Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation

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Bibtex

@article{3261439737b743558384668ec7ae84fd,
title = "Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation",
abstract = "We have developed the Yeast Pathway Kit (YPK) for rational and random metabolic pathway assembly in Saccharomyces cerevisiae using reusable and redistributable genetic elements. Genetic elements are cloned in a suicide vector in a rapid process that omits PCR product purification. Single-gene expression cassettes are assembled in vivo using genetic elements that are both promoters and terminators (TP). Cassettes sharing genetic elements are assembled by recombination into multigene pathways. A wide selection of prefabricated TP elements makes assembly both rapid and inexpensive. An innovative software tool automatically produces detailed self-contained executable documentation in the form of pydna code in the narrative Jupyter notebook format to facilitate planning and sharing YPK projects. A d-xylose catabolic pathway was created using YPK with four or eight genes that resulted in one of the highest growth rates reported on d-xylose (0.18 h-1) for recombinant S. cerevisiae without adaptation. The two-step assembly of single-gene expression cassettes into multigene pathways may improve the yield of correct pathways at the cost of adding overall complexity, which is offset by the supplied software tool.",
keywords = "bioinformatics, d -xylose, metabolic engineering, Saccharomyces cerevisiae, synthetic biology",
author = "Filipa Pereira and Fl{\'a}vio Azevedo and Parachin, {Nadia Skorupa} and B{\"a}rbel Hahn-H{\"a}gerdal and Gorwa-Grauslund, {Marie F.} and Bj{\"o}rn Johansson",
year = "2016",
month = "5",
day = "20",
doi = "10.1021/acssynbio.5b00250",
language = "English",
volume = "5",
pages = "386--394",
journal = "ACS Synthetic Biology",
issn = "2161-5063",
publisher = "The American Chemical Society (ACS)",
number = "5",

}