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Metabolite damage and repair in metabolic engineering design.

Metabolic engineering

Sun J, Jeffryes JG, Henry CS, Bruner SD, Hanson AD.
PMID: 29030275
Metab Eng. 2017 Nov;44:150-159. doi: 10.1016/j.ymben.2017.10.006. Epub 2017 Oct 10.

The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such...

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Sun J, Jeffryes JG, Henry CS, et al. Metabolite damage and repair in metabolic engineering design. Metab Eng. 2017;44:150-159doi: 10.1016/j.ymben.2017.10.006.
Sun, J., Jeffryes, J. G., Henry, C. S., Bruner, S. D., & Hanson, A. D. (2017). Metabolite damage and repair in metabolic engineering design. Metabolic engineering, 44150-159. https://doi.org/10.1016/j.ymben.2017.10.006
Sun, Jiayi, et al. "Metabolite damage and repair in metabolic engineering design." Metabolic engineering vol. 44 (2017): 150-159. doi: https://doi.org/10.1016/j.ymben.2017.10.006
Sun J, Jeffryes JG, Henry CS, Bruner SD, Hanson AD. Metabolite damage and repair in metabolic engineering design. Metab Eng. 2017 Nov;44:150-159. doi: 10.1016/j.ymben.2017.10.006. Epub 2017 Oct 10. PMID: 29030275.
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Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies.

World journal of microbiology & biotechnology

Horvat P, Koller M, Braunegg G.
PMID: 26066363
World J Microbiol Biotechnol. 2015 Sep;31(9):1315-28. doi: 10.1007/s11274-015-1887-1. Epub 2015 Jun 12.

A review of the use of elementary flux modes (EFMs) and their applications in metabolic engineering covered with yield space analysis (YSA) is presented. EFMs are an invaluable tool in mathematical modeling of biochemical processes. They are described from...

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Horvat P, Koller M, Braunegg G. Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies. World J Microbiol Biotechnol. 2015;31(9):1315-28doi: 10.1007/s11274-015-1887-1.
Horvat, P., Koller, M., & Braunegg, G. (2015). Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies. World journal of microbiology & biotechnology, 31(9), 1315-28. https://doi.org/10.1007/s11274-015-1887-1
Horvat, Predrag, et al. "Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies." World journal of microbiology & biotechnology vol. 31,9 (2015): 1315-28. doi: https://doi.org/10.1007/s11274-015-1887-1
Horvat P, Koller M, Braunegg G. Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies. World J Microbiol Biotechnol. 2015 Sep;31(9):1315-28. doi: 10.1007/s11274-015-1887-1. Epub 2015 Jun 12. PMID: 26066363.
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CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli.

Metabolic engineering

Liang L, Liu R, Garst AD, Lee T, Nogué VSI, Beckham GT, Gill RT.
PMID: 28216108
Metab Eng. 2017 May;41:1-10. doi: 10.1016/j.ymben.2017.02.009. Epub 2017 Feb 16.

Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and...

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Liang L, Liu R, Garst AD, et al. CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab Eng. 2017;41:1-10doi: 10.1016/j.ymben.2017.02.009.
Liang, L., Liu, R., Garst, A. D., Lee, T., Nogué, V. S. I., Beckham, G. T., & Gill, R. T. (2017). CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metabolic engineering, 411-10. https://doi.org/10.1016/j.ymben.2017.02.009
Liang, Liya, et al. "CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli." Metabolic engineering vol. 41 (2017): 1-10. doi: https://doi.org/10.1016/j.ymben.2017.02.009
Liang L, Liu R, Garst AD, Lee T, Nogué VSI, Beckham GT, Gill RT. CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab Eng. 2017 May;41:1-10. doi: 10.1016/j.ymben.2017.02.009. Epub 2017 Feb 16. PMID: 28216108.
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Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review.

Microbial cell factories

Qiu XY, Xie SS, Min L, Wu XM, Zhu LY, Zhu L.
PMID: 30064437
Microb Cell Fact. 2018 Jul 31;17(1):120. doi: 10.1186/s12934-018-0965-0.

For years, microbes have been widely applied as chassis in the construction of synthetic metabolic pathways. However, the lack of in vivo enzyme clustering of heterologous metabolic pathways in these organisms often results in low local concentrations of enzymes...

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Qiu XY, Xie SS, Min L, et al. Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review. Microb Cell Fact. 2018;17(1):120doi: 10.1186/s12934-018-0965-0.
Qiu, X. Y., Xie, S. S., Min, L., Wu, X. M., Zhu, L. Y., & Zhu, L. (2018). Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review. Microbial cell factories, 17(1), 120. https://doi.org/10.1186/s12934-018-0965-0
Qiu, Xin-Yuan, et al. "Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review." Microbial cell factories vol. 17,1 (2018): 120. doi: https://doi.org/10.1186/s12934-018-0965-0
Qiu XY, Xie SS, Min L, Wu XM, Zhu LY, Zhu L. Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review. Microb Cell Fact. 2018 Jul 31;17(1):120. doi: 10.1186/s12934-018-0965-0. PMID: 30064437; PMCID: PMC6066912.
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User guides for biologists to learn computational methods.

Journal of microbiology (Seoul, Korea)

Na D.
PMID: 32108313
J Microbiol. 2020 Mar;58(3):173-175. doi: 10.1007/s12275-020-9723-1. Epub 2020 Feb 27.

System-wide studies of a given molecular type are referred to as "omics." These include genomics, proteomics, and metabolomics, among others. Recent biotechnological advances allow for high-throughput measurement of cellular components, and thus it becomes possible to take a snapshot...

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Na D. User guides for biologists to learn computational methods. J Microbiol. 2020;58(3):173-175doi: 10.1007/s12275-020-9723-1.
Na, D. (2020). User guides for biologists to learn computational methods. Journal of microbiology (Seoul, Korea), 58(3), 173-175. https://doi.org/10.1007/s12275-020-9723-1
Na, Dokyun. "User guides for biologists to learn computational methods." Journal of microbiology (Seoul, Korea) vol. 58,3 (2020): 173-175. doi: https://doi.org/10.1007/s12275-020-9723-1
Na D. User guides for biologists to learn computational methods. J Microbiol. 2020 Mar;58(3):173-175. doi: 10.1007/s12275-020-9723-1. Epub 2020 Feb 27. PMID: 32108313.
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CRISPR-based metabolic editing: Next-generation metabolic engineering in plants.

Gene

Sabzehzari M, Zeinali M, Naghavi MR.
PMID: 32717311
Gene. 2020 Oct 30;759:144993. doi: 10.1016/j.gene.2020.144993. Epub 2020 Jul 24.

Plants generate many secondary metabolites, so called phyto-metabolites, which can be used as toxins, dyes, drugs, and insecticides in bio-warfare plus bio-terrorism, industry, medicine, and agriculture, respectively. To 2013, the first generation metabolic engineering approaches like miRNA-based manipulation were...

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Sabzehzari M, Zeinali M, Naghavi MR. CRISPR-based metabolic editing: Next-generation metabolic engineering in plants. Gene. 2020;759:144993doi: 10.1016/j.gene.2020.144993.
Sabzehzari, M., Zeinali, M., & Naghavi, M. R. (2020). CRISPR-based metabolic editing: Next-generation metabolic engineering in plants. Gene, 759144993. https://doi.org/10.1016/j.gene.2020.144993
Sabzehzari, Mohammad, et al. "CRISPR-based metabolic editing: Next-generation metabolic engineering in plants." Gene vol. 759 (2020): 144993. doi: https://doi.org/10.1016/j.gene.2020.144993
Sabzehzari M, Zeinali M, Naghavi MR. CRISPR-based metabolic editing: Next-generation metabolic engineering in plants. Gene. 2020 Oct 30;759:144993. doi: 10.1016/j.gene.2020.144993. Epub 2020 Jul 24. PMID: 32717311.
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Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations.

Metabolic engineering

Hameri T, Fengos G, Ataman M, Miskovic L, Hatzimanikatis V.
PMID: 30455161
Metab Eng. 2019 Mar;52:29-41. doi: 10.1016/j.ymben.2018.10.005. Epub 2018 Oct 26.

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other types of models...

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Hameri T, Fengos G, Ataman M, et al. Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations. Metab Eng. 2018;52:29-41doi: 10.1016/j.ymben.2018.10.005.
Hameri, T., Fengos, G., Ataman, M., Miskovic, L., & Hatzimanikatis, V. (2019). Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations. Metabolic engineering, 5229-41. https://doi.org/10.1016/j.ymben.2018.10.005
Hameri, Tuure, et al. "Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations." Metabolic engineering vol. 52 (2019): 29-41. doi: https://doi.org/10.1016/j.ymben.2018.10.005
Hameri T, Fengos G, Ataman M, Miskovic L, Hatzimanikatis V. Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations. Metab Eng. 2019 Mar;52:29-41. doi: 10.1016/j.ymben.2018.10.005. Epub 2018 Oct 26. PMID: 30455161.
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Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies.

Biotechnology journal

Saa PA, Cortés MP, López J, Bustos D, Maass A, Agosin E.
PMID: 31140756
Biotechnol J. 2019 Sep;14(9):e1800734. doi: 10.1002/biot.201800734. Epub 2019 Jul 01.

Design and selection of efficient metabolic pathways is critical for the success of metabolic engineering endeavors. Convenient pathways should not only produce the target metabolite in high yields but also are required to be thermodynamically feasible under production conditions,...

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Saa PA, Cortés MP, López J, et al. Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies. Biotechnol J. 2019;14(9):e1800734doi: 10.1002/biot.201800734.
Saa, P. A., Cortés, M. P., López, J., Bustos, D., Maass, A., & Agosin, E. (2019). Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies. Biotechnology journal, 14(9), e1800734. https://doi.org/10.1002/biot.201800734
Saa, Pedro A, et al. "Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies." Biotechnology journal vol. 14,9 (2019): e1800734. doi: https://doi.org/10.1002/biot.201800734
Saa PA, Cortés MP, López J, Bustos D, Maass A, Agosin E. Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies. Biotechnol J. 2019 Sep;14(9):e1800734. doi: 10.1002/biot.201800734. Epub 2019 Jul 01. PMID: 31140756.
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Identification of metabolites identical and similar to drugs as candidates for metabolic engineering.

Journal of biotechnology

Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS.
PMID: 31254549
J Biotechnol. 2019 Aug 20;302:67-76. doi: 10.1016/j.jbiotec.2019.06.303. Epub 2019 Jun 26.

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....

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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;302:67-76doi: 10.1016/j.jbiotec.2019.06.303.
Sinatti, V. V. C., Gonçalves, C. A. X., & Romão-Dumaresq, A. S. (2019). Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. Journal of biotechnology, 30267-76. https://doi.org/10.1016/j.jbiotec.2019.06.303
Sinatti, Vanessa V C, et al. "Identification of metabolites identical and similar to drugs as candidates for metabolic engineering." Journal of biotechnology vol. 302 (2019): 67-76. doi: https://doi.org/10.1016/j.jbiotec.2019.06.303
Sinatti VVC, Gonçalves CAX, Romão-Dumaresq AS. Identification of metabolites identical and similar to drugs as candidates for metabolic engineering. J Biotechnol. 2019 Aug 20;302:67-76. doi: 10.1016/j.jbiotec.2019.06.303. Epub 2019 Jun 26. PMID: 31254549.
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Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered .

Proceedings of the National Academy of Sciences of the United States of America

Dinh CV, Prather KLJ.
PMID: 31796590
Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25562-25568. doi: 10.1073/pnas.1911144116. Epub 2019 Dec 03.

Metabolic engineering seeks to reprogram microbial cells to efficiently and sustainably produce value-added compounds. Since chemical production can be at odds with the cell's natural objectives, strategies have been developed to balance conflicting goals. For example, dynamic regulation modulates...

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Dinh CV, Prather KLJ. Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered . Proc Natl Acad Sci U S A. 2019;116(51):25562-25568doi: 10.1073/pnas.1911144116.
Dinh, C. V., & Prather, K. L. J. (2019). Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered . Proceedings of the National Academy of Sciences of the United States of America, 116(51), 25562-25568. https://doi.org/10.1073/pnas.1911144116
Dinh, Christina V, and Prather, Kristala L J. "Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered ." Proceedings of the National Academy of Sciences of the United States of America vol. 116,51 (2019): 25562-25568. doi: https://doi.org/10.1073/pnas.1911144116
Dinh CV, Prather KLJ. Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered . Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25562-25568. doi: 10.1073/pnas.1911144116. Epub 2019 Dec 03. PMID: 31796590; PMCID: PMC6926038.
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Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production.

Critical reviews in biochemistry and molecular biology

Wang Y, Ren H, Zhao H.
PMID: 29411648
Crit Rev Biochem Mol Biol. 2018 Apr;53(2):115-129. doi: 10.1080/10409238.2018.1431201. Epub 2018 Feb 07.

Biocatalysts have been increasingly used in the synthesis of fine chemicals and medicinal compounds due to significant advances in enzyme discovery and engineering. To mimic the synergistic effects of cascade reactions catalyzed by multiple enzymes in nature, researchers have...

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Wang Y, Ren H, Zhao H. Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Crit Rev Biochem Mol Biol. 2018;53(2):115-129doi: 10.1080/10409238.2018.1431201.
Wang, Y., Ren, H., & Zhao, H. (2018). Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Critical reviews in biochemistry and molecular biology, 53(2), 115-129. https://doi.org/10.1080/10409238.2018.1431201
Wang, Yajie, et al. "Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production." Critical reviews in biochemistry and molecular biology vol. 53,2 (2018): 115-129. doi: https://doi.org/10.1080/10409238.2018.1431201
Wang Y, Ren H, Zhao H. Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Crit Rev Biochem Mol Biol. 2018 Apr;53(2):115-129. doi: 10.1080/10409238.2018.1431201. Epub 2018 Feb 07. PMID: 29411648; PMCID: PMC6112242.
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Metabolic ensemble modeling for strain engineers.

Biotechnology journal

Tan Y, Liao JC.
PMID: 22021171
Biotechnol J. 2012 Mar;7(3):343-53. doi: 10.1002/biot.201100186. Epub 2011 Oct 21.

Previous mathematical modeling efforts have made significant contributions to the development of systems biology for predicting biological behavior quantitatively. However, dynamic metabolic model construction remains challenging due to uncertainties in mechanistic structures and parameters. In addition, parameter estimation and...

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Tan Y, Liao JC. Metabolic ensemble modeling for strain engineers. Biotechnol J. 2011;7(3):343-53doi: 10.1002/biot.201100186.
Tan, Y., & Liao, J. C. (2012). Metabolic ensemble modeling for strain engineers. Biotechnology journal, 7(3), 343-53. https://doi.org/10.1002/biot.201100186
Tan, Yikun, and Liao, James C. "Metabolic ensemble modeling for strain engineers." Biotechnology journal vol. 7,3 (2012): 343-53. doi: https://doi.org/10.1002/biot.201100186
Tan Y, Liao JC. Metabolic ensemble modeling for strain engineers. Biotechnol J. 2012 Mar;7(3):343-53. doi: 10.1002/biot.201100186. Epub 2011 Oct 21. PMID: 22021171.
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Showing 1 to 12 of 36 entries