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Jin, Yong-Su

Publications and source records attributed to Jin, Yong-Su.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

Kim, Haseong↗
DOE OSTI2024

Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates

Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid- tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low- pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Data for Self-Buffering System for Cost-Effective Production of Lactic Acid from Glucose and Xylose Using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis . I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

Conversion↗
DOE OSTI2023

Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

ABSTRACT Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dissecting the Division of Labor in Microbial Consortia for the Production of Biofuels and Chemicals (Final Technical Report)

The overarching objective of this project is to elucidate the fundamental design rules for microbial division of labor (DOL), the core of ecosystem organization, in the context of artificial yeast—lactic acid bacteria consortia that produce advanced biofuel and chemical from cellulosic biomass. Over the course of four years, we have successfully achieved the objective through three lines of research that combines experiment with mathematical modeling. Specifically, we have shown that compositional and temporal DOL is effective in modulating mixed sugar fermentation by an engineered consortium and uncovered general quantitative criteria for conditions under which microbial DOL outperforms single superbugs for simultaneous utilization of mixed substrates. We also demonstrated, in synthetic consortia of yeast and lactic acid bacteria, that partitioning the labor for substrate breakdown and end-product synthesis can allow an efficient production of 2-butanol that is difficult otherwise for a single yeast strain. Additionally, by systematically probing the stability of an engineered cooperative consortium, we found that the stability of microbial symbiosis is governed by the topological structure of the underlying cellular interactions rather than specific microbial species and that rational modulation of the interactions may facilitate the restoration of collapsed consortia as well as the intervention of target communities. Together, this project has advanced the fundamental knowledge of microbial DOL in terms of its strength in mixed substrate fermentation, production of complex chemicals, and ecological system stability in the context of microbial consortia. It also provides valuable insights into the design, construction and optimization of artificial consortia for the utilization of cellulosic biomass and economic production of biofuel and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

ABSTRACT Lipomyces tetrasporous is an oleaginous yeast that can utilize a variety of plant-based sugars. It accumulates lipids during growth on lignocellulosic biomass hydrolysates. We present the annotated genome sequence of L. tetrasporous NRRL Y-64009 to aid in its development as a platform organism for producing lipids and lipid-based bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Construction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloides

A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides. Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm 3 ) capable of generating an electron density of greater than 10 13 cm –3 was constructed to produce reactive species (N 2 *, N 2 +, O, OH, and H α ) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. In conclusion, this compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for Construction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloides

A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides . Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm3) capable of generating an electron density of greater than 1013 cm–3 was constructed to produce reactive species (N2*, N2+, O, OH, and Hα) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. This compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.

Conversion↗
DOE OSTI2023

Data for Glucose Assimilation Rate Determines the Partition of Flux at Pyruvate Between Lactic Acid and Ethanol in Saccharomyces cerevisiae

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L−1 from the 12 g L−1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.

Conversion↗
DOE OSTI2022

Data for A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach

A wide range of inorganic and organic chemicals are used during the pretreatment and enzymatic hydrolysis of lignocellulosic biomass to produce biofuels. Developing an industrially relevant 2G biorefinery process using such chemicals is challenging and requires more unit operations for downstream processing. A sustainable process has been developed to achieve industrially relevant titers of bioethanol with significant ethanol yield. The pretreatment of sorghum biomass was performed by a continuous pilot-scale hydrothermal reactor followed by disk milling. Enzymatic hydrolysis was performed without washing the pretreated biomass. Moreover, citrate buffer strength was reduced to 100-fold (50 mM to 0.5 mM) during the enzymatic hydrolysis. Enzymatic hydrolysis at 0.5 mM citrate buffer strength showed that significant sugar concentrations of 222 ± 2.3 to 241 ± 2.3 g/L (glucose + xylose) were attained at higher solids loadings of 50 to 60% (w/v). Furthermore, hydrolysates were fermented to produce bioethanol using two different xylose-fermenting Saccharomyces cerevisiae strains and a co-culture of xylose-fermenting and non-GMO yeast cultures. Bioethanol titer of 81.7 g/L was achieved with an ethanol yield of 0.48 gp/gs. Additionally, lipids were produced using the oleaginous yeast Rhodosporidium toruloides , yielding 13.2 g/L lipids with cellular lipid accumulation of 38.5% w/w from 100 g/L of sugar concentration. In summary, reducing the strength of the citrate buffer during enzymatic hydrolysis and omitting inorganic chemicals from the pretreatment process enhances the fermentability of hydrolysates and can also reduce operating costs.

Conversion↗
DOE OSTI2022

A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach

A wide range of inorganic and organic chemicals are used during the pretreatment and enzymatic hydrolysis of lignocellulosic biomass to produce biofuels. Developing an industrially relevant 2G biorefinery process using such chemicals is challenging and requires more unit operations for downstream processing. A sustainable process has been developed to achieve industrially relevant titers of bioethanol with significant ethanol yield. The pretreatment of sorghum biomass was performed by a continuous pilot-scale hydrothermal reactor followed by disk milling. Enzymatic hydrolysis was performed without washing the pretreated biomass. Moreover, citrate buffer strength was reduced to 100-fold (50 mM to 0.5 mM) during the enzymatic hydrolysis. Enzymatic hydrolysis at 0.5 mM citrate buffer strength showed that significant sugar concentrations of 222 ± 2.3 to 241 ± 2.3 g/L (glucose + xylose) were attained at higher solids loadings of 50 to 60% (w/v). Furthermore, hydrolysates were fermented to produce bioethanol using two different xylose-fermenting Saccharomyces cerevisiae strains and a co-culture of xylose-fermenting and non-GMO yeast cultures. Bioethanol titer of 81.7 g/L was achieved with an ethanol yield of 0.48 gp/gs. Additionally, lipids were produced using the oleaginous yeast Rhodosporidium toruloides, yielding 13.2 g/L lipids with cellular lipid accumulation of 38.5% w/w from 100 g/L of sugar concentration. In summary, reducing the strength of the citrate buffer during enzymatic hydrolysis and omitting inorganic chemicals from the pretreatment process enhances the fermentability of hydrolysates and can also reduce operating costs.

Deshavath, Narendra Naik↗
DOE OSTI2022

Data for Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides

Engineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2-pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value-added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency, and yield.

Conversion↗
DOE OSTI2022

Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates

Issatchenkia orientalis, exhibiting high tolerance against harsh environmental conditions, is a promising metabolic engineering host for producing fuels and chemicals from cellulosic hydrolysates containing fermentation inhibitors under acidic conditions. Although genetic tools for I. orientalis exist, they require auxotrophic mutants so that the selection of a host strain is limited. We developed a drug resistance gene (cloNAT)-based genome-editing method for engineering any I. orientalis strains and engineered I. orientalis strains isolated from various sources for xylose fermentation. Specifically, xylose reductase, xylitol dehydrogenase, and xylulokinase from Scheffersomyces stipitis were integrated into an intended chromosomal locus in four I. orientalis strains (SD108, IO21, IO45, and IO46) through Cas9-based genome editing. Furthermore, the resulting strains (SD108X, IO21X, IO45X, and IO46X) efficiently produced ethanol from cellulosic and hemicellulosic hydrolysates even though the pH adjustment and nitrogen source were not provided. As they presented different fermenting capacities, selection of a host I. orientalis strain was crucial for producing fuels and chemicals using cellulosic hydrolysates.

09 BIOMASS FUELS↗
DOE OSTI2022

Rewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant production

Rising concerns for sustainability and global climate change have driven the development of sustainable pro- duction pathways for biofuels and chemicals from lignocellulosic biomass via integrated biological and chemical processes. We constructed an engineered Saccharomyces cerevisiae capable of producing 2,3-butanediol (2,3-BDO) from glucose without accumulating ethanol and glycerol, which hinder downstream processing of 2,3-BDO, through extensive metabolic reprogramming. Specifically, we introduced heterologous 2,3-BDO biosynthetic enzymes and deleted the major isozymes of ethanol and glycerol biosynthetic enzymes. In addition, we introduced an NAD + regenerating Pyruvate-Malate (PM) cycle and enhanced the NAD + regenerating capability of the PM cycle to resolve the redox imbalance from the deletion of ethanol and glycerol production pathways. The resulting engineered yeast produced 109.9 g/L of 2,3-BDO with a productivity of 1.0 g/L/h and a yield of 0.36 g/ g glucose in a fed-batch fermentation. We also conducted techno-economic analysis (TEA) and life cycle assessment (LCA) of the production of methyl ethyl ketone (MEK) through catalytic dehydration of 2,3-BDO. A TEA based on the experimental results indicated that the minimum product selling price (MPSP) was estimated to be $1.90/kg. Regarding cradle-to-grave LCA, 100-year global warming potential (GWP100) and fossil energy consumption (FEC) were found to be 0.37 kg CO 2 eq/kg and 3.1 MJ/kg, respectively. These results demonstrated the feasibility of cost-competitive and sustainable bio-based MEK production via yeast fermentation. In addition, we explored the possibility of using the fermentation broth containing 2,3-BDO as a biostimulant inducing drought tolerance in plants. As a result, the yeast 2,3-BDO fermentation broth can induce drought tolerance in Arabidopsis thaliana without a complicated purification process.

2,3-butanediol (2,3-BDO)↗
DOE OSTI2022

Systems analysis of Lipomyces starkeyi during growth on various plant-based sugars

Oleaginous yeasts have received significant attention due to their substantial lipid storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. Furthermore, this analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

raogroupuiuc/lipo11557_growth

Project: Systems analysis of Lipomyces starkeyi during growth on various plant-based sugars Authors: Anshu Deewan*, Jing-Jing Liu*, Sujit Sadashiv Jagtap, Eun Ju Yun, Hanna E Walukiewicz, Yong-Su Jin, Christopher V Rao (* - co-authors) Abstract : Oleaginous yeasts have received significant attention due to their substantial lipids storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. This analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels.

Deewan, Anshu↗