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  1. Article: A deoxynucleoside triphosphate triphosphohydrolase promotes cell cycle progression in

    Hellenbrand, Chandler N / Stevenson, David M / Gromek, Katarzyna A / Amador-Noguez, Daniel / Hershey, David M

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Intracellular pools of deoxynucleoside triphosphates (dNTPs) are strictly maintained throughout the cell cycle to ensure accurate and efficient DNA replication. DNA synthesis requires an abundance of dNTPs, but elevated dNTP concentrations in ... ...

    Abstract Intracellular pools of deoxynucleoside triphosphates (dNTPs) are strictly maintained throughout the cell cycle to ensure accurate and efficient DNA replication. DNA synthesis requires an abundance of dNTPs, but elevated dNTP concentrations in nonreplicating cells delay entry into S phase. Enzymes known as deoxyguanosine triphosphate triphosphohydrolases (Dgts) hydrolyze dNTPs into deoxynucleosides and triphosphates, and we propose that Dgts restrict dNTP concentrations to promote the G1 to S phase transition. We characterized a Dgt from the bacterium
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.25.591158
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Efficiency of Lactiplantibacillus plantarum JT-PN39 and Paenibacillus motobuensis JT-A29 for Fermented Coffee Applications and Fermented Coffee Characteristics

    Ngamnok, Teerawat / Nimlamool, Wutigri / Amador-Noguez, Daniel / Palaga, Tanapat / Meerak, Jomkhwan

    Foods. 2023 July 29, v. 12, no. 15

    2023  

    Abstract: To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, ... ...

    Abstract To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, pectinase, and cellulase activities. By analyzing 16S rDNA phylogeny, those bacteria were identified to be Lactiplantibacillus plantarum JT-PN39 (LP) and Paenibacillus motobuensis JT-A29 (PM), where their potency (pure or mixed bacterial culture) for fermenting 5 L of arabica parchment coffee in 48–72 h was further determined. To characterize the role of bacteria in coffee fermentation, growth and pH were also determined. For mixed starter culture conditions, the growth of PM was not detected after 36 h of fermentation due to the low acid conditions generated by LP. Coffee quality was evaluated using a cupping test, and LP-fermented coffee expressed a higher cupping score, with a main fruity and sour flavor, and a dominant caramel-honey-like aroma. Antioxidant and anti-foodborne pathogenic bacteria activity, including total phenolic compounds of PM and LP fermented coffee extracts, was significantly higher than those of ordinary coffee. In addition, LP-fermented coffee expressed the highest antibacterial and antioxidant activities among the fermented coffee. The toxicity test was examined in the murine macrophage RAW 264.7 cell, and all fermented coffee revealed 80–90% cell variability, which means that the fermentation process does not generate any toxicity. In addition, qualifications of non-volatile and volatile compounds in fermented coffee were examined by LC-MS and GC-MS to discriminate the bacterial role during the process by PCA plot. The flavors of fermented coffee, including volatile and non-volatile compounds, were totally different between the non-fermented and fermented conditions. Moreover, the PCA plot showed slightly different flavors among fermentations with different starter cultures. For both the cupping test and biological activities, this study suggests that LP has potential for health benefits in coffee fermentation.
    Keywords Paenibacillus ; amylases ; antioxidants ; bacterial culture ; carboxylic ester hydrolases ; digestive system ; endo-1,4-beta-glucanase ; feces ; fermentation ; macrophages ; mice ; multiple strain starters ; odors ; pH ; phylogeny ; polygalacturonase ; proteinases ; sourness ; toxicity ; toxicity testing
    Language English
    Dates of publication 2023-0729
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods12152894
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: C-di-AMP accumulation disrupts glutathione metabolism and inhibits virulence program expression in

    Siletti, Cheta / Freeman, Matthew / Tu, Zepeng / Stevenson, David M / Amador-Noguez, Daniel / Sauer, John-Demian / Huynh, TuAnh N

    bioRxiv : the preprint server for biology

    2024  

    Abstract: C-di-AMP is an essential second messenger in many bacteria but its levels must be regulated. Unregulated c-di-AMP accumulation attenuates the virulence of many bacterial pathogens, including those that do not require c-di-AMP for growth. However, the ... ...

    Abstract C-di-AMP is an essential second messenger in many bacteria but its levels must be regulated. Unregulated c-di-AMP accumulation attenuates the virulence of many bacterial pathogens, including those that do not require c-di-AMP for growth. However, the mechanisms by which c-di-AMP regulates bacterial pathogenesis remain poorly understood. In
    Importance: C-di-AMP regulates both bacterial pathogenesis and interactions with the host. Although c-di-AMP is essential in many bacteria, its accumulation also attenuates the virulence of many bacterial pathogens. Therefore, disrupting c-di-AMP homeostasis is a promising antibacterial treatment strategy, and has inspired several studies that screened for chemical inhibitors of c-di-AMP phosphodiesterases. However, the mechanisms by which c-di-AMP accumulation diminishes bacterial pathogenesis are poorly understood. Such understanding will reveal the molecular function of c-di-AMP, and inform therapeutic development strategies. Here, we identify GSH metabolism as a pathway regulated by c-di-AMP that is pertinent to
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.18.576247
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in

    Pensinger, Daniel A / Dobrila, Horia A / Stevenson, David M / Hryckowian, Nicole D / Amador-Noguez, Daniel / Hryckowian, Andrew J

    mBio

    2024  Volume 15, Issue 3, Page(s) e0253523

    Abstract: The gut microbiome engenders colonization resistance against the diarrheal ... ...

    Abstract The gut microbiome engenders colonization resistance against the diarrheal pathogen
    MeSH term(s) Humans ; Animals ; Mice ; Clostridioides difficile ; Clostridioides ; Clostridium Infections ; Butyrates ; Virulence ; Diarrhea
    Chemical Substances Butyrates
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02535-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis.

    Rivera Vazquez, Julio / Trujillo, Edna / Williams, Jonathan / She, Fukang / Getahun, Fitsum / Callaghan, Melanie M / Coon, Joshua J / Amador-Noguez, Daniel

    Biotechnology for biofuels and bioproducts

    2024  Volume 17, Issue 1, Page(s) 14

    Abstract: Background: Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism's vulnerability to isobutanol toxicity, adversely affecting its growth ... ...

    Abstract Background: Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism's vulnerability to isobutanol toxicity, adversely affecting its growth and productivity. The limited understanding of the physiological impacts of isobutanol on Z. mobilis constrains our ability to overcome these production barriers.
    Results: We utilized a systems-level approach comprising LC-MS/MS-based lipidomics, metabolomics, and shotgun proteomics, to investigate how exposure to ethanol and isobutanol impact the lipid membrane composition and overall physiology of Z. mobilis. Our analysis revealed significant and distinct alterations in membrane phospholipid and fatty acid composition resulting from ethanol and isobutanol exposure. Notably, ethanol exposure increased membrane cyclopropane fatty acid content and expression of cyclopropane fatty acid (CFA) synthase. Surprisingly, isobutanol decreased cyclopropane fatty acid content despite robust upregulation of CFA synthase. Overexpression of the native Z. mobilis' CFA synthase increased cyclopropane fatty acid content in all phospholipid classes and was associated with a significant improvement in growth rates in the presence of added ethanol and isobutanol. Heterologous expression of CFA synthase from Clostridium acetobutylicum resulted in a near complete replacement of unsaturated fatty acids with cyclopropane fatty acids, affecting all lipid classes. However, this did not translate to improved growth rates under isobutanol exposure. Correlating with its greater susceptibility to isobutanol, Z. mobilis exhibited more pronounced alterations in its proteome, metabolome, and overall cell morphology-including cell swelling and formation of intracellular protein aggregates -when exposed to isobutanol compared to ethanol. Isobutanol triggered a broad stress response marked by the upregulation of heat shock proteins, efflux transporters, DNA repair systems, and the downregulation of cell motility proteins. Isobutanol also elicited widespread dysregulation of Z. mobilis' primary metabolism evidenced by increased levels of nucleotide degradation intermediates and the depletion of biosynthetic and glycolytic intermediates.
    Conclusions: This study provides a comprehensive, systems-level evaluation of the impact of ethanol and isobutanol exposure on the lipid membrane composition and overall physiology of Z. mobilis. These findings will guide engineering of Z. mobilis towards the creation of isobutanol-tolerant strains that can serve as robust platforms for the industrial production of isobutanol from lignocellulosic sugars.
    Language English
    Publishing date 2024-01-28
    Publishing country England
    Document type Journal Article
    ISSN 2731-3654
    ISSN (online) 2731-3654
    DOI 10.1186/s13068-023-02450-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Efficiency of

    Ngamnok, Teerawat / Nimlamool, Wutigri / Amador-Noguez, Daniel / Palaga, Tanapat / Meerak, Jomkhwan

    Foods (Basel, Switzerland)

    2023  Volume 12, Issue 15

    Abstract: To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, ... ...

    Abstract To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, pectinase, and cellulase activities. By analyzing 16S rDNA phylogeny, those bacteria were identified to be
    Language English
    Publishing date 2023-07-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods12152894
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Listeria monocytogenes

    Smith, Hans B / Lee, Kijeong / Stevenson, David M / Amador-Noguez, Daniel / Sauer, John-Demian

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... Listeria ... ...

    Abstract Listeria monocytogenes
    Language English
    Publishing date 2023-01-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.13.524026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism.

    Jacobson, Tyler B / Callaghan, Melanie M / Amador-Noguez, Daniel

    Annual review of microbiology

    2021  Volume 75, Page(s) 515–539

    Abstract: To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential ... ...

    Abstract To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection.
    MeSH term(s) Prokaryotic Cells ; Viruses
    Language English
    Publishing date 2021-08-04
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 207931-8
    ISSN 1545-3251 ; 0066-4227
    ISSN (online) 1545-3251
    ISSN 0066-4227
    DOI 10.1146/annurev-micro-060621-043448
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks.

    Khana, Daven B / Callaghan, Melanie M / Amador-Noguez, Daniel

    Current opinion in microbiology

    2021  Volume 66, Page(s) 21–31

    Abstract: Thermodynamic analysis of metabolic networks has emerged as a useful new tool for pathway design and metabolic engineering. Understanding the relationship between the thermodynamic driving force of biochemical reactions and metabolic flux has generated ... ...

    Abstract Thermodynamic analysis of metabolic networks has emerged as a useful new tool for pathway design and metabolic engineering. Understanding the relationship between the thermodynamic driving force of biochemical reactions and metabolic flux has generated new insights regarding the design principles of microbial carbon metabolism. This review summarizes the various lessons that can be obtained from the thermodynamic analysis of metabolic pathways, illustrates concepts of computational thermodynamic tools, and highlights recent applications of thermodynamic analysis to pathway design in industrially relevant microbes.
    MeSH term(s) Carbon ; Computational Biology ; Metabolic Engineering ; Metabolic Networks and Pathways ; Models, Biological ; Thermodynamics
    Chemical Substances Carbon (7440-44-0)
    Language English
    Publishing date 2021-12-30
    Publishing country England
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2021.11.007
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    In stock of ZB MED Cologne/Königswinter

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  10. Article: Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks

    Khana, Daven B / Callaghan, Melanie M / Amador-Noguez, Daniel

    Current opinion in microbiology. 2022 Apr., v. 66

    2022  

    Abstract: Thermodynamic analysis of metabolic networks has emerged as a useful new tool for pathway design and metabolic engineering. Understanding the relationship between the thermodynamic driving force of biochemical reactions and metabolic flux has generated ... ...

    Abstract Thermodynamic analysis of metabolic networks has emerged as a useful new tool for pathway design and metabolic engineering. Understanding the relationship between the thermodynamic driving force of biochemical reactions and metabolic flux has generated new insights regarding the design principles of microbial carbon metabolism. This review summarizes the various lessons that can be obtained from the thermodynamic analysis of metabolic pathways, illustrates concepts of computational thermodynamic tools, and highlights recent applications of thermodynamic analysis to pathway design in industrially relevant microbes.
    Keywords carbon metabolism ; microbial carbon ; thermodynamics
    Language English
    Dates of publication 2022-04
    Size p. 21-31.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2021.11.007
    Database NAL-Catalogue (AGRICOLA)

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