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

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Yeast Pathway Kit : A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. / Pereira, Filipa; Azevedo, Flávio; Parachin, Nadia Skorupa; Hahn-Hägerdal, Bärbel; Gorwa-Grauslund, Marie F.; Johansson, Björn.

In: ACS Synthetic Biology, Vol. 5, No. 5, 20.05.2016, p. 386-394.

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Pereira, Filipa ; Azevedo, Flávio ; Parachin, Nadia Skorupa ; Hahn-Hägerdal, Bärbel ; Gorwa-Grauslund, Marie F. ; Johansson, Björn. / Yeast Pathway Kit : A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. In: ACS Synthetic Biology. 2016 ; Vol. 5, No. 5. pp. 386-394.

RIS

TY - JOUR

T1 - Yeast Pathway Kit

T2 - ACS Synthetic Biology

AU - Pereira, Filipa

AU - Azevedo, Flávio

AU - Parachin, Nadia Skorupa

AU - Hahn-Hägerdal, Bärbel

AU - Gorwa-Grauslund, Marie F.

AU - Johansson, Björn

PY - 2016/5/20

Y1 - 2016/5/20

N2 - 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.

AB - 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.

KW - bioinformatics

KW - d -xylose

KW - metabolic engineering

KW - Saccharomyces cerevisiae

KW - synthetic biology

UR - http://www.scopus.com/inward/record.url?scp=84973164107&partnerID=8YFLogxK

U2 - 10.1021/acssynbio.5b00250

DO - 10.1021/acssynbio.5b00250

M3 - Article

VL - 5

SP - 386

EP - 394

JO - ACS Synthetic Biology

JF - ACS Synthetic Biology

SN - 2161-5063

IS - 5

ER -