A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

D'Ambrosio, Vasil; Hansen, Lea G.; Zhang, Jie; Jensen, Emil D.; Arsovska, Dushica; Laloux, Marcos; Jakočiūnas, Tadas; Hjort, Pernille; De Lucrezia, Davide; Marletta, Serena; Keasling, Jay D.; Jensen, Michael K.

doi:10.1016/j.synbio.2022.02.001

Title: A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

Journal Article · 15 February 2022 · Synthetic and Systems Biotechnology

DOI: https://doi.org/10.1016/j.synbio.2022.02.001 · OSTI ID:2470800

D'Ambrosio, Vasil ^[1];

^[1]; Zhang, Jie ^[1]; Jensen, Emil D. ^[1]; Arsovska, Dushica ^[1]; Laloux, Marcos ^[1];

^[1]; Hjort, Pernille ^[1];

^[2]; Marletta, Serena ^[2];

^[3];

^[1]

Technical University of Denmark, Lyngby (Denmark)
Explora Biotech Srl (Italy)
Technical University of Denmark, Lyngby (Denmark); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California, Berkeley, CA (United States); Shenzhen Institutes of Advanced Technologies (China)

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: BioInnovation Institute Foundation; Horizon 2020; Novo Nordisk Foundation; USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2470800

Journal Information:: Synthetic and Systems Biotechnology, Journal Name: Synthetic and Systems Biotechnology Journal Issue: 2 Vol. 7; ISSN 2405-805X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
Promoter
Standardization
Terminator
Yeast
gRNA

Title: A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

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