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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 LU ; Hahn-Hägerdal, Bärbel LU ; Gorwa-Grauslund, Marie F. LU and Johansson, Björn LU (2016) In ACS Synthetic Biology 5(5). p.386-394
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... (More)

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.

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Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
bioinformatics, d -xylose, metabolic engineering, Saccharomyces cerevisiae, synthetic biology
in
ACS Synthetic Biology
volume
5
issue
5
pages
9 pages
publisher
American Chemical Society (ACS)
external identifiers
  • scopus:84973164107
  • wos:000376476900003
ISSN
2161-5063
DOI
10.1021/acssynbio.5b00250
language
English
LU publication?
yes
id
32614397-37b7-4355-8384-668ec7ae84fd
date added to LUP
2017-01-30 10:27:16
date last changed
2017-09-18 11:34:41
@article{32614397-37b7-4355-8384-668ec7ae84fd,
  abstract     = {<p>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<sup>-1</sup>) 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.</p>},
  author       = {Pereira, Filipa and Azevedo, Flávio and Parachin, Nadia Skorupa and Hahn-Hägerdal, Bärbel and Gorwa-Grauslund, Marie F. and Johansson, Björn},
  issn         = {2161-5063},
  keyword      = {bioinformatics,d -xylose,metabolic engineering,Saccharomyces cerevisiae,synthetic biology},
  language     = {eng},
  month        = {05},
  number       = {5},
  pages        = {386--394},
  publisher    = {American Chemical Society (ACS)},
  series       = {ACS Synthetic Biology},
  title        = {Yeast Pathway Kit : A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation},
  url          = {http://dx.doi.org/10.1021/acssynbio.5b00250},
  volume       = {5},
  year         = {2016},
}