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  1. Book ; Online ; Thesis: Development of a xylose inducible promoter system to study ribosome biogenesis in Chaetomium thermophilum

    Reislöhner, Sven [Verfasser] / Hurt, Ed [Akademischer Betreuer]

    2022  

    Author's details Sven Reislöhner ; Betreuer: Ed Hurt
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek Heidelberg
    Publishing place Heidelberg
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  2. Article ; Online: Identification and characterization of sugar-regulated promoters in Chaetomium thermophilum.

    Reislöhner, Sven / Schermann, Geza / Kilian, Max / Santamaría-Muñoz, Daniela / Zimmerli, Christian / Kellner, Nikola / Baßler, Jochen / Brunner, Michael / Hurt, Ed

    BMC biotechnology

    2023  Volume 23, Issue 1, Page(s) 19

    Abstract: The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of ... ...

    Abstract The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of genetic tools compatible with this thermophile, which are typically suited to other mesophilic eukaryotic model organisms, in particular the yeast Saccharomyces cerevisiae. Hence, we aimed to find genes from C. thermophilum that are expressed under the control of different sugars and examine their associated 5' untranslated regions as promoters responsible for sugar-regulated gene expression. To identify sugar-regulated promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes with induced expression in the presence of xylose but repressed expression in glucose-supplemented media. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of a thermostable yellow fluorescent protein (YFP) reporter. With this, we demonstrated xylose-dependent YFP expression by both Western blotting and live-cell imaging fluorescence microscopy. Prompted by these results, we expressed the C. thermophilum orthologue of a well-characterized dominant-negative ribosome assembly factor mutant, under the control of the XDH promoter, which allowed us to induce a nuclear export defect on the pre-60S subunit when C. thermophilum cells were grown in xylose- but not glucose-containing medium. Altogether, our study identified xylose-regulatable promoters in C. thermophilum, which might facilitate functional studies of genes of interest in this thermophilic eukaryotic model organism.
    MeSH term(s) Sugars/metabolism ; Xylose/metabolism ; Chaetomium/genetics ; Chaetomium/metabolism ; Saccharomyces cerevisiae/genetics ; Glucose/metabolism
    Chemical Substances Sugars ; Xylose (A1TA934AKO) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2023-07-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2052746-9
    ISSN 1472-6750 ; 1472-6750
    ISSN (online) 1472-6750
    ISSN 1472-6750
    DOI 10.1186/s12896-023-00791-9
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  3. Article: Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum

    Singh, Amit / Schermann, Géza / Reislöhner, Sven / Kellner, Nikola / Hurt, Ed / Brunner, Michael

    Genes. 2021 Sept. 29, v. 12, no. 10

    2021  

    Abstract: A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames ...

    Abstract A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of C. thermophilum by deep RNA sequencing. We annotated 7044 coding genes and 4567 noncoding genes. Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes as well as 2878 novel noncoding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help to understand the gene regulatory landscape in C. thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.
    Keywords Chaetomium ; enzymes ; gene ontology ; genes ; structural biology ; transcriptome
    Language English
    Dates of publication 2021-0929
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12101549
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete

    Singh, Amit / Schermann, Géza / Reislöhner, Sven / Kellner, Nikola / Hurt, Ed / Brunner, Michael

    Genes

    2021  Volume 12, Issue 10

    Abstract: A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome ... ...

    Abstract A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of
    MeSH term(s) Chaetomium/genetics ; Chaetomium/metabolism ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Regulatory Networks ; Molecular Sequence Annotation ; Transcriptome
    Chemical Substances Fungal Proteins
    Language English
    Publishing date 2021-09-29
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12101549
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  5. Article ; Online: In vivo localization studies in the stramenopile alga Nannochloropsis oceanica.

    Moog, Daniel / Stork, Simone / Reislöhner, Sven / Grosche, Christopher / Maier, Uwe-G

    Protist

    2015  Volume 166, Issue 1, Page(s) 161–171

    Abstract: The tiny eustigmatophyte Nannochloropsis sp. recently emerged as a promising model organism for biotechnology as it possesses a considerably high cellular oil content interesting for biodiesel production. Furthermore, the alga was shown to be genetically ...

    Abstract The tiny eustigmatophyte Nannochloropsis sp. recently emerged as a promising model organism for biotechnology as it possesses a considerably high cellular oil content interesting for biodiesel production. Furthermore, the alga was shown to be genetically well accessible providing powerful tools for biotechnological engineering as well as basic research. Nannochloropsis sp. can be transformed very efficiently taking advantage of homologous recombination, however, so far it remained unclear whether these organisms are also suitable model systems for in vivo protein localization studies due to their small cell size. Here we present, to our knowledge, the first protein localization studies based on the expression of chimeric fluorescent fusion proteins in the genus Nannochloropsis using N. oceanica CCMP1779 as a model organism. Besides expressing a cytosolic green fluorescent protein (GFP), the reporter could be directed into subcellular structures such as the mitochondria, the endoplasmic reticulum and secretory pathway as well as the complex plastid including the periplastidal compartment and the stroma via fusion of specific N-terminal targeting sequences. These results expand the potential of N. oceanica as a model system in biotechnology as well as cellular biology for which now an almost complete molecular tool set exists.
    MeSH term(s) Algal Proteins/genetics ; Algal Proteins/metabolism ; Genes, Reporter ; Genetics, Microbial/methods ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Metabolic Engineering/methods ; Protein Transport ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Stramenopiles/genetics ; Stramenopiles/metabolism
    Chemical Substances Algal Proteins ; Luminescent Proteins ; Recombinant Proteins
    Language English
    Publishing date 2015-02
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2036014-9
    ISSN 1618-0941 ; 1434-4610
    ISSN (online) 1618-0941
    ISSN 1434-4610
    DOI 10.1016/j.protis.2015.01.003
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