A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories
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 de...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2014-08-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037014000257 |
| _version_ | 1811193435622735872 |
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| author | Amanda K. Fisher Benjamin G. Freedman David R. Bevan Ryan S. Senger |
| author_facet | Amanda K. Fisher Benjamin G. Freedman David R. Bevan Ryan S. Senger |
| author_sort | Amanda K. Fisher |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T00:08:19Z |
| format | Article |
| id | doaj.art-84f99023410f44b38d2fdfe93ec44ee3 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-12T00:08:19Z |
| publishDate | 2014-08-01 |
| publisher | Elsevier |
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| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-84f99023410f44b38d2fdfe93ec44ee32022-12-22T03:56:02ZengElsevierComputational and Structural Biotechnology Journal2001-03702014-08-011118919910.1016/j.csbj.2014.08.010A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factoriesAmanda K. Fisher0Benjamin G. Freedman1David R. Bevan2Ryan S. Senger3Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United StatesDepartment of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United StatesDepartment of Biochemistry, Virginia Tech, Blacksburg, VA, United StatesDepartment of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United StatesMicrobial 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.http://www.sciencedirect.com/science/article/pii/S2001037014000257Metabolic engineeringEnzyme engineeringMicrobial cell factoryGenome-scale modelDockingMolecular dynamics |
| spellingShingle | Amanda K. Fisher Benjamin G. Freedman David R. Bevan Ryan S. Senger A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories Computational and Structural Biotechnology Journal Metabolic engineering Enzyme engineering Microbial cell factory Genome-scale model Docking Molecular dynamics |
| title | A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| title_full | A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| title_fullStr | A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| title_full_unstemmed | A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| title_short | A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| title_sort | review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories |
| topic | Metabolic engineering Enzyme engineering Microbial cell factory Genome-scale model Docking Molecular dynamics |
| url | http://www.sciencedirect.com/science/article/pii/S2001037014000257 |
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