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Molecular and Systems Biotechnology Lab @ UIUC

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Kew words Peer-reviewed articles 2015 Li, X., Vivian, Y.Y., Lin, Y., Chomvong, K., Estrela, R., Liang, J.M., Znameroski, E.A., Feehan, J., Kim, S.R., Jin, Y.S., Glass, N.L., Cate, J.H.D. (2014). Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels. eLife Link Lewis, Z.T., Totten, S.M., Smilowitz, J.T., Popovic, M., Parker, E., Lemay, D.G., Van Tassell, M.L., Miller, M.J., Jin, Y.S., German, J.B., Lebrilla, C.B., Mills, D.A. Maternal Fucosyltransferase 2 Status Affects the Gut Bifidobacterial Communities of Breastfed Infants. Microbiome (accepted) Yi, W., Zhang, X., Seo, S., Choi, K., Ting, L., Jin, Y.S., Hans, B. Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system. Journal of Biotechnology (accepted) Wei, N., Oh, E.J., Million, G., Cate, J., Jin, Y.S. Simultaneous utilization of cellobiose, xylose, and acetic acid from lignocellulosic biomass for biofuel production by an engineered yeast platform. ACS Synthetic Biology (accepted) 2014 Kim, S.R., Xu, H., Lesmana, A., Kuzmanovic, U., Au, M., Florencia, C., Oh, E.J., Zhang, G., Kim, H.K., and Jin, Y.S. Deletion of PHO13 encoding HAD type IIA phosphatase results in upregulation of the pentose phosphate pathway in yeast. Applied and Environmental Microbiology (accepted) Quarterman, J., Kim, S.R., Kim, P.J., Jin, Y.S. Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening. Journal of Biotechnology Link Kim, T. Y., Oh, E. J., Jin, Y. S., Oh, M. K. Improved resistance against oxidative stress of engineered cellobiose-fermenting Saccharomyces cerevisiae revealed by metabolite profiling. Biotechnology and Bioprocess Engineering, 19(6), 951-957. Link Lane, S., Zhang, S., Wei, N., Rao, C., Jin, Y.S. Development and Physiological Characterization of Cellobiose-Consuming Yarrowia lipolytica. Biotechnology & Bioengineering (in press) Zhang, G., Kong, I.I., Kim, H., Liu, J., Cate, J.H.D., Jin, Y.S. Construction of a quadruple auxotrophic mutant of an industrial polyploidy Saccharomyces cerevisiae using RNA-guided Cas9 nuclease. Applied and Environmental Microbiology Link Tsai, C.S., Kwak, S., Turner, T.L., Jin, Y.S. Yeast synthetic biology toolbox and applications for biofuel production. FEMS Yeast Research (accepted) Link Lin, Y., Chomvong, L., Acosta-Sampson, L., Estrela, R., Galazka, J.M., Kim, S.R., Jin, Y.S., Cate, J.H.D. Leveraging transcription factors to speed cellobiose fermentation by Saccharomyces cerevisiae. Biotechnology for Biofuels Link Chomvong, K., Kordic, V., Li, X., Bauer, S., Gillespie. A.E., Ha, S.J., Oh, E.J., Galazka, J.M., Jin, Y.S., Cate, J.H. Overcoming inefficient cellobiose fermentation by cellobiose phosphorylase in the presence of xylose. Biotechnology for Biofuels Link Hong, N., Seo, S.S., Oh, E.J., Seo, J.H., Cate, J.H., Jin, Y.S. 2,3-Butanediol production from cellobiose by engineered Saccharomyces cerevisiae. Applied Microbiology and Biotechnology Link Kim, S.J., Seo, S.O., Park, Y.C., Jin, Y.S., Seo, J.H. Production of 2,3-Butanediol from xylose by engineered Saccharomyces cerevisiae. Journal of Biotechnology Link 2013 Bae, Y.H., Kang, K.H., Jin, Y.S., Seo, J.H. Molecular cloning and expression of fungal cellobiose transporters and β-glucosidases conferring efficient cellobiose fermentation in Saccharomyces cerevisiae. Journal of Biotechnology, 169, 34-41 Link Kim, H., Lee, W.H., Galazka, J.M., Cate, J.H., Jin, Y.S. Analysis of cellodextrin transporters from Neurospora crassa in Saccharomyces cerevisiae for cellobiose fermentation. Applied Microbiology and Biotechnology, 1-8 Link Ha, S.J., Kim, S.R., Kim, H., Du, J., Cate, J.H., Jin, Y.S. Continuous co-fermentation of cellobiose and xylose by engineered Saccharomyces cerevisiae. Bioresource Technology, 149, 525-531 Link Wei, N., Quarterman, J., Kim, S.R., Cate, J.H., Jin, Y.S. Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast. Nature Communications 4, 2580. Link, News Release from Natureasia, Inside Illinois, BBC News Li, S., Ha, S.J., Kim, H.J., Galazka, J.M., Cate, J.H., Jin, Y.S., Zhao, H. Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization. Journal of Biotechnology 168, 1-6. Link Kim, H.J., Lee, H.R., Kim, C.S., Jin, Y.S., Seo, J.H. Investigation of protein expression profiles of erythritol-producing Candida magnoliae in response to glucose perturbation. Enzyme and Microbial Technology 53, 174-180 Link Kim, H.J., Turner, T.L., Jin, Y.S. Combinatorial genetic perturbation to refince metabolic circuits for producing biofuels and biochemicals. Biotechnology Advances 31, 976-985 Link Kim, S.J., Seo, S.O., Jin, Y.S., Seo, J.H. Production of 2,3-butanediol by engineered Saccharomyces cerevisiae. Bioresource Technology 146, 274-281 Link Wang, Y., Li, X.Z., Milne, C., Janssen, H., Lin, W., Phan, G., Hu, H., Jin, Y.S., Price, N., Blaschek, H. Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. Applied and Environmental Microbiology 79, 5853-5863 Link Lee, W.H., Nan, H., Kim, H.J., Jin, Y.S. Simultaneous saccharification and fermentation by engineered Saccharomyces cerevisiae without supplementing extracellular beta-glucosidase. Journal of Biotechnology 167, 316-322 Link Kim, S.R., Park, Y.C., Jin, Y.S., Seo, J.H. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnology Advances 31, 851-861 Link Wei, N., Xu, H., Kim, S.R., & Jin, Y.S. Deletion of FPS1 coding for aquaglyceroporin Fps1p improves xylose fermentation by engineered Saccharomyces cerevisiae. Applied and Environmental Microbiology Link Kim, S.R., Kwee, N.R., Kim, H.J. & Jin, Y.S. Feasibility of xylose fermentation by engineered Saccharomyces cerevisiae overexpressing endogenous aldose reductase (GRE3), xylitol dehydrogenase (XYL2) and xylulokinase (XYL3) from Scheffersomyces stipitis. FEMS Yeast Research Link Lee, W.H., Kim, M.D., Jin, Y.S. & Seo, J.H. Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation. Applied Microbiology and Biotechnology Link Kim, S.R., Skerker, J.M., Kang, W., Lesmana, A., Wei, N., Arkin, A.P. & Jin, Y.S. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLOS One Link Kim, S.R., Lee, K.S., Kong, I.K., Lesmana, A., Lee, W.H., Seo, J.H., Kweon, D.H. & Jin, Y.S. Construction of an efficient xylose-fermenting diploid Saccharomyces cerevisiae strain through mating of two engineered haploid strains capable of xylose assimilation. Journal of Biotechnology Link 2012 Guo, B., Zhang, Y., Yu, G., Lee, W.H., Jin, Y.S.& Morgenroth, E., Two-stage acidic-alkaline hydrothermal pretreatment of lignocellulose for the high recovery of cellulose and hemicellulose sugars. Applied Biochemistry and Biotechnology Link Ha,S.J., Kim, H., Lin, Y., Jang, M.U., Galazka, J.M., Kim, T.J., Cate. J.H. & Jin, Y.S. Single amino acid substitutions of HXT2.4 from Scheffersomyces stipitis lead to improved cellobiose fermentation by engineered Saccharomyces cerevisiae. Applied and Environmental Microbiology Link Ha, S.J., Galazka, J.M., Oh, E.J., Kordic, V., Kim, H., Jin, Y.S., & Cate, J.H. Energetic benefits and rapid cellobiose fermentation by Saccharomyces cerevisiae expressing cellobiose phosphorylase and mutant cellodextrin transporters. Metabolic Engineering Link Wei, N. Quarterman, J., & Jin, Y.S. Marine macroalgae: an untapped resource for producing fuels and chemicals. Trends in Biotechnol. Link Oh, E.J., Ha, S.J., Kim, S.R., Lee, W.H., Galazka, J.M., Cate, J.H. & Jin, Y.S. Enhanced xylitol production through simultaneous co-utilization of cellobiose and xylose by engineered Saccharomyces cerevisiae. Metabolic Engineering Link Lee, K.S., Kim, J.S., Heo, P., Yang, T.J., Sung, Y.J., Cheon, Y., Koo, H.M., Yu, B.J., Seo, J.H., Jin, Y.S., Park, J.C., Kweon, D.H. Characterization of Saccharomyces cerevisiae promoters for heterologous gene expression in Kluyveromyces marxianus. Appl Microbiol Biotechnol Link Lee, W.H., Pathanibul, P., Quarterman, J., Jo, J.H., Han, N.S., Miller, M.J., Jin, Y.S.& Seo, J.H. Whole cell biosynthesis of a functional oligosaccharide, 2-fucosyllactose, using engineered Escherichia coli. Microbial Cell Factories 11, 48 Link Lee, W.H., Seo, S.O., Bae, Y.H., Nan, H., Jin, Y.S.& Seo, J.H. Isobutanol production in engineered Saccharomyces cerevisiae by overexpression of 2-ketoisovalerate decarboxylase and valine biosynthetic enzymes. Bioprocess and Biosystems Engineering 35, 1467-75 Link Kim, S.R., Ha, S.J., Kong, I.I., & Jin, Y.S. High expression of XYL2 coding for xylitol dehydrogenase is necessary for efficient xylose fermentation by engineered Saccharomyces cerevisiae Metab. Eng. 14, 336-343 Link Guo, B., Zhang, Y., Ha, S. J., Jin, Y.S.& Morgenroth, E. Combined biomimetic and inorganic acids hydrolysis of hemicellulose in Miscanthus for bioethanol production. Bioresource Technol 110,278-87 Link Kim, S.R., Ha, S.J., Wei, N., Oh, E.J., & Jin, Y.S. Simultaneous co-fermenation of mixed sugars: a promising strategy for producing cellulosic ethnaol. Trend Biotechnol 30,274–282 Link Jin, Y.S. & Cate, J.H. Model-guided strain improvement: Simultaneous hydrolysis and co-fermentation of cellulosic sugars. Biotechnol. J. 7,361-73. Link Cha, C., Kim, S.R., Jin, Y.S. & Kong, H.J. Tuning structural durability of yeast-encapsulating alginate gel beads with interpenetrating networks for sustained bioethanol production. Biotechnol. Bioeng. 109,63-73 Link 2011 Lu, C.H., Choi, J.H., Engelmann Moran, N., Jin, Y.S. & Erdman, J. Laboratory-scale production of 13C-labeled lycopene and phytoene by bioengineered Escherichia. J Agric Food Chem Link Kim, J.S., Heo P., Yang. T.J., Lee, K.S., Jin Y.S., Kim, S. K., Shin, D. & Kweon, D.H. Bacterial persisters tolerate antibiotics by not producing hydroxyl radicals. Biochem. Biophys. Res. Commun. Link Milne, C.B., Eddy, J.A., Raju, R., Ardekani,S., Kim, P.J., Senger, R. S., Jin, Y.S., Blaschek, H.P. & Price, N.D. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 BMC Systems Biology 5:130. Link Ha, S.J., Wei, Q., Kim, S.R., Galazka, J., Cate, J.H. & Jin, Y.S. Co-fermentation of cellobiose and galactose by an engineered Saccharomyces cerevisiae. Appl. Environ. Microbiol. 77, 5822-5826. Link, Related News Ha, S.J., Kim, S.R., Choi J.H., Park, M.S. & Jin Y.S. Xylitol does not inhibit xylose fermentation by engineered Saccharomyces cerevisiae expressing xylA as severely as it inhibits xylose isomerase reaction in vitro. Appl Microbiol Biotechnol Link Ha, S.J., Galazka J.M., Rin Kim S., Choi J.H., Yang X., Seo J.H., Louise Glass N., Cate J.H., & Jin Y.S.Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci U S A. 108, 504-509 (2011) Link,In This Issue-PNAS, Related News Lee, K.S., Hong, M.E., Jung, S.C., Ha, S.J., Yu, B.J., Koo, H.M., Park, S.M., Seo, J.H., Kweon, D.H., Park, J.C. & Jin, Y.S. Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering. Biotechnol Bioeng. 108, 621-632. Link 2010 Kim, S.R., Lee, K.S., Choi, J.H., Ha, S.J., Kweon, D.H., Seo, J.H. & Jin, Y.S. Repeated-batch fermentations of xylose and glucose-xylose mixtures using a respiration-deficient Saccharomyces cerevisiae engineered for xylose metabolism. J Biotechnol 150, 404-407 (2010). Link Jung, S.C., Smith, C.L., Lee, K.S., Hong, M.E., Kweon, D.H., Stephanopoulos, G. & Jin, Y.S. Restoration of growth phenotypes of Escherichia coli DH5alpha in minimal media through reversal of a point mutation in purB. Appl Environ Microbiol 76, 6307-6309 (2010). Link, Related News1, Related News2 Hong, M.E., Lee, K.S., Yu, B.J., Sung, Y.J., Park, S.M., Koo, H.M., Kweon, D.H., Park, J.C. & Jin, Y.S. Identification of gene targets eliciting improved alcohol tolerance in Saccharomyces cerevisiae through inverse metabolic engineering. J Biotechnol 149, 52-59 (2010). Link, Related News 2009 Tyo, K.E., Jin, Y.S., Espinoza, F.A. & Stephanopoulos, G. Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803. Biotechnol Prog 25, 1236-1243 (2009). Link Shin, J.Y., Shin, J.I., Kim, J.S., Yang, Y.S., Hwang, Y., Yang, J.S., Shin, D., Seo, J.H., Jin, Y.S., Park, Y.C., Hwang, J.S. & Kweon, D.H. Assembly of Coenzyme Q10 nanostructure resembling nascent discoidal high density lipoprotein particle. Biochem Biophys Res Commun 388, 217-221 (2009). Link Lee, K., Shin, J.Y., Yang, Y.S., Shin, J.I., Park, Y.C., Seo, J.H., Park, T.H., Shin, C.S., Jin, Y.S. & Kweon, D.H. Towards a microarray of functional membrane proteins: Assembly of a surface-attachable, membrane-protein-anchored membrane structure using apolipoprotein A-1. Enz. Microb Tech 44, 217-222 (2009). Link Lee, J., Seo, E., Kweon, D.H., Park, K. & Jin, Y.S. Fermentation of rice bran and defatted rice rran for butanol production using Clostridium beijerinckii NCIMB 8052. J. Microbiol. Biotechnol. 19, 482-490 (2009). Link 2008 Lee, K.S., Chang, E.H., Shin, J.Y., Kweon, D.H., Park, K.M. & Jin, Y.S. Production of casein phosphopeptides using Streptococcus faecalis var. liquefaciens cell immobilization. Korean J Biotechnol Bioeng 23, 59-64 (2008). Link Jung, C.H., Yang, Y.S., Kim, J.S., Shin, J.I., Jin, Y.S., Shin, J.Y., Lee, J.H., Chung, K.M., Hwang, J.S., Oh, J.M., Shin, Y.K. & Kweon, D.H. A search for synthetic peptides that inhibit soluble N-ethylmaleimide sensitive-factor attachment receptor-mediated membrane fusion. FEBS J 275, 3051-3063 (2008). Link 2006-2007 Jung, S.C., Chung, C.Y., Kim, J.S., Kweon, D.H., Park, K.M. & Jin, Y.S. Policosanol production from rice bran oil byproducts. Food Eng Prog 11, 293-297 (2007) Link Jin, Y.S. & Stephanopoulos, G. Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab Eng 9, 337-347 (2007). Link Jeffries, T.W., Grigoriev, I.V., Grimwood, J., Laplaza, J.M., Aerts, A., Salamov, A., Schmutz, J., Lindquist, E., Dehal, P., Shapiro, H., Jin, Y.S., Passoth, V. & Richardson, P.M. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25, 319-326 (2007). Link Laplaza, J.M., Torres, B.R., Jin, Y.S. & Jeffries, T.W. Sh ble and Cre adapted for functional genomics and metabolic engineering of Pichia stipitis. Enz Microb Tech 38, 741-747 (2006). Link Jin, Y.S., Cruz, J. & Jeffries, T.W. Xylitol production by a Pichia stipitis D-xylulokinase mutant. Appl Microbiol Biotechnol 68, 42-45 (2005). Link Jin, Y.S., Alper, H., Yang, Y.T. & Stephanopoulos, G. Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol 71, 8249-8256 (2005). Link Alper, H., Jin, Y.S., Moxley, J.F. & Stephanopoulos, G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 7, 155-164 (2005). Link Jin, Y.S., Laplaza, J.M. & Jeffries, T.W. Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response. Appl Environ Microbiol 70, 6816-6825 (2004). Link Jin, Y.S. & Jeffries, T.W. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab Eng 6, 229-238 (2004). Link Jeffries, T.W. & Jin, Y.S. Metabolic engineering for improved fermentation of pentoses by yeasts. Appl Microbiol Biotechnol 63, 495-509 (2004). Link Jin, Y.S., Ni, H., Laplaza, J.M. & Jeffries, T.W. Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate D-xylulokinase activity. Appl Environ Microbiol 69, 495-503 (2003). Link Jin, Y.S. & Jeffries, T.W. Changing flux of xylose metabolites by altering expression of xylose reductase and xylitol dehydrogenase in recombinant Saccharomyces cerevisiae. Appl Biochem Biotechnol 105 -108, 277-286 (2003). Link Jin, Y.S., Jones, S., Shi, N.Q. & Jeffries, T.W. Molecular cloning of XYL3 (D-xylulokinase) from Pichia stipitis and characterization of its physiological function. Appl Environ Microbiol 68, 1232-1239 (2002). Link Jin, Y.S., Lee, T.H., Choi, Y.D., Ryu, Y.W. & Seo, J.H. Conversion of xylose to ethanol by recombinant Saccharomyces cerevisiae containing genes for xylose reductase and xylitol dehydrogenase from Pichia stipitis. J Microbiol Biotechnol 10, 564-567 (2000). Link Jeffries, T.W. & Jin, Y.S. Ethanol and thermotolerance in the bioconversion of xylose by yeasts. Adv Appl Microbiol 47, 221-268 (2000). Link