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Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis has emerged as a potential platform microorganism for production of organic acids due to its ability to grow robustly under highly acidic conditions. However, lack of efficient genetic tools remains a major bottleneck in metabolic engineering of this...

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Autores principales: Tran, Vinh G., Cao, Mingfeng, Fatma, Zia, Song, Xiaofei, Zhao, Huimin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595149/
https://www.ncbi.nlm.nih.gov/pubmed/31243078
http://dx.doi.org/10.1128/mSphere.00345-19
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author Tran, Vinh G.
Cao, Mingfeng
Fatma, Zia
Song, Xiaofei
Zhao, Huimin
author_facet Tran, Vinh G.
Cao, Mingfeng
Fatma, Zia
Song, Xiaofei
Zhao, Huimin
author_sort Tran, Vinh G.
collection PubMed
description The nonconventional yeast Issatchenkia orientalis has emerged as a potential platform microorganism for production of organic acids due to its ability to grow robustly under highly acidic conditions. However, lack of efficient genetic tools remains a major bottleneck in metabolic engineering of this organism. Here we report that the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) was functional for plasmid replication in I. orientalis, and the resulting episomal plasmid enabled efficient genome editing by the CRISPR/Cas9 system. The optimized CRISPR/Cas9-based system employed a fusion RPR1′-tRNA promoter for single guide RNA (sgRNA) expression and could attain greater than 97% gene disruption efficiency for various gene targets. Additionally, we demonstrated multiplexed gene deletion with disruption efficiencies of 90% and 47% for double gene and triple gene knockouts, respectively. This genome editing tool can be used for rapid strain development and metabolic engineering of this organism for production of biofuels and chemicals. IMPORTANCE Microbial production of fuels and chemicals from renewable and readily available biomass is a sustainable and economically attractive alternative to petroleum-based production. Because of its unusual tolerance to highly acidic conditions, I. orientalis is a promising potential candidate for the manufacture of valued organic acids. Nevertheless, reliable and efficient genetic engineering tools in I. orientalis are limited. The results outlined in this paper describe a stable episomal ARS-containing plasmid and the first CRISPR/Cas9-based system for gene disruptions in I. orientalis, paving the way for applying genome engineering and metabolic engineering strategies and tools in this microorganism for production of fuels and chemicals.
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spelling pubmed-65951492019-07-03 Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis Tran, Vinh G. Cao, Mingfeng Fatma, Zia Song, Xiaofei Zhao, Huimin mSphere Research Article The nonconventional yeast Issatchenkia orientalis has emerged as a potential platform microorganism for production of organic acids due to its ability to grow robustly under highly acidic conditions. However, lack of efficient genetic tools remains a major bottleneck in metabolic engineering of this organism. Here we report that the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) was functional for plasmid replication in I. orientalis, and the resulting episomal plasmid enabled efficient genome editing by the CRISPR/Cas9 system. The optimized CRISPR/Cas9-based system employed a fusion RPR1′-tRNA promoter for single guide RNA (sgRNA) expression and could attain greater than 97% gene disruption efficiency for various gene targets. Additionally, we demonstrated multiplexed gene deletion with disruption efficiencies of 90% and 47% for double gene and triple gene knockouts, respectively. This genome editing tool can be used for rapid strain development and metabolic engineering of this organism for production of biofuels and chemicals. IMPORTANCE Microbial production of fuels and chemicals from renewable and readily available biomass is a sustainable and economically attractive alternative to petroleum-based production. Because of its unusual tolerance to highly acidic conditions, I. orientalis is a promising potential candidate for the manufacture of valued organic acids. Nevertheless, reliable and efficient genetic engineering tools in I. orientalis are limited. The results outlined in this paper describe a stable episomal ARS-containing plasmid and the first CRISPR/Cas9-based system for gene disruptions in I. orientalis, paving the way for applying genome engineering and metabolic engineering strategies and tools in this microorganism for production of fuels and chemicals. American Society for Microbiology 2019-06-26 /pmc/articles/PMC6595149/ /pubmed/31243078 http://dx.doi.org/10.1128/mSphere.00345-19 Text en Copyright © 2019 Tran et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Tran, Vinh G.
Cao, Mingfeng
Fatma, Zia
Song, Xiaofei
Zhao, Huimin
Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title_full Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title_fullStr Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title_full_unstemmed Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title_short Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis
title_sort development of a crispr/cas9-based tool for gene deletion in issatchenkia orientalis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595149/
https://www.ncbi.nlm.nih.gov/pubmed/31243078
http://dx.doi.org/10.1128/mSphere.00345-19
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