020] [Indexed: 02/08/2023]
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Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS. Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. J Biotechnol 2019; 302:67-76. [PMID: 31254549 DOI: 10.1016/j.jbiotec.2019.06.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/20/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022]
Abstract
Natural compounds and derivatives play an essential role in the pharmaceutical industry, however, the difficulty in resynthesizing natural products or isolate them from the native host, often limit their availability, elevate costs and slow down the pharmaceutical manufacturing process. In this context, application of synthetic biology could enable the efficient production of large amounts of drugs or drug precursors in heterologous microorganisms aiming to accelerate the entire manufacturing process. Considering this perspective, here we developed a pipeline to automatically search for metabolites available in the metabolic space that are structurally similar to worldwide approved drugs. This pipeline involved the in silico screening of metabolites from a metabolic pathway meta-database using both Tanimoto coefficients based on Daylight like fingerprints and Maximum Common Substructure algorithm. The method was successfully applied to identify metabolites sharing essential scaffolds with one or more drugs as potential candidates for metabolic engineering. Three of these metabolites (Festuclavine, Scopolamine, and Baccatin III) were identified as similar to many drugs like Cabergoline, Oxitropium, Paclitaxel and had their metabolic pathways computationally mapped for their production in Saccharomyces cerevisiae with our proprietary pathway design software. These compounds are examples of new opportunities for the application of synthetic biology in pharmaceutical production.
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Affiliation(s)
- Vanessa V C Sinatti
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil.
| | - Carlos Alberto X Gonçalves
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
| | - Aline S Romão-Dumaresq
- SENAI Innovation Institute for Biosynthetics, Technology Center for Chemical and Textile Industry, Rio de Janeiro, Brazil
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Shanks BH, Broadbelt LJ. A Robust Strategy for Sustainable Organic Chemicals Utilizing Bioprivileged Molecules. CHEMSUSCHEM 2019; 12:2970-2975. [PMID: 30964228 DOI: 10.1002/cssc.201900323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/28/2019] [Indexed: 06/09/2023]
Abstract
Biobased chemicals will inevitably be an important part of a sustainable organic chemical industry. Current efforts in biobased chemicals are largely driven by opportunistic chemical product targets requiring complete technology development from feedstock to final product for a specific molecule. To enhance the development of biobased chemicals, it is important to create strategies that can be more systematic and can leverage advancements across multiple final products. Discussed here is the concept of bioprivileged molecules, which are chemical intermediates that have the potential to be efficiently converted into a range of product molecules that can both directly replace existing petrochemicals and are novel molecules that impart enhanced performance properties in end-use applications.
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Affiliation(s)
- Brent H Shanks
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa, 50011, USA
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, USA
| | - Linda J Broadbelt
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa, 50011, USA
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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19
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Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. Proc Natl Acad Sci U S A 2019; 116:13996-14001. [PMID: 31221760 DOI: 10.1073/pnas.1821905116] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
High-quality and high-throughput prediction of enzyme commission (EC) numbers is essential for accurate understanding of enzyme functions, which have many implications in pathologies and industrial biotechnology. Several EC number prediction tools are currently available, but their prediction performance needs to be further improved to precisely and efficiently process an ever-increasing volume of protein sequence data. Here, we report DeepEC, a deep learning-based computational framework that predicts EC numbers for protein sequences with high precision and in a high-throughput manner. DeepEC takes a protein sequence as input and predicts EC numbers as output. DeepEC uses 3 convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers that cannot be classified by the CNNs. Comparative analyses against 5 representative EC number prediction tools show that DeepEC allows the most precise prediction of EC numbers, and is the fastest and the lightest in terms of the disk space required. Furthermore, DeepEC is the most sensitive in detecting the effects of mutated domains/binding site residues of protein sequences. DeepEC can be used as an independent tool, and also as a third-party software component in combination with other computational platforms that examine metabolic reactions.
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20
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Vernuccio S, Broadbelt LJ. Discerning complex reaction networks using automated generators. AIChE J 2019. [DOI: 10.1002/aic.16663] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sergio Vernuccio
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
| | - Linda J. Broadbelt
- Department of Chemical and Biological Engineering Northwestern University Evanston Illinois
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21
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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22
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Gupta U, Le T, Hu WS, Bhan A, Daoutidis P. Automated network generation and analysis of biochemical reaction pathways using RING. Metab Eng 2018; 49:84-93. [DOI: 10.1016/j.ymben.2018.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
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23
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Kumar A, Wang L, Ng CY, Maranas CD. Pathway design using de novo steps through uncharted biochemical spaces. Nat Commun 2018; 9:184. [PMID: 29330441 PMCID: PMC5766603 DOI: 10.1038/s41467-017-02362-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously considering any combination of the aforementioned design criteria. First, we track and codify as rules all reaction centers using a prime factorization-based encoding technique (rePrime). Reaction rules and known biotransformations are then simultaneously used by the pathway design algorithm (novoStoic) to trace both metabolites and molecular moieties through balanced bio-conversion strategies. We demonstrate the use of novoStoic in bypassing steps in existing pathways through putative transformations, assembling complex pathways blending both known and putative steps toward pharmaceuticals, and postulating ways to biodegrade xenobiotics.
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Affiliation(s)
- Akhil Kumar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
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24
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Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metab Eng 2018; 45:158-170. [DOI: 10.1016/j.ymben.2017.12.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/03/2017] [Accepted: 12/05/2017] [Indexed: 12/01/2022]
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25
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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Abstract
There is a number of global environmental problems that could be tackled through advanced Microbial Biotechnology.
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Affiliation(s)
- Víctor de Lorenzo
- Centro Nacional de Biotecnología (CNB-CSIC), Systems Biology Program, 28049, Campus de Cantoblanco-Madrid 28049, Spain
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27
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Islam MA, Hadadi N, Ataman M, Hatzimanikatis V, Stephanopoulos G. Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas. Metab Eng 2017; 41:173-181. [PMID: 28433737 DOI: 10.1016/j.ymben.2017.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/28/2016] [Accepted: 04/16/2017] [Indexed: 10/19/2022]
Abstract
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a greener and more sustainable alternative to the current production methods. Technologies of synthetic biology and metabolic engineering of microorganisms can be deployed for the expression of new biochemical pathways for MEG-synthesis from gases, provided that such promising alternative routes are first identified. We used the BNICE.ch algorithm to develop novel and previously unknown biological pathways to MEG from synthesis gas by leveraging the Wood-Ljungdahl pathway of carbon fixation of acetogenic bacteria. We developed a set of useful pathway pruning and analysis criteria to systematically assess thousands of pathways generated by BNICE.ch. Published genome-scale models of Moorella thermoacetica and Clostridium ljungdahlii were used to perform the pathway yield calculations and in-depth analyses of seven (7) newly developed biological MEG-producing pathways from gases, including CO2, CO, and H2. These analyses helped identify not only better candidate pathways, but also superior chassis organisms that can be used for metabolic engineering of the candidate pathways. The pathway generation, pruning, and detailed analysis procedures described in this study can also be used to develop biochemical pathways for other commodity chemicals from gaseous substrates.
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Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Noushin Hadadi
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Meric Ataman
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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28
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Latino DARS, Wicker J, Gütlein M, Schmid E, Kramer S, Fenner K. Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:449-464. [PMID: 28229138 DOI: 10.1039/c6em00697c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Developing models for the prediction of microbial biotransformation pathways and half-lives of trace organic contaminants in different environments requires as training data easily accessible and sufficiently large collections of respective biotransformation data that are annotated with metadata on study conditions. Here, we present the Eawag-Soil package, a public database that has been developed to contain all freely accessible regulatory data on pesticide degradation in laboratory soil simulation studies for pesticides registered in the EU (282 degradation pathways, 1535 reactions, 1619 compounds and 4716 biotransformation half-life values with corresponding metadata on study conditions). We provide a thorough description of this novel data resource, and discuss important features of the pesticide soil degradation data that are relevant for model development. Most notably, the variability of half-life values for individual compounds is large and only about one order of magnitude lower than the entire range of median half-life values spanned by all compounds, demonstrating the need to consider study conditions in the development of more accurate models for biotransformation prediction. We further show how the data can be used to find missing rules relevant for predicting soil biotransformation pathways. From this analysis, eight examples of reaction types were presented that should trigger the formulation of new biotransformation rules, e.g., Ar-OH methylation, or the extension of existing rules, e.g., hydroxylation in aliphatic rings. The data were also used to exemplarily explore the dependence of half-lives of different amide pesticides on chemical class and experimental parameters. This analysis highlighted the value of considering initial transformation reactions for the development of meaningful quantitative-structure biotransformation relationships (QSBR), which is a novel opportunity offered by the simultaneous encoding of transformation reactions and corresponding half-lives in Eawag-Soil. Overall, Eawag-Soil provides an unprecedentedly rich collection of manually extracted and curated biotransformation data, which should be useful in a great variety of applications.
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Affiliation(s)
- Diogo A R S Latino
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
| | - Jörg Wicker
- Institute of Computer Science, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Martin Gütlein
- Institute of Computer Science, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Emanuel Schmid
- Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland
| | - Stefan Kramer
- Institute of Computer Science, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland. and Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
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29
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Chibwe L, Titaley IA, Hoh E, Massey Simonich SL. Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2017; 4:32-43. [PMID: 35600207 PMCID: PMC9119311 DOI: 10.1021/acs.estlett.6b00455] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Complex environmental mixtures consist of hundreds to thousands of unknown and unregulated organic compounds that may have toxicological relevance, including transformation products (TPs) of anthropogenic organic pollutants. Non-targeted analysis and suspect screening analysis offer analytical approaches for potentially identifying these toxic transformation products. However, additional tools and strategies are needed in order to reduce the number of chemicals of interest and focus analytical efforts on chemicals that may pose risks to humans and the environment. This brief review highlights recent developments in this field and suggests an integrated framework that incorporates complementary instrumental techniques, computational chemistry, and toxicity analysis, for prioritizing and identifying toxic TPs in the environment.
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Affiliation(s)
- Leah Chibwe
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Ivan A. Titaley
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Eunha Hoh
- Graduate School of Public Health, San Diego State University, San Diego, CA, 92182, USA
| | - Staci L. Massey Simonich
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
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30
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Thijs S, Sillen W, Weyens N, Vangronsveld J. Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:23-38. [PMID: 27484694 DOI: 10.1080/15226514.2016.1216076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.
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Affiliation(s)
- Sofie Thijs
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Wouter Sillen
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Nele Weyens
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Jaco Vangronsveld
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
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31
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Noor E, Flamholz A, Bar-Even A, Davidi D, Milo R, Liebermeister W. The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PLoS Comput Biol 2016; 12:e1005167. [PMID: 27812109 PMCID: PMC5094713 DOI: 10.1371/journal.pcbi.1005167] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/27/2016] [Indexed: 02/03/2023] Open
Abstract
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell’s capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and bioengineering. It depends on enzyme parameters (such as kcat and KM constants), but also on metabolite concentrations. Moreover, similar amounts of different enzymes might incur different costs for the cell, depending on enzyme-specific properties such as protein size and half-life. Here, we developed enzyme cost minimization (ECM), a scalable method for computing enzyme amounts that support a given metabolic flux at a minimal protein cost. The complex interplay of enzyme and metabolite concentrations, e.g. through thermodynamic driving forces and enzyme saturation, would make it hard to solve this optimization problem directly. By treating enzyme cost as a function of metabolite levels, we formulated ECM as a numerically tractable, convex optimization problem. Its tiered approach allows for building models at different levels of detail, depending on the amount of available data. Validating our method with measured metabolite and protein levels in E. coli central metabolism, we found typical prediction fold errors of 4.1 and 2.6, respectively, for the two kinds of data. This result from the cost-optimized metabolic state is significantly better than randomly sampled metabolite profiles, supporting the hypothesis that enzyme cost is important for the fitness of E. coli. ECM can be used to predict enzyme levels and protein cost in natural and engineered pathways, and could be a valuable computational tool to assist metabolic engineering projects. Furthermore, it establishes a direct connection between protein cost and thermodynamics, and provides a physically plausible and computationally tractable way to include enzyme kinetics into constraint-based metabolic models, where kinetics have usually been ignored or oversimplified. “Enzyme cost”, the amount of protein needed for a given metabolic flux, is crucial for the metabolic choices cells have to make. However, due to the technical limitations of linear optimization methods, this cost has traditionally been ignored by constraint-based metabolic models such as Flux Balance Analysis. On the other hand, more detailed kinetic models which use ordinary differential equations to simulate fluxes for different choices of enzyme allocation, are computationally demanding and not scalable enough. In this work, we developed a method which utilizes the full kinetic model to predict steady-state enzyme costs, using a scalable and robust algorithm based on convex optimization. We show that the minimization of enzyme cost is a meaningful optimality principle by comparing our predictions to measured enzyme and metabolite levels in exponentially growing E. coli. This method could be used to quantify the enzyme cost of many other pathways and explain why evolution has selected some low-yield metabolic strategies, including aerobic fermentation in yeast and cancer cells. Furthermore, future metabolic engineering projects could benefit from our method by choosing pathways that reduce the total amount of enzyme required for the synthesis of a value-added product.
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Affiliation(s)
- Elad Noor
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Avi Flamholz
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Arren Bar-Even
- Max Planck Institute for Molecular Plant Physiology, Golm, Germany
| | - Dan Davidi
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ron Milo
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Wolfram Liebermeister
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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32
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Sivakumar TV, Giri V, Park JH, Kim TY, Bhaduri A. ReactPRED: a tool to predict and analyze biochemical reactions. Bioinformatics 2016; 32:3522-3524. [DOI: 10.1093/bioinformatics/btw491] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/24/2016] [Accepted: 07/19/2016] [Indexed: 01/19/2023] Open
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33
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Morgado G, Gerngross D, Roberts TM, Panke S. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:117-146. [PMID: 27757475 DOI: 10.1007/10_2016_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).
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Affiliation(s)
- Gaspar Morgado
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Gerngross
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania M Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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34
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Wicker J, Lorsbach T, Gütlein M, Schmid E, Latino D, Kramer S, Fenner K. enviPath--The environmental contaminant biotransformation pathway resource. Nucleic Acids Res 2015; 44:D502-8. [PMID: 26582924 PMCID: PMC4702869 DOI: 10.1093/nar/gkv1229] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS) has been a unique resource covering microbial biotransformation pathways of primarily xenobiotic chemicals for over 15 years. This paper introduces the successor system, enviPath (The Environmental Contaminant Biotransformation Pathway Resource), which is a complete redesign and reimplementation of UM-BBD/PPS. enviPath uses the database from the UM-BBD/PPS as a basis, extends the use of this database, and allows users to include their own data to support multiple use cases. Relative reasoning is supported for the refinement of predictions and to allow its extensions in terms of previously published, but not implemented machine learning models. User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases. enviPath is publicly available at https://envipath.org with free and open access to its core data.
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Affiliation(s)
- Jörg Wicker
- Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Tim Lorsbach
- Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Martin Gütlein
- Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Emanuel Schmid
- Scientific IT Services, ETH Zürich, Weinbergstrasse 11, 8092 Zürich, Switzerland
| | - Diogo Latino
- Department of Environmental Chemistry, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Stefan Kramer
- Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Kathrin Fenner
- Department of Environmental Chemistry, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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35
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Hadadi N, Hatzimanikatis V. Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr Opin Chem Biol 2015; 28:99-104. [DOI: 10.1016/j.cbpa.2015.06.025] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/16/2015] [Accepted: 06/21/2015] [Indexed: 12/28/2022]
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Zisaki A, Miskovic L, Hatzimanikatis V. Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches. Curr Pharm Des 2015; 21:806-22. [PMID: 25341854 PMCID: PMC4435036 DOI: 10.2174/1381612820666141024151119] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/09/2014] [Indexed: 02/07/2023]
Abstract
Drug discovery and development is a high-risk enterprise that requires significant investments in capital, time and scientific expertise. The studies of xenobiotic metabolism remain as one of the main topics in the research and development of drugs, cosmetics and nutritional supplements. Antihypertensive drugs are used for the treatment of high blood pressure, which is one the most frequent symptoms of the patients that undergo cardiovascular diseases such as myocardial infraction and strokes. In current cardiovascular disease pharmacology, four drug clusters - Angiotensin Converting Enzyme Inhibitors, Beta-Blockers, Calcium Channel Blockers and Diuretics - cover the major therapeutic characteristics of the most antihypertensive drugs. The pharmacokinetic and specifically the metabolic profile of the antihypertensive agents are intensively studied because of the broad inter-individual variability on plasma concentrations and the diversity on the efficacy response especially due to the P450 dependent metabolic status they present. Several computational methods have been developed with the aim to: (i) model and better understand the human drug metabolism; and (ii) enhance the experimental investigation of the metabolism of small xenobiotic molecules. The main predictive tools these methods employ are rule-based approaches, quantitative structure metabolism/activity relationships and docking approaches. This review paper provides detailed metabolic profiles of the major clusters of antihypertensive agents, including their metabolites and their metabolizing enzymes, and it also provides specific information concerning the computational approaches that have been used to predict the metabolic profile of several antihypertensive drugs.
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Affiliation(s)
| | | | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne, EPFL/SB/ISIC/LCSB, CH H4 624/ Station 6/ CH-1015 Lausanne/ Switzerland.
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37
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Nazem-Bokaee H, S. Senger R. ToMI-FBA: A genome-scale metabolic flux based algorithm to select optimum hosts and media formulations for expressing pathways of interest. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Gudmundsson S, Nogales J. Cyanobacteria as photosynthetic biocatalysts: a systems biology perspective. MOLECULAR BIOSYSTEMS 2015; 11:60-70. [DOI: 10.1039/c4mb00335g] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A review of cyanobacterial biocatalysts highlighting their metabolic features that argues for the need for systems-level metabolic engineering.
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Affiliation(s)
| | - Juan Nogales
- Department of Environmental Biology
- Centro de Investigaciones Biológicas-CSIC
- 28040 Madrid
- Spain
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39
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Satpathy R, Konkimalla VB, Ratha J. Application of bioinformatics tools and databases in microbial dehalogenation research: A review. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683815010147] [Citation(s) in RCA: 6] [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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A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol 2014; 10:e1003837. [PMID: 25232952 PMCID: PMC4168981 DOI: 10.1371/journal.pcbi.1003837] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 07/29/2014] [Indexed: 02/08/2023] Open
Abstract
Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succinate dehydrogenase (SDH), and fumarate hydratase (FH) that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes), expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers. Cancer and metabolism have been considered to be associated for a long period since Otto Warburg observed that tumor cells consume glucose and convert most of it to lactate, despite the presence of oxygen. However, the role of the Warburg effect in oncogenesis had been under doubt because no solid links between genetic variations in metabolic genes and cancer had been observed until recent days. When with the development of sequencing technologies, researchers found mutations in IDH1, IDH2 (isocitrate dehydrogenase) in medium-grade glioma and acute leukemia. As these mutated metabolic genes initiate unexpected enzymatic reactions, cancer cells show altered concentration of particular metabolites, here called “oncometabolites”. The oncometabolites regulate the epigenetic controls of cell differentiations. In this study, we predict potential oncometabolites that might originate from loss or gain-of-function mutations in nine types of cancer from massive scale cancer mutation data with a systems biology approach.
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41
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A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. Comput Struct Biotechnol J 2014; 11:91-9. [PMID: 25379147 PMCID: PMC4212277 DOI: 10.1016/j.csbj.2014.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Microbial cell factories (MCFs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity. In particular, the rational design of an MCF involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) MCF chassis selection, (iv) enzyme engineering of promiscuity to enable the formation of new products, and (v) metabolic engineering to ensure optimal use of the pathway by the MCF host. Computational tools such as (i) de novo biosynthetic pathway builders, (ii) docking, (iii) molecular dynamics (MD) and steered MD (SMD), and (iv) genome-scale metabolic flux modeling all play critical roles in the rational design of an MCF. Genome-scale metabolic flux models are of considerable use to the design process since they can reveal metabolic capabilities of MCF hosts. These can be used for host selection as well as optimizing precursors and cofactors of artificial de novo biosynthetic pathways. In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.
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42
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Wu D, Yue D, You F, Broadbelt LJ. Computational evaluation of factors governing catalytic 2-keto acid decarboxylation. J Mol Model 2014; 20:2310. [PMID: 24912593 DOI: 10.1007/s00894-014-2310-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/19/2014] [Indexed: 11/25/2022]
Abstract
Recent advances in computational approaches for creating pathways for novel biochemical reactions has motivated the development of approaches for identifying enzyme-substrate pairs that are attractive candidates for effecting catalysis. We present an improved structural-based strategy to probe and study enzyme-substrate binding based on binding geometry, energy, and molecule characteristics, which allows for in silico screening of structural features that imbue higher catalytic potential with specific substrates. The strategy is demonstrated using 2-keto acid decarboxylation with various pairs of 2-keto acids and enzymes. We show that this approach fitted experimental values for a wide range of 2-keto acid decarboxylases for different 2-keto acid substrates. In addition, we show that the structure-based methods can be used to select specific enzymes that may be promising candidates to catalyze decarboxylation of certain 2-keto acids. The key features and principles of the candidate enzymes evaluated by the strategy can be used to design novel biosynthesis pathways, to guide enzymatic mutation or to guide biomimetic catalyst design.
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Affiliation(s)
- Di Wu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
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43
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Vieira G, Carnicer M, Portais JC, Heux S. FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. Bioinformatics 2014; 30:2986-8. [DOI: 10.1093/bioinformatics/btu422] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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44
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45
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Hadadi N, Cher Soh K, Seijo M, Zisaki A, Guan X, Wenk MR, Hatzimanikatis V. A computational framework for integration of lipidomics data into metabolic pathways. Metab Eng 2014; 23:1-8. [DOI: 10.1016/j.ymben.2013.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/26/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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46
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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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47
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The path of anti-tuberculosis drugs: from blood to lesions to mycobacterial cells. Nat Rev Microbiol 2014; 12:159-67. [PMID: 24487820 DOI: 10.1038/nrmicro3200] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For the successful treatment of pulmonary tuberculosis, drugs need to penetrate complex lung lesions and permeate the mycobacterial cell wall in order to reach their intracellular targets. However, most currently used anti-tuberculosis drugs were introduced into clinical use without considering the pharmacokinetic and pharmacodynamic properties that influence drug distribution, and this has contributed to the long duration and limited success of current therapies. In this Progress article, I describe new methods to quantify and image drug distribution in infected lung tissue and in mycobacterial cells, and I explore how this technology could be used to design optimized multidrug regimens.
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48
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McClymont K, Soyer OS. Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Res 2013; 41:e113. [PMID: 23580552 PMCID: PMC3675468 DOI: 10.1093/nar/gkt234] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
One of the primary aims of synthetic biology is to (re)design metabolic pathways towards the production of desired chemicals. The fast pace of developments in molecular biology increasingly makes it possible to experimentally redesign existing pathways and implement de novo ones in microbes or using in vitro platforms. For such experimental studies, the bottleneck is shifting from implementation of pathways towards their initial design. Here, we present an online tool called ‘Metabolic Tinker’, which aims to guide the design of synthetic metabolic pathways between any two desired compounds. Given two user-defined ‘target’ and ‘source’ compounds, Metabolic Tinker searches for thermodynamically feasible paths in the entire known metabolic universe using a tailored heuristic search strategy. Compared with similar graph-based search tools, Metabolic Tinker returns a larger number of possible paths owing to its broad search base and fast heuristic, and provides for the first time thermodynamic feasibility information for the discovered paths. Metabolic Tinker is available as a web service at http://osslab.ex.ac.uk/tinker.aspx. The same website also provides the source code for Metabolic Tinker, allowing it to be developed further or run on personal machines for specific applications.
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Affiliation(s)
- Kent McClymont
- Computer Science, College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter EX4 4QF, UK
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49
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Lo TM, Teo WS, Ling H, Chen B, Kang A, Chang MW. Microbial engineering strategies to improve cell viability for biochemical production. Biotechnol Adv 2013; 31:903-14. [PMID: 23403071 DOI: 10.1016/j.biotechadv.2013.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 11/16/2022]
Abstract
Efficient production of biochemicals using engineered microbes as whole-cell biocatalysts requires robust cell viability. Robust viability leads to high productivity and improved bioprocesses by allowing repeated cell recycling. However, cell viability is negatively affected by a plethora of stresses, namely chemical toxicity and metabolic imbalances, primarily resulting from bio-synthesis pathways. Chemical toxicity is caused by substrates, intermediates, products, and/or by-products, and these compounds often interfere with important metabolic processes and damage cellular infrastructures such as cell membrane, leading to poor cell viability. Further, stresses on engineered cells are accentuated by metabolic imbalances, which are generated by heavy metabolic resource consumption due to enzyme overexpression, redistribution of metabolic fluxes, and impaired intracellular redox state by co-factor imbalance. To address these challenges, herein, we discuss a range of key microbial engineering strategies, substantiated by recent advances, to improve cell viability for commercially sustainable production of biochemicals from renewable resources.
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Affiliation(s)
- Tat-Ming Lo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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50
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Affiliation(s)
- Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering, Dept. of Biological Sciences, and the Delaware Biotechnology Institute; University of Delaware; 15 Innovation Way; Newark; DE; 19711
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