Abstract
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.
Highlights
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
We used the DNA assembler method [14] to construct a plasmid, which was derived from pRS415, containing the I. orientalis uracil auxotrophic selection marker (IoURA3), Saccharomyces cerevisiae (ScARS), S. cerevisiae LEU2 (ScLEU2), and a green fluorescent protein (GFP) gene as a reporter (Fig. 1A)
1000 colonies were obtained with 500 ng pIo-UG by heat shock transformation, and around 55% of the cells cultured in liquid media could express the GFP at a symmetric peak for at least 5 days (Fig. 1B)
Summary
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. 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. The results outlined in this paper describe a stable episomal ARScontaining 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. Owing to its extraordinary tolerance to multiple stresses, including extremely low-pH conditions, Issatchenkia orientalis is a promising platform microorganism for the production of organic acids It was previously used in ethanol fermentation at pH 2 [1] and engineered to produce succinic acid [2] and lactic acid [3]. Our optimized CRISPR/Cas system represents a powerful tool for comprehensive metabolic engineering of I. orientalis to produce biofuels and chemicals
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