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  1. Article ; Online: The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.

    Gao, Ye / Bang, Ina / Seif, Yara / Kim, Donghyuk / Palsson, Bernhard O

    Nucleic acids research

    2023  Volume 51, Issue 8, Page(s) 3618–3630

    Abstract: While global transcription factors (TFs) have been studied extensively in Escherichia coli model strains, conservation and diversity in TF regulation between strains is still unknown. Here we use a combination of ChIP-exo-to define ferric uptake ... ...

    Abstract While global transcription factors (TFs) have been studied extensively in Escherichia coli model strains, conservation and diversity in TF regulation between strains is still unknown. Here we use a combination of ChIP-exo-to define ferric uptake regulator (Fur) binding sites-and differential gene expression-to define the Fur regulon in nine E. coli strains. We then define a pan-regulon consisting of 469 target genes that includes all Fur target genes in all nine strains. The pan-regulon is then divided into the core regulon (target genes found in all the strains, n = 36), the accessory regulon (target found in two to eight strains, n = 158) and the unique regulon (target genes found in one strain, n = 275). Thus, there is a small set of Fur regulated genes common to all nine strains, but a large number of regulatory targets unique to a particular strain. Many of the unique regulatory targets are genes unique to that strain. This first-established pan-regulon reveals a common core of conserved regulatory targets and significant diversity in transcriptional regulation amongst E. coli strains, reflecting diverse niche specification and strain history.
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Iron/metabolism ; Regulon/genetics ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Transcription Factors
    Chemical Substances Iron (E1UOL152H7) ; Repressor Proteins ; Escherichia coli Proteins ; ferric uptake regulating proteins, bacterial ; Transcription Factors
    Language English
    Publishing date 2023-04-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad253
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  2. Article ; Online: Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

    Bang, Ina / Lee, Sang-Mok / Park, Seojoung / Park, Joon Young / Nong, Linh Khanh / Gao, Ye / Palsson, Bernhard O / Kim, Donghyuk

    Briefings in bioinformatics

    2023  Volume 24, Issue 2

    Abstract: Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair ... ...

    Abstract Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions. Here, we report the development of DEOCSU (DEep-learning Optimized ChIP-exo peak calling SUite), a novel machine learning-based ChIP-exo peak calling suite. DEOCSU entails the deep convolutional neural network model which was trained with curated ChIP-exo peak data to distinguish the visualized data of bona fide peaks from false ones. Performance validation of the trained deep-learning model indicated its high accuracy, high precision and high recall of over 95%. Applying the new suite to both in-house and publicly available ChIP-exo datasets obtained from bacteria, eukaryotes and archaea revealed an accurate prediction of peaks containing canonical motifs, highlighting the versatility and efficiency of DEOCSU. Furthermore, DEOCSU can be executed on a cloud computing platform or the local environment. With visualization software included in the suite, adjustable options such as the threshold of peak probability, and iterable updating of the pre-trained model, DEOCSU can be optimized for users' specific needs.
    MeSH term(s) Chromatin Immunoprecipitation Sequencing ; Deep Learning ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/metabolism ; Software ; Algorithms ; Binding Sites ; Sequence Analysis, DNA
    Chemical Substances DNA-Binding Proteins
    Language English
    Publishing date 2023-01-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbad024
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  3. Article: Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network

    Park, Joon Young / Rimal, Hemraj / Bang, Ina / Nong, Linh Khanh / Kim, Donghyuk

    Biotechnology and bioprocess engineering. 2020 Dec., v. 25, no. 6

    2020  

    Abstract: The development and innovative use of next-generation sequencing technologies have opened the doors for genetic and epigenetic research at the next level. These technologies can be used to study gene expression regulation at the transcriptional and post- ... ...

    Abstract The development and innovative use of next-generation sequencing technologies have opened the doors for genetic and epigenetic research at the next level. These technologies can be used to study gene expression regulation at the transcriptional and post-transcriptional levels in both prokaryotic and eukaryotic systems. In this review, we focused on the various tools and techniques for DNA-binding proteins such as RNA polymerase, sigma factors, nucleoid-associated proteins, and transcription factors in bacteria. Descriptions on series of Chromatin ImmunoPrecipitation (ChIP) technologies, including ChIP followed by microarray hybridization (ChIP-chip), ChIP followed by deep sequencing (ChIP-seq), and ChIP with exonuclease digestion and deep sequencing (ChIP-exo) has been given. Furthermore, recent investigations on transcriptional regulatory networks of a wide range of bacteria with ChIP technologies are discussed for the model bacteria Escherichia coli followed by pathogenic and other non-pathogenic bacteria. In conclusion, ChIP technologies have proven effective and efficient to reconstruct and to delineate transcriptional regulatory network in a variety of bacteria.
    Keywords DNA-directed RNA polymerase ; Escherichia coli ; bioprocessing ; biotechnology ; chromatin immunoprecipitation ; digestion ; epigenetics ; gene expression regulation ; microarray technology ; transcription (genetics)
    Language English
    Dates of publication 2020-12
    Size p. 944-954.
    Publishing place The Korean Society for Biotechnology and Bioengineering
    Document type Article
    Note NAL-AP-2-clean ; Review
    ZDB-ID 2125481-3
    ISSN 1976-3816 ; 1226-8372
    ISSN (online) 1976-3816
    ISSN 1226-8372
    DOI 10.1007/s12257-020-0030-9
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  4. Article: Genome sequence of the potential probiotic eukaryote Saccharomyces cerevisiae KCCM 51299

    Hwang, Junsang / Bang, Ina / Kim, Donghyuk / Shin, Seung Chul / Chin, Young-Wook / Kim, Tae-Wan / Kim, Hyo Jin

    3 Biotech. 2020 Apr., v. 10, no. 4

    2020  

    Abstract: Saccharomyces cerevisiae KCCM 51299, a potential probiotic yeast overproducing glutathione, has been isolated from among 272 yeast strains from the relatively safe Nuruk. The genome sequence of S. cerevisiae KCCM 51299 was analyzed and a near-complete ... ...

    Abstract Saccharomyces cerevisiae KCCM 51299, a potential probiotic yeast overproducing glutathione, has been isolated from among 272 yeast strains from the relatively safe Nuruk. The genome sequence of S. cerevisiae KCCM 51299 was analyzed and a near-complete genome (12 Mb) with 19 contigs was assembled after PacBio single-molecule real-time (SMRT) sequencing. The genome of S. cerevisiae KCCM 51299 was compared to the S. cerevisiae s288c reference genome. Additionally, genes involved in glutathione biosynthesis were identified, and the glutathione biosynthesis pathway was constructed in silico based on these genes. Furthermore, S. cerevisiae KCCM 51299 genes were compared with those in other yeast genomes. Finally, genome-scale in silico flux analysis was carried out, and a metabolic engineering strategy for glutathione biosynthesis was generated. These results provide useful information to further develop eukaryotic probiotics to overproduce glutathione.
    Keywords Saccharomyces cerevisiae ; biosynthesis ; computer simulation ; eukaryotic cells ; genes ; glutathione ; metabolic engineering ; nucleotide sequences ; probiotics ; yeasts
    Language English
    Dates of publication 2020-04
    Size p. 185.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-020-02174-9
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  5. Article ; Online: Enhanced production of nonanedioic acid from nonanoic acid by engineered Escherichia coli.

    Lee, Yongjoo / Sathesh-Prabu, Chandran / Kwak, Geun Hwa / Bang, Ina / Jung, Hyun Wook / Kim, Donghyuk / Lee, Sung Kuk

    Biotechnology journal

    2021  Volume 17, Issue 3, Page(s) e2000416

    Abstract: In this study, whole-cell biotransformation was conducted to produce nonanedioic acid from nonanoic acid by expressing the alkane hydroxylating system (AlkBGT) from Pseudomonas putida GPo1 in Escherichia coli. Following adaptive laboratory evolution, an ... ...

    Abstract In this study, whole-cell biotransformation was conducted to produce nonanedioic acid from nonanoic acid by expressing the alkane hydroxylating system (AlkBGT) from Pseudomonas putida GPo1 in Escherichia coli. Following adaptive laboratory evolution, an efficient E. coli mutant strain, designated as MRE, was successfully obtained, demonstrating the fastest growth (27-fold higher) on nonanoic acid as the sole carbon source compared to the wild-type strain. Additionally, the MRE strain was engineered to block nonanoic acid degradation by deleting fadE. The resulting strain exhibited a 12.8-fold increase in nonanedioic acid production compared to the wild-type strain. Six mutations in acrR, P
    MeSH term(s) Dicarboxylic Acids/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Fatty Acids
    Chemical Substances Dicarboxylic Acids ; Fatty Acids ; pelargonic acid (97SEH7577T) ; azelaic acid (F2VW3D43YT)
    Language English
    Publishing date 2021-05-28
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2221885-3
    ISSN 1860-7314 ; 1860-6768
    ISSN (online) 1860-7314
    ISSN 1860-6768
    DOI 10.1002/biot.202000416
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  6. Article ; Online: Fermentation product with new equol-producing Lactobacillus paracasei as a probiotic-like product candidate for prevention of skin and intestinal disorder.

    Kwon, Jeong Eun / Lim, Jaewon / Bang, Ina / Kim, Inhye / Kim, Donghyuk / Kang, Se Chan

    Journal of the science of food and agriculture

    2019  Volume 99, Issue 9, Page(s) 4200–4210

    Abstract: Background: Equol is a major isoflavone metabolite, and equol-producing bacteria have been isolated and characterized; however, fermentation has been performed with soybean-based products as substrates. Pueraria lobata has been reported as a plant with ... ...

    Abstract Background: Equol is a major isoflavone metabolite, and equol-producing bacteria have been isolated and characterized; however, fermentation has been performed with soybean-based products as substrates. Pueraria lobata has been reported as a plant with higher content of isoflavones.
    Results: The genome of new equol-producing bacteria, Lactobacillus paracasei JS1, was analyzed. Also, the effect of P. lobata extract fermented with L. paracasei JS1 (FPE) on the skin and intestinal immune response was examined. With gene expression analysis, it was proven that seven skin-related proteins, hyaluronan synthase-1, -2, -3, collagen, elastin, epidermal growth factor, and epidermal growth factor receptor were differentially expressed upon FPE treatment. The messenger RNA expression increased with treatment with the FPE, and a skin moisturizing effect was confirmed by a hematoxylin-eosin staining experiment. In addition, such an experiment showed that proinflammatory cytokines, tumor necrosis factor-α, cyclooxygenase-2, inducible nitric oxide synthase, interleukin-1β, -4, and -6, were reduced in large intestine when treated with FPE.
    Conclusion: L. paracasei JS1 has the ability to produce equol having beneficial effects on the skin. Moreover, FPE also has an inhibitory effect on inflammation cytokines in the large intestine. Thus, the novel and edible equol-producing L. paracasei JS1 and FPE have thepotential to be developed as nutricosmetic resources. © 2019 Society of Chemical Industry.
    MeSH term(s) Animals ; Collagen/genetics ; Collagen/metabolism ; Elastin/genetics ; Elastin/metabolism ; Equol/metabolism ; Fermentation ; Humans ; Hyaluronan Synthases/genetics ; Hyaluronan Synthases/metabolism ; Interleukin-1beta/genetics ; Interleukin-1beta/metabolism ; Intestinal Diseases/genetics ; Intestinal Diseases/metabolism ; Intestinal Diseases/prevention & control ; Lactobacillus paracasei/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Nitric Oxide Synthase Type II/genetics ; Nitric Oxide Synthase Type II/metabolism ; Probiotics/administration & dosage ; Skin Diseases/genetics ; Skin Diseases/metabolism ; Skin Diseases/prevention & control
    Chemical Substances Interleukin-1beta ; Equol (531-95-3) ; Collagen (9007-34-5) ; Elastin (9007-58-3) ; Nitric Oxide Synthase Type II (EC 1.14.13.39) ; Hyaluronan Synthases (EC 2.4.1.212)
    Language English
    Publishing date 2019-04-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 184116-6
    ISSN 1097-0010 ; 0022-5142
    ISSN (online) 1097-0010
    ISSN 0022-5142
    DOI 10.1002/jsfa.9648
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  7. Article ; Online: Characterization of an Entner-Doudoroff pathway-activated Escherichia coli.

    Kim, Ye Eun / Cho, Kyung Hyun / Bang, Ina / Kim, Chang Hee / Ryu, Young Shin / Kim, Yuchan / Choi, Eun Mi / Nong, Linh Khanh / Kim, Donghyuk / Lee, Sung Kuk

    Biotechnology for biofuels and bioproducts

    2022  Volume 15, Issue 1, Page(s) 120

    Abstract: Background: Escherichia coli have both the Embden-Meyerhof-Parnas pathway (EMPP) and Entner-Doudoroff pathway (EDP) for glucose breakdown, while the EDP primarily remains inactive for glucose metabolism. However, EDP is a more favorable route than EMPP ... ...

    Abstract Background: Escherichia coli have both the Embden-Meyerhof-Parnas pathway (EMPP) and Entner-Doudoroff pathway (EDP) for glucose breakdown, while the EDP primarily remains inactive for glucose metabolism. However, EDP is a more favorable route than EMPP for the production of certain products.
    Results: EDP was activated by deleting the pfkAB genes in conjunction with subsequent adaptive laboratory evolution (ALE). The evolved strains acquired mutations in transcriptional regulatory genes for glycolytic process (crp, galR, and gntR) and in glycolysis-related genes (gnd, ptsG, and talB). The genotypic, transcriptomic and phenotypic analyses of those mutations deepen our understanding of their beneficial effects on cellulosic biomass bio-conversion. On top of these scientific understandings, we further engineered the strain to produce higher level of lycopene and 3-hydroxypropionic acid.
    Conclusions: These results indicate that the E. coli strain has innate capability to use EDP in lieu of EMPP for glucose metabolism, and this versatility can be harnessed to further engineer E. coli for specific biotechnological applications.
    Language English
    Publishing date 2022-11-09
    Publishing country England
    Document type Journal Article
    ISSN 2731-3654
    ISSN (online) 2731-3654
    DOI 10.1186/s13068-022-02219-6
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  8. Article: Genome sequence of the potential probiotic eukaryote

    Hwang, Junsang / Bang, Ina / Kim, Donghyuk / Shin, Seung Chul / Chin, Young-Wook / Kim, Tae-Wan / Kim, Hyo Jin

    3 Biotech

    2020  Volume 10, Issue 4, Page(s) 185

    Abstract: Saccharomyces ... ...

    Abstract Saccharomyces cerevisiae
    Language English
    Publishing date 2020-03-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-020-02174-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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