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  1. Article ; Online: Targeting intracellular nontuberculous mycobacteria and

    Bartlett, Helen P / Dawson, Clinton C / Glickman, Cody M / Osborn, David W / Evans, Christopher R / Garcia, Benjamin J / Frost, Lauren C / Cummings, Jason E / Whittel, Nicholas / Slayden, Richard A / Holder, Jason W

    Microbiology spectrum

    2024  Volume 12, Issue 5, Page(s) e0353423

    Abstract: To address intracellular mycobacterial infections, we developed a cocktail of four enzymes that catalytically attack three layers of the mycobacterial envelope. This cocktail is delivered to macrophages, through a targeted liposome presented here as ... ...

    Abstract To address intracellular mycobacterial infections, we developed a cocktail of four enzymes that catalytically attack three layers of the mycobacterial envelope. This cocktail is delivered to macrophages, through a targeted liposome presented here as ENTX_001. Endolytix Cocktail 1 (EC1) leverages mycobacteriophage lysin enzymes LysA and LysB, while also including α-amylase and isoamylase for degradation of the mycobacterial envelope from outside of the cell. The LysA family of proteins from mycobacteriophages has been shown to cleave the peptidoglycan layer, whereas LysB is an esterase that hydrolyzes the linkage between arabinogalactan and mycolic acids of the mycomembrane. The challenge of gaining access to the substrates of LysA and LysB provided exogenously was addressed by adding amylase enzymes that degrade the extracellular capsule shown to be present in
    MeSH term(s) Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/enzymology ; Mycobacteriophages/genetics ; Mycobacteriophages/enzymology ; Macrophages/microbiology ; Macrophages/virology ; Humans ; Nontuberculous Mycobacteria/drug effects ; Liposomes/chemistry ; Anti-Bacterial Agents/pharmacology ; Peptidoglycan/metabolism ; Microbial Sensitivity Tests ; Endopeptidases/metabolism ; Endopeptidases/pharmacology ; Endopeptidases/genetics ; Galactans
    Chemical Substances Liposomes ; Anti-Bacterial Agents ; endolysin (EC 3.4.99.-) ; Peptidoglycan ; arabinogalactan (SL4SX1O487) ; Endopeptidases (EC 3.4.-) ; Galactans
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.03534-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Architecture of the Tn7 posttransposition complex: an elaborate nucleoprotein structure.

    Holder, Jason W / Craig, Nancy L

    Journal of molecular biology

    2010  Volume 401, Issue 2, Page(s) 167–181

    Abstract: Four transposition proteins encoded by the bacterial transposon Tn7, TnsA, TnsB, TnsC, and TnsD, mediate its site- and orientation-specific insertion into the chromosomal site attTn7. To establish which Tns proteins are actually present in the ... ...

    Abstract Four transposition proteins encoded by the bacterial transposon Tn7, TnsA, TnsB, TnsC, and TnsD, mediate its site- and orientation-specific insertion into the chromosomal site attTn7. To establish which Tns proteins are actually present in the transpososome that executes DNA breakage and joining, we have determined the proteins present in the nucleoprotein product of transposition, the posttransposition complex (PTC), using fluorescently labeled Tns proteins. All four required Tns proteins are present in the PTC in which we also find that the Tn7 ends are paired by protein-protein contacts between Tns proteins bound to the ends. Quantification of the relative amounts of the fluorescent Tns proteins in the PTC indicates that oligomers of TnsA, TnsB, and TnsC mediate Tn7 transposition. High-resolution DNA footprinting of the DNA product of transposition attTn7Colon, two colonsTn7 revealed that about 350 bp of DNA on the transposon ends and on attTn7 contact the Tns proteins. All seven binding sites for TnsB, the component of the transposase that specifically binds the ends and mediates 3' end breakage and joining, are occupied in the PTC. However, the protection pattern of the sites closest to the Tn7 ends in the PTC are different from that observed with TnsB alone, likely reflecting the pairing of the ends and their interaction with the target nucleoprotein complex necessary for activation of the breakage and joining steps. We also observe extensive protection of the attTn7 sequences in the PTC and that alternative DNA structures in substrate attTn7 that are imposed by TnsD are maintained in the PTC.
    MeSH term(s) Base Sequence ; Binding Sites ; DNA Footprinting ; DNA Transposable Elements/genetics ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Microscopy, Atomic Force ; Molecular Sequence Data ; Molecular Structure ; Multiprotein Complexes/chemistry ; Nucleoproteins/chemistry ; Nucleoproteins/genetics ; Nucleoproteins/metabolism ; Transposases/chemistry ; Transposases/genetics ; Transposases/metabolism
    Chemical Substances DNA Transposable Elements ; DNA, Bacterial ; Escherichia coli Proteins ; Multiprotein Complexes ; Nucleoproteins ; Transposases (EC 2.7.7.-)
    Language English
    Publishing date 2010-06-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2010.06.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article ; Online: Elucidation of beta-oxidation pathways in Ralstonia eutropha H16 by examination of global gene expression.

    Brigham, Christopher J / Budde, Charles F / Holder, Jason W / Zeng, Qiandong / Mahan, Alison E / Rha, Chokyun / Sinskey, Anthony J

    Journal of bacteriology

    2010  Volume 192, Issue 20, Page(s) 5454–5464

    Abstract: Ralstonia eutropha H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We compare whole-cell gene expression ...

    Abstract Ralstonia eutropha H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We compare whole-cell gene expression levels of R. eutropha H16 during growth and polyhydroxyalkanoate production on trioleate and fructose. Trioleate is a triacylglycerol that serves as a model for plant oils. Among the genes of note, two potential fatty acid β-oxidation operons and two putative lipase genes were shown to be upregulated in trioleate cultures. The genes of the glyoxylate bypass also exhibit increased expression during growth on trioleate. We observed that single β-oxidation operon deletion mutants of R. eutropha could grow using palm oil or crude palm kernel oil as the sole carbon source, regardless of which operon was present in the genome, but a double mutant was unable to grow under these conditions. A lipase deletion mutant did not exhibit a growth defect in emulsified oil cultures but did exhibit a phenotype in cultures containing nonemulsified oil. Mutants of the glyoxylate shunt gene for isocitrate lyase were able to grow in the presence of oils, while a malate synthase (aceB) deletion mutant grew more slowly than wild type. Gene expression under polyhydroxyalkanoate storage conditions was also examined. Many findings of this analysis confirm results from previous studies by our group and others. This work represents the first examination of global gene expression involving triacylglycerol and fatty acid catabolism genes in R. eutropha.
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cloning, Molecular ; Cupriavidus necator/classification ; Cupriavidus necator/genetics ; Cupriavidus necator/metabolism ; Fatty Acids/metabolism ; Fructose ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/physiology ; Hydroxybutyrates/metabolism ; Mutation ; Oxidation-Reduction ; Plant Oils/metabolism ; Polyesters/metabolism ; Protein Array Analysis
    Chemical Substances Bacterial Proteins ; Fatty Acids ; Hydroxybutyrates ; Plant Oils ; Polyesters ; poly-beta-hydroxybutyrate (26063-00-3) ; Fructose (30237-26-4)
    Language English
    Publishing date 2010-08-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00493-10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.50: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.

    Holder, Jason W / Ulrich, Jil C / DeBono, Anthony C / Godfrey, Paul A / Desjardins, Christopher A / Zucker, Jeremy / Zeng, Qiandong / Leach, Alex L B / Ghiviriga, Ion / Dancel, Christine / Abeel, Thomas / Gevers, Dirk / Kodira, Chinnappa D / Desany, Brian / Affourtit, Jason P / Birren, Bruce W / Sinskey, Anthony J

    PLoS genetics

    2011  Volume 7, Issue 9, Page(s) e1002219

    Abstract: The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of ... ...

    Abstract The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.
    MeSH term(s) Biofuels ; Fatty Acids/genetics ; Fatty Acids/metabolism ; Genome, Bacterial ; Genomics ; Lipids/biosynthesis ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Rhodococcus/genetics ; Rhodococcus/metabolism ; Triglycerides/biosynthesis ; Triglycerides/genetics
    Chemical Substances Biofuels ; Fatty Acids ; Lipids ; Triglycerides
    Language English
    Publishing date 2011-09-08
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1002219
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

    Desjardins, Christopher A / Champion, Mia D / Holder, Jason W / Muszewska, Anna / Goldberg, Jonathan / Bailão, Alexandre M / Brigido, Marcelo Macedo / Ferreira, Márcia Eliana da Silva / Garcia, Ana Maria / Grynberg, Marcin / Gujja, Sharvari / Heiman, David I / Henn, Matthew R / Kodira, Chinnappa D / León-Narváez, Henry / Longo, Larissa V G / Ma, Li-Jun / Malavazi, Iran / Matsuo, Alisson L /
    Morais, Flavia V / Pereira, Maristela / Rodríguez-Brito, Sabrina / Sakthikumar, Sharadha / Salem-Izacc, Silvia M / Sykes, Sean M / Teixeira, Marcus Melo / Vallejo, Milene C / Walter, Maria Emília Machado Telles / Yandava, Chandri / Young, Sarah / Zeng, Qiandong / Zucker, Jeremy / Felipe, Maria Sueli / Goldman, Gustavo H / Haas, Brian J / McEwen, Juan G / Nino-Vega, Gustavo / Puccia, Rosana / San-Blas, Gioconda / Soares, Celia Maria de Almeida / Birren, Bruce W / Cuomo, Christina A

    PLoS genetics

    2011  Volume 7, Issue 10, Page(s) e1002345

    Abstract: Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally ... ...

    Abstract Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
    MeSH term(s) Carbohydrate Metabolism/genetics ; Drug Delivery Systems ; Evolution, Molecular ; Genome, Fungal ; Genome, Mitochondrial/genetics ; Humans ; Multigene Family/genetics ; Onygenales/enzymology ; Onygenales/genetics ; Paracoccidioides/enzymology ; Paracoccidioides/genetics ; Paracoccidioidomycosis/microbiology ; Phylogeny ; Protein Kinases/genetics ; Proteolysis ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA
    Chemical Substances Protein Kinases (EC 2.7.-)
    Language English
    Publishing date 2011-10-27
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1002345
    Database MEDical Literature Analysis and Retrieval System OnLINE

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