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    PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes

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    Name:
    PATHcre8 for KAUST Repository.pdf
    Size:
    1.328Mb
    Format:
    PDF
    Description:
    Accepted manuscript
    Embargo End Date:
    2021-11-17
    Download
    Type
    Article
    Authors
    Motwalli, Olaa Amin cc
    Uludag, Mahmut cc
    Mijakovic, Ivan cc
    Alazmi, Meshari cc
    Bajic, Vladimir B. cc
    Gojobori, Takashi cc
    Gao, Xin cc
    Essack, Magbubah cc
    KAUST Department
    Applied Mathematics and Computational Science Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Structural and Functional Bioinformatics Group
    KAUST Grant Number
    BAS/1/1059-01-01
    BAS/1/1606-01-01
    BAS/1/1624-01-01
    FCC/1/1976-02-01
    FCC/1/1976-17-01
    FCC/1/1976-26-01
    Date
    2020-11-16
    Embargo End Date
    2021-11-17
    Submitted Date
    2020-02-02
    Permanent link to this record
    http://hdl.handle.net/10754/666037
    
    Metadata
    Show full item record
    Abstract
    Developing computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand, the preferred host organisms may not have the native metabolic reactions needed to produce the compound of interest; thus, the computational tool needs to identify the metabolic reactions that will most efficiently produce the desired product. In this regard, we developed the generic tool PATHcre8 to facilitate an optimized search for heterologous biosynthetic pathway routes. PATHcre8 finds and ranks biosynthesis routes in a large number of organisms, including Cyanobacteria. The tool ranks the pathways based on feature scores that reflect reaction thermodynamics, the potentially toxic products in the pathway (compound toxicity), intermediate products in the pathway consumed by competing reactions (product consumption), and host-specific information such as enzyme copy number. A comparison with several other similar tools shows that PATHcre8 is more efficient in ranking functional pathways. To illustrate the effectiveness of PATHcre8, we further provide case studies focused on isoprene production and the biodegradation of cocaine. PATHcre8 is free for academic and nonprofit users and can be accessed at https://www.cbrc.kaust.edu.sa/pathcre8/.
    Citation
    Motwalli, O., Uludag, M., Mijakovic, I., Alazmi, M., Bajic, V. B., Gojobori, T., … Essack, M. (2020). PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes. ACS Synthetic Biology. doi:10.1021/acssynbio.0c00058
    Sponsors
    This work has been supported by the King Abdullah University of Science and Technology (KAUST) Base Research Fund BAS/1/1606-01-01, BAS/1/1059-01-01, BAS/1/1624-01-01, as well as through the Awards No. FCC/1/1976-02-01, FCC/1/1976-17-01, FCC/1/1976-16-01, and FCC/1/1976-26-01 from the KAUST Office of Sponsored Research (OSR). Also, the Novo Nordisk Foundation Grant NNF10CC1016517 awarded to IM.
    Publisher
    American Chemical Society (ACS)
    Journal
    ACS Synthetic Biology
    DOI
    10.1021/acssynbio.0c00058
    PubMed ID
    33198455
    Additional Links
    https://pubs.acs.org/doi/10.1021/acssynbio.0c00058
    ae974a485f413a2113503eed53cd6c53
    10.1021/acssynbio.0c00058
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Structural and Functional Bioinformatics Group; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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