Pathway design

Pathway design (also called metabolic engineering ) is a method of biochemistry in which the metabolic pathways are changed by protein design . Pathway design is a form of rational design .

properties

In pathway design, protein design changes existing enzymes in such a way that the substrate or product is also changed. Likewise, by supplementing the genome with genes from enzymes, new enzymes can be introduced into an organism; in the case of bacteria, this is usually done with a plasmid . As a result, new metabolic pathways can be constructed in an organism or existing ones can be modified, e.g. B. to avoid metabolite damage . The development process can be accelerated through a modular approach.

Selenzyme is an online database for selecting enzymes in pathway design.

literature

Huimin Zhao: Synthetic Biology - Metabolic Engineering. Springer, 2017, ISBN 978-3-319-55318-4 , p. 81.
A. Kumar, L. Wang, CY Ng, CD Maranas: Pathway design using de novo steps through uncharted biochemical spaces. In: Nature Communications . Volume 9, number 1, 01 2018, p. 184, doi : 10.1038 / s41467-017-02362-x , PMID 29330441 , PMC 5766603 (free full text).
Z. Chen, AP Zeng: Protein engineering approaches to chemical biotechnology. In: Current Opinion in Biotechnology. Volume 42, December 2016, pp. 198–205, doi : 10.1016 / j.copbio.2016.07.007 , PMID 27525565 .
B. Delépine, T. Duigou, P. Carbonell, JL Faulon: RetroPath2.0: A retrosynthesis workflow for metabolic engineers. In: Metabolic engineering. Volume 45, January 2018, pp. 158-170, doi : 10.1016 / j.ymben.2017.12.002 , PMID 29233745 .

Individual evidence

↑ J. Sun, JG Jeffryes, CS Henry, SD Bruner, AD Hanson metabolites damage and repair in metabolic engineering design. In: Metabolic engineering. Volume 44, November 2017, pp. 150-159, doi : 10.1016 / j.ymben.2017.10.006 , PMID 29030275 .
↑ JT Boock, A. Gupta, KL Prather: Screening and modular design for metabolic pathway optimization. In: Current Opinion in Biotechnology. Volume 36, December 2015, pp. 189-198, doi : 10.1016 / j.copbio.2015.08.013 , PMID 26432992 .
^ H. Taniguchi, K. Okano, K. Honda: Modules formetabolic engineering: Pathway assembly for bio-based production of value-added chemicals. In: Synthetic and systems biotechnology. Volume 2, number 2, June 2017, pp. 65-74, doi : 10.1016 / j.synbio.2017.06.002 , PMID 29062963 , PMC 5636945 (free full text).
^ P. Carbonell, J. Wong, N. Swainston, E. Takano, NJ Turner, NS Scrutton, DB Kell, R. Breitling, JL Faulon, O. Stegle: Selenzyme: Enzyme selection tool for pathway design. In: Bioinformatics. [electronic publication before printing] February 2018, doi : 10.1093 / bioinformatics / bty065 , PMID 29425325 .

[1] J. Sun, JG Jeffryes, CS Henry, SD Bruner, AD Hanson metabolites damage and repair in metabolic engineering design. In: Metabolic engineering. Volume 44, November 2017, pp. 150-159, doi : 10.1016 / j.ymben.2017.10.006 , PMID 29030275 .

[2] JT Boock, A. Gupta, KL Prather: Screening and modular design for metabolic pathway optimization. In: Current Opinion in Biotechnology. Volume 36, December 2015, pp. 189-198, doi : 10.1016 / j.copbio.2015.08.013 , PMID 26432992 .

[3] H. Taniguchi, K. Okano, K. Honda: Modules formetabolic engineering: Pathway assembly for bio-based production of value-added chemicals. In: Synthetic and systems biotechnology. Volume 2, number 2, June 2017, pp. 65-74, doi : 10.1016 / j.synbio.2017.06.002 , PMID 29062963 , PMC 5636945 (free full text).

[4] P. Carbonell, J. Wong, N. Swainston, E. Takano, NJ Turner, NS Scrutton, DB Kell, R. Breitling, JL Faulon, O. Stegle: Selenzyme: Enzyme selection tool for pathway design. In: Bioinformatics. [electronic publication before printing] February 2018, doi : 10.1093 / bioinformatics / bty065 , PMID 29425325 .