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Now showing items 1 - 16 of 592

  • A Conversation with Sang Yup Lee

    Lee, Sang Yup  

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  • A Conversation with Sang Yup Lee

    Lee, Sang Yup  

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  • MEMOTE for standardized genome-scale metabolic model testing

    Lieven, Christian   Beber, Moritz E.   Olivier, Brett G.   Bergmann, Frank T.   Ataman, Meric   Babaei, Parizad   Bartell, Jennifer A.   Blank, Lars M.   Chauhan, Siddharth   Correia, Kevin   Diener, Christian   Draeger, Andreas   Ebert, Birgitta E.   Edirisinghe, Janaka N.   Faria, Jose P.   Feist, Adam M.   Fengos, Georgios   Fleming, Ronan M. T.   Garcia-Jimenez, Beatriz   Hatzimanikatis, Vassily   van Helvoirt, Wout   Henry, Christopher S.   Hermjakob, Henning   Herrgard, Markus J.   Kaafarani, Ali   Kim, Hyun Uk   King, Zachary   Klamt, Steffen   Klipp, Edda   Koehorst, Jasper J.   Koenig, Matthias   Lakshmanan, Meiyappan   Lee, Dong-Yup   Lee, Sang Yup   Lee, Sunjae   Lewis, Nathan E.   Liu, Filipe   Ma, Hongwu   Machado, Daniel   Mahadevan, Radhakrishnan   Maia, Paulo   Mardinoglu, Adil   Medlock, Gregory L.   Monk, Jonathan M.   Nielsen, Jens   Nielsen, Lars Keld   Nogales, Juan   Nookaew, Intawat   Palsson, Bernhard O.   Papin, Jason A.   Patil, Kiran R.   Poolman, Mark   Price, Nathan D.   Resendis-Antonio, Osbaldo   Richelle, Anne   Rocha, Isabel   Sanchez, Benjamin J.   Schaap, Peter J.   Malik Sheriff, Rahuman S.   Shoaie, Saeed   Sonnenschein, Nikolaus   Teusink, Bas   Vilaca, Paulo   Vik, Jon Olav   Wodke, Judith A. H.   Xavier, Joana C.   Yuan, Qianqian   Zakhartsev, Maksim   Zhang, Cheng  

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  • Microbial production of methyl anthranilate, a grape flavor compound

    Luo, Zi Wei   Cho, Jae Sung   Lee, Sang Yup  

    Methyl anthranilate (MANT) is a widely used compound to give grape scent and flavor, but is currently produced by petroleum-based processes. Here, we report the direct fermentative production of MANT from glucose by metabolically engineered Escherichia coli and Corynebacterium glutamicum strains harboring a synthetic plantderived metabolic pathway. Optimizing the key enzyme anthranilic acid (ANT) methyltransferasel (AAMT1) expression, increasing the direct precursor ANT supply, and enhancing the intracellular availability and salvage of the cofactor S-adenosyl-L-methionine required by AAMT1, results in improved MANT production in both engineered microorganisms. Furthermore, in situ two-phase extractive fermentation using tributyrin as an extractant is developed to overcome MANT toxicity. Fed-batch cultures of the final engineered E. coli and C glutamicum strains in two-phase cultivation mode led to the production of 4.47 and 5.74 g/L MANT, respectively, in minimal media containing glucose. The metabolic engineering strategies developed here will be useful for the production of volatile aromatic esters including MANT.
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  • Advances in CRISPR-Cas systems for RNA targeting, tracking and editing

    Wang, Fei   Wang, Lianrong   Zou, Xuan   Duan, Suling   Li, Zhiqiang   Deng, Zixin   Luo, Jie   Lee, Sang Yup   Chen, Shi  

    Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only similar to 930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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  • Metabolomics for industrial fermentation

    Choi, Kyeong Rok   Kim, Won Jun   Lee, Sang Yup  

    Metabolomics is essential to understand the metabolism and identify engineering targets to improve the performances of strains and bioprocesses. Although numerous metabolomics techniques have been developed and applied to various organisms, the metabolome of Saccharopolyspora erythraea, a native producer of erythromycin, had never been studied. The 2017 best paper of Bioprocess and Biosystems Engineering reports examination of three methods for quenching and extraction to analyze the intracellular metabolome of S. erythraea, and identified the most reliable methods for studying different groups of the metabolites. Subsequent studies on the dynamics of the intracellular metabolome of S. erythraea during the fed-batch fermentation identified a positive correlation between the specific erythromycin production rate and the pool size of intracellular propionyl-CoA and other precursors of erythromycin. A series of follow-up studies, such as demonstrating the applicability of the quenching/extraction methods in other related antibiotic producers, demonstrating the generality of the best matches between the quenching/extraction methods and the metabolite groups, and combining metabolomics approaches with the fluxomics and systems metabolic engineering approaches, will facilitate the metabolomics studies on important antibiotic producers, enable standardization of the quenching/extraction protocols, and improve the performance of the antibiotic production with deeper insight into their metabolism.
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  • Advances in CRISPR-Cas systems for RNA targeting, tracking and editing

    Wang, Fei   Wang, Lianrong   Zou, Xuan   Duan, Suling   Li, Zhiqiang   Deng, Zixin   Luo, Jie   Lee, Sang Yup   Chen, Shi  

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  • CRISPR/Cas-based genome engineering in natural product discovery

    Tong, Yaojun   Weber, Tilmann   Lee, Sang Yup  

    This review briefly introduces and summarizes current knowledge about the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) - CRISPR/Cas system and how it was engineered to become one of the most important and versatile genome editing techniques that are currently revolutionizing the whole field of molecular biology. It aims to highlight and discuss the applications and remaining challenges of CRISPR/Cas (mainly focusing on CRISPR/SpCas9)-based genome editing in natural product discovery. The organisms covered include bacteria such as Streptomyces, Corynebacteria, and Myxobacteria; filamentous fungi such as Aspergillus, Beauveria, and Ganoderma; microalgae; and some plants. As closing remarks, the prospects of using CRISPR/Cas in natural product discovery will be discussed.
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  • A comprehensive metabolic map for production of bio-based chemicals

    Lee, Sang Yup   Kim, Hyun Uk   Chae, Tong Un   Cho, Jae Sung   Kim, Je Woong   Shin, Jae Ho   Kim, Dong In   Ko, Yoo-Sung   Jang, Woo Dae   Jang, Yu-Sin  

    Production of industrial chemicals using renewable biomass feedstock is becoming increasingly important to address limited fossil resources, climate change and other environmental problems. To develop high-performance microbial cell factories, equivalent to chemical plants, microorganisms undergo systematic metabolic engineering to efficiently convert biomass-derived carbon sources into target chemicals. Over the past two decades, many engineered microorganisms capable of producing natural and non-natural chemicals have been developed. This Review details the current status of representative industrial chemicals that are produced through biological and/or chemical reactions. We present a comprehensive bio-based chemicals map that highlights the strategies and pathways of single or multiple biological reactions, chemical reactions and combinations thereof towards production of particular chemicals of interest. Future challenges are also discussed to enable production of even more diverse chemicals and more efficient production of chemicals from renewable feedstocks.
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  • Document vectorization method using network information of words

    Lee, Sang Yup  

    We propose a new method for vectorizing a document using the relational characteristics of the words in the document. For the relational characteristics, we use two types of relational information of a word: 1) the centrality measures of the word and 2) the number of times that the word is used with other words in the document. We propose these methods mainly because information regarding the relations of a word to other words in the document are likely to better represent the unique characteristics of the document than the frequency-based methods (e.g., term frequency and term frequency-inverse document frequency). In experiments using a corpus consisting of 14 documents pertaining to four different topics, the results of clustering analysis using cosine similarities between vectors of relational information for words were comparable to (and more accurate than in some cases) those obtained using vectors of frequency-based methods. The clustering analysis using vectors of tie weights between words yielded the most accurate result. Although the results obtained for the small dataset used in this study can hardly be generalized, they suggest that at least in some cases, vectorization of a document using the relational characteristics of the words can provide more accurate results than the frequency-based vectors.
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  • A comprehensive metabolic map for production of bio-based chemicals

    Lee, Sang Yup   Kim, Hyun Uk   Chae, Tong Un   Cho, Jae Sung   Kim, Je Woong   Shin, Jae Ho   Kim, Dong In   Ko, Yoo-Sung   Jang, Woo Dae   Jang, Yu-Sin  

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  • Current status and applications of genome-scale metabolic models.

    Gu, Changdai   Kim, Gi Bae   Kim, Won Jun   Kim, Hyun Uk   Lee, Sang Yup  

    Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applications, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases.=20
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  • The urgent need for microbiology literacy in society

    Timmis, Kenneth   Cavicchioli, Ricardo   Garcia, José Luis   Nogales, Balbina   Chavarría, Max   Stein, Lisa   McGenity, Terry J.   Webster, Nicole   Singh, Brajesh   Handelsman, Jo   Lorenzo, Victor   Pruzzo, Carla   Timmis, James   Martín, Juan Luis Ramos   Verstraete, Willy   Jetten, Mike   Danchin, Antoine   Huang, Wei   Gilbert, Jack   Lal, Rup   Santos, Helena   Lee, Sang Yup   Sessitsch, Angela   Bonfante, Paola   Gram, Lone   Lin, Raymond T. P.   Ron, Eliora   Karahan, Ceren   Meer, Jan Roelof   Artunkal, Seza   Jahn, Dieter   Harper, Lucy  

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  • CRISPR/Cas-based genome engineering in natural product discovery

    Tong, Yaojun   Weber, Tilmann   Lee, Sang Yup  

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  • Microbial production of butyl butyrate, a flavor and fragrance compound

    Noh, Hyeon Ji   Lee, Sang Yup   Jang, Yu-Sin  

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  • METHOD FOR PRODUCING LACTAM

    The present invention relates to a recombinant microorganism having a lactam production capacity from omega-amino acid, into which a gene for coating a beta-alanine coenzyme A transferase on a microorganism having an omega-amino acid biosynthetic metabolic pathway from amino acid is introduced, and a method for producing a variety of lactams and omega-aminoacyl-CoAs using the same. The recombinant microorganism and the method for producing lactam according to the present invention are useful in producing a variety of lactams such as propiolactam, 2-pyrrolidone, valerolactam, carprolactam, heptanolactam, etc. from a variety of omega-amino acids.
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