Yeast Pathway Kit : A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation
(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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- author
- Pereira, Filipa ; Azevedo, Flávio ; Parachin, Nadia Skorupa LU ; Hahn-Hägerdal, Bärbel LU ; Gorwa-Grauslund, Marie F. LU and Johansson, Björn LU
- organization
- publishing date
- 2016-05-20
- 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
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:84973164107
- pmid:26916955
- 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
- 2024-03-07 21:17:25
@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}},
keywords = {{bioinformatics; d -xylose; metabolic engineering; Saccharomyces cerevisiae; synthetic biology}},
language = {{eng}},
month = {{05}},
number = {{5}},
pages = {{386--394}},
publisher = {{The 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}},
doi = {{10.1021/acssynbio.5b00250}},
volume = {{5}},
year = {{2016}},
}