51
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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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52
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Purdy HM, Reed JL. Evaluating the capabilities of microbial chemical production using genome-scale metabolic models. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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53
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Libis V, Delépine B, Faulon JL. Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS Synth Biol 2016; 5:1076-1085. [PMID: 27028723 DOI: 10.1021/acssynbio.5b00225] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Detection of chemical signals is critical for cells in nature as well as in synthetic biology, where they serve as inputs for designer circuits. Important progress has been made in the design of signal processing circuits triggering complex biological behaviors, but the range of small molecules recognized by sensors as inputs is limited. The ability to detect new molecules will increase the number of synthetic biology applications, but direct engineering of tailor-made sensors takes time. Here we describe a way to immediately expand the range of biologically detectable molecules by systematically designing metabolic pathways that transform nondetectable molecules into molecules for which sensors already exist. We leveraged computer-aided design to predict such sensing-enabling metabolic pathways, and we built several new whole-cell biosensors for molecules such as cocaine, parathion, hippuric acid, and nitroglycerin.
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Affiliation(s)
- Vincent Libis
- Micalis
Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Institute
of Systems and Synthetic Biology, Genopole, CNRS, UEVE, Université Paris-Saclay, F-91030 Évry, France
| | - Baudoin Delépine
- Micalis
Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Institute
of Systems and Synthetic Biology, Genopole, CNRS, UEVE, Université Paris-Saclay, F-91030 Évry, France
| | - Jean-Loup Faulon
- Micalis
Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Institute
of Systems and Synthetic Biology, Genopole, CNRS, UEVE, Université Paris-Saclay, F-91030 Évry, France
- SYNBIOCHEM
Center, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
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Abstract
BACKGROUND The term 'metabolome' was introduced to the scientific literature in September 1998. AIM AND KEY SCIENTIFIC CONCEPTS OF THE REVIEW To mark its 18-year-old 'coming of age', two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131, Princess St, Manchester, M1 7DN UK
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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55
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Carbonell P, Currin A, Jervis AJ, Rattray NJW, Swainston N, Yan C, Takano E, Breitling R. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Nat Prod Rep 2016; 33:925-32. [PMID: 27185383 PMCID: PMC5063057 DOI: 10.1039/c6np00018e] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/11/2022]
Abstract
Covering: 2000 to 2016Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted.
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Affiliation(s)
- Pablo Carbonell
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Andrew Currin
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Adrian J. Jervis
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Nicholas J. W. Rattray
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Neil Swainston
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Cunyu Yan
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Eriko Takano
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Rainer Breitling
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
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56
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Delépine B, Libis V, Carbonell P, Faulon JL. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic Acids Res 2016; 44:W226-31. [PMID: 27106061 PMCID: PMC5741204 DOI: 10.1093/nar/gkw305] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 12/17/2022] Open
Abstract
Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications.
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Affiliation(s)
- Baudoin Delépine
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Vincent Libis
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Pablo Carbonell
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, M1 7DN Manchester, UK
| | - Jean-Loup Faulon
- iSSB, Genopole, CNRS, UEVE, Université Paris Saclay, 91000 Évry, France Micalis Institute, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, M1 7DN Manchester, UK
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57
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Kuwahara H, Alazmi M, Cui X, Gao X. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Res 2016; 44:W217-25. [PMID: 27131375 PMCID: PMC4987905 DOI: 10.1093/nar/gkw342] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
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Affiliation(s)
- Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Meshari Alazmi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Xuefeng Cui
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
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58
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Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl 2016; 2:16009. [PMID: 28725470 PMCID: PMC5516863 DOI: 10.1038/npjsba.2016.9] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 01/08/2023] Open
Abstract
The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.
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Affiliation(s)
- Victor Chubukov
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Héctor García Martín
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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59
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Toogood HS, Tait S, Jervis A, Ní Cheallaigh A, Humphreys L, Takano E, Gardiner JM, Scrutton NS. Natural Product Biosynthesis in Escherichia coli: Mentha Monoterpenoids. Methods Enzymol 2016; 575:247-70. [PMID: 27417932 DOI: 10.1016/bs.mie.2016.02.020] [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] [Indexed: 03/07/2024]
Abstract
The era of synthetic biology heralds in a new, more "green" approach to fine chemical and pharmaceutical drug production. It takes the knowledge of natural metabolic pathways and builds new routes to chemicals, enables nonnatural chemical production, and/or allows the rapid production of chemicals in alternative, highly performing organisms. This route is particularly useful in the production of monoterpenoids in microorganisms, which are naturally sourced from plant essential oils. Successful pathways are constructed by taking into consideration factors such as gene selection, regulatory elements, host selection and optimization, and metabolic considerations of the host organism. Seamless pathway construction techniques enable a "plug-and-play" switching of genes and regulatory parts to optimize the metabolic functioning in vivo. Ultimately, synthetic biology approaches to microbial monoterpenoid production may revolutionize "natural" compound formation.
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Affiliation(s)
- H S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - S Tait
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - A Jervis
- Manchester Institute of Biotechnology, SYNBIOCHEM, University of Manchester, Manchester, United Kingdom
| | - A Ní Cheallaigh
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - L Humphreys
- GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - E Takano
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - J M Gardiner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - N S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
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60
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Moura M, Finkle J, Stainbrook S, Greene J, Broadbelt LJ, Tyo KE. Evaluating enzymatic synthesis of small molecule drugs. Metab Eng 2016; 33:138-147. [DOI: 10.1016/j.ymben.2015.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/02/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
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61
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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62
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Designing overall stoichiometric conversions and intervening metabolic reactions. Sci Rep 2015; 5:16009. [PMID: 26530953 PMCID: PMC4632160 DOI: 10.1038/srep16009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/07/2015] [Indexed: 02/07/2023] Open
Abstract
Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.
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63
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Shih SCC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol 2015; 4:1151-64. [PMID: 26075958 DOI: 10.1021/acssynbio.5b00062] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.
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Affiliation(s)
- Steve C. C. Shih
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Garima Goyal
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Peter W. Kim
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Nicolas Koutsoubelis
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Paul D. Adams
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Anup K. Singh
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
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64
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Liu R, Bassalo MC, Zeitoun RI, Gill RT. Genome scale engineering techniques for metabolic engineering. Metab Eng 2015; 32:143-154. [PMID: 26453944 DOI: 10.1016/j.ymben.2015.09.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/15/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022]
Abstract
Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications.
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Affiliation(s)
- Rongming Liu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Ramsey I Zeitoun
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
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65
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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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66
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Ng CY, Khodayari A, Chowdhury A, Maranas CD. Advances in de novo strain design using integrated systems and synthetic biology tools. Curr Opin Chem Biol 2015; 28:105-14. [DOI: 10.1016/j.cbpa.2015.06.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/13/2015] [Accepted: 06/21/2015] [Indexed: 11/17/2022]
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67
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Ataman M, Hatzimanikatis V. Heading in the right direction: thermodynamics-based network analysis and pathway engineering. Curr Opin Biotechnol 2015; 36:176-82. [PMID: 26360871 DOI: 10.1016/j.copbio.2015.08.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 11/28/2022]
Abstract
Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods.
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Affiliation(s)
- Meric Ataman
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
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68
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Petzold CJ, Chan LJG, Nhan M, Adams PD. Analytics for Metabolic Engineering. Front Bioeng Biotechnol 2015; 3:135. [PMID: 26442249 PMCID: PMC4561385 DOI: 10.3389/fbioe.2015.00135] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/20/2022] Open
Abstract
Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.
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Affiliation(s)
- Christopher J Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Melissa Nhan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Paul D Adams
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
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Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T. DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinformatics 2015; 16:96. [PMID: 25888481 PMCID: PMC4389672 DOI: 10.1186/s12859-015-0499-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/18/2015] [Indexed: 12/27/2022] Open
Abstract
Background Computational predictions of catalytic function are vital for in-depth understanding of enzymes. Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we hypothesized that there is a large gap between the number of known annotated enzymes and the actual number in the protein universe, which significantly limits our ability to extract additional biologically relevant functional information from the available sequencing data. To reliably expand the enzyme space, we developed DomSign, a highly accurate domain signature–based enzyme functional prediction tool to assign Enzyme Commission (EC) digits. Results DomSign is a top-down prediction engine that yields results comparable, or superior, to those from many benchmark EC number prediction tools, including BLASTP, when a homolog with an identity >30% is not available in the database. Performance tests showed that DomSign is a highly reliable enzyme EC number annotation tool. After multiple tests, the accuracy is thought to be greater than 90%. Thus, DomSign can be applied to large-scale datasets, with the goal of expanding the enzyme space with high fidelity. Using DomSign, we successfully increased the percentage of EC-tagged enzymes from 12% to 30% in UniProt-TrEMBL. In the Kyoto Encyclopedia of Genes and Genomes bacterial database, the percentage of EC-tagged enzymes for each bacterial genome could be increased from 26.0% to 33.2% on average. Metagenomic mining was also efficient, as exemplified by the application of DomSign to the Human Microbiome Project dataset, recovering nearly one million new EC-labeled enzymes. Conclusions Our results offer preliminarily confirmation of the existence of the hypothesized huge number of “hidden enzymes” in the protein universe, the identification of which could substantially further our understanding of the metabolisms of diverse organisms and also facilitate bioengineering by providing a richer enzyme resource. Furthermore, our results highlight the necessity of using more advanced computational tools than BLAST in protein database annotations to extract additional biologically relevant functional information from the available biological sequences. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0499-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianmin Wang
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
| | - Hiroshi Mori
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-E3-10 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
| | - Ken Kurokawa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-E3-10 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
| | - Takuji Yamada
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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70
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Li M, Borodina I. Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res 2015; 15:1-12. [PMID: 25238571 DOI: 10.1111/1567-1364.12213] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/13/2014] [Accepted: 09/15/2014] [Indexed: 11/29/2022] Open
Abstract
Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae We describe computational tools for the prediction of biochemical pathways, molecular biology methods for assembly of DNA parts into pathways, and for introducing the pathways into the host, and finally approaches for optimizing performance of the introduced pathways.
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Affiliation(s)
- Mingji Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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71
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Muschiol J, Peters C, Oberleitner N, Mihovilovic MD, Bornscheuer UT, Rudroff F. Cascade catalysis – strategies and challenges en route to preparative synthetic biology. Chem Commun (Camb) 2015; 51:5798-811. [DOI: 10.1039/c4cc08752f] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this feature article recent progress and future perspectives of cascade catalysis combining bio/bio or bio/chemo catalysts are presented.
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Affiliation(s)
- Jan Muschiol
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Christin Peters
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Nikolin Oberleitner
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
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72
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Ding Y, Wu F, Tan C. Synthetic Biology: A Bridge between Artificial and Natural Cells. Life (Basel) 2014; 4:1092-116. [PMID: 25532531 PMCID: PMC4284483 DOI: 10.3390/life4041092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022] Open
Abstract
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications.
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Affiliation(s)
- Yunfeng Ding
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, One Shields Ave., Davis, CA 95616-5270, USA.
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Lewis DD, Villarreal FD, Wu F, Tan C. Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol 2014; 2:66. [PMID: 25538941 PMCID: PMC4260521 DOI: 10.3389/fbioe.2014.00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/23/2014] [Indexed: 12/22/2022] Open
Abstract
As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.
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Affiliation(s)
- Daniel D. Lewis
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | | | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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Araki M, Cox RS, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A. M-path: a compass for navigating potential metabolic pathways. Bioinformatics 2014; 31:905-11. [DOI: 10.1093/bioinformatics/btu750] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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