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  • 1
    Electronic Resource
    Electronic Resource
    Glycerol conversion to 1,3-propanediol by Clostridium pasteurianum: cloning and expression of the gene encoding 1,3-propanediol dehydrogenase (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 154 (1997), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: When grown on glycerol as sole carbon and energy source, cell extracts of Clostridium pasteurianum exhibited activities of glycerol dehydrogenase, dihydroxyacetone kinase, glycerol dehydratase and 1,3-propanediol dehydrogenase. The genes encoding the latter two enzymes were cloned by colony hybridization using the dhaT gene of Citrobacter freundii as a heterologous DNA probe and expressed in Escherichia coli. The native molecular mass of 1,3-propanediol dehydrogenase (DhaT) is 440 000 Da. The dhaT gene of C. pasteurianum was subcloned and its nucleotide sequence (1158 bp) was determined. The deduced gene product (41 776 Da) revealed high similarity to DhaT of C. freundii (80.5% identity; 89.8% similarity).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1997.tb12665.x
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  • 2
    Electronic Resource
    Electronic Resource
    Biochemistry of coenzyme B12-dependent glycerol and diol dehydratases and organization of the encoding genes (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 22 (1998), S. 0 
    Details
    ISSN: 1574-6976
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Glycerol and diol dehydratases exhibit a subunit composition of α2β2γ2 and contain coenzyme B12 in the base-on form. The dehydratase reaction proceeds via a radical mechanism. The dehydratases are subject to reaction inactivation by the substrate glycerol which is caused by a cessation of the catalytic cycle because coenzyme B12 is not regenerated, instead 5′-deoxyadenosine and a catalytically inactive cobalamin are formed. The genetic organization of the dehydratase genes is quite similar in all organisms. Downstream of the dehydratase genes an open reading frame encoding a polypeptide of approximately 600 amino acids was identified which is apparently involved in the reactivation of suicide-inactivated enzyme.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6976.1998.tb00387.x
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  • 3
    Electronic Resource
    Electronic Resource
    Identification of the syntrophic partners in a coculture coupling anaerobic methanol oxidation to Fe(III) reduction (1999)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 180 (1999), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: From enrichments with methanol and ferric pyrophosphate a coculture was isolated which coupled methanol oxidation to carbon dioxide with the reduction of Fe(III) to Fe(II). 16S rRNA gene analysis of the isolated syntrophic partners revealed 99.5% similarity to Clostridium sphenoides and 98.5% to Shewanella putrefaciens. Formation of Fe(II) coupled to methanol oxidation was confirmed by using strains of culture collections (C. sphenoides DSM 632 and S. putrefaciens DSM 9461). The importance of this process is discussed, also with respect to the anaerobic oxidation of methane.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1999.tb08796.x
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  • 4
    Electronic Resource
    Electronic Resource
    Properties and sequence of the coenzyme B12-dependent glycerol dehydratase of Clostridium pasteurianum (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 164 (1998), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The genes encoding coenzyme B12-dependent glycerol dehydratase of Clostridium pasteurianum were subcloned and expressed in Escherichia coli. The native molecular mass of the enzyme is 190 000 Da. The enzyme converts glycerol, 1,2-propanediol and 1,2-ethanediol to 3-hydroxypropionaldehyde, propionaldehyde and acetaldehyde, respectively, but glycerol is the preferred substrate. The nucleotide sequences of the dhaBCE genes encoding the three subunits of glycerol dehydratase and of orfZ whose function is unknown were determined. The deduced products of the dhaBCE genes with calculated molecular masses of 60 813, 19 549 and 16 722 Da, respectively, revealed high similarity to amino acid sequences of subunits of coenzyme B12-dependent glycerol and diol dehydratases from other organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1998.tb13062.x
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  • 5
    Electronic Resource
    Electronic Resource
    Growth temperature-dependent activity of glycerol dehydratase in Escherichia coli expressing the Citrobacter freundii dha regulon (1992)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 100 (1992), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Using the cosmid pWE15, a genomic library of Citrobacter freundii DNA in Escherichia coli ECL707 was prepared and screened for glycerol utilization. Six out of approximately 3000 clones were positive. One clone, harboring the recombinant cosmid pRD1, expressed glycerol dehydratase in high activity when grown at 28°C but not at 37°C. The growth temperature had little effect on the activity of the other enzymes encoded by the dha regulon. When the glycerol-containing medium was supplemented with corrinoids, the recombinant E. coli strain produced 1,3-propanediol in high amounts at 28°C.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1992.tb14053.x
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  • 6
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    Prokaryotic Diversity and Community Patterns in Antarctic Continental Shelf Sponges (2019)
    Frontiers Media S.A.
    In:  EPIC3Frontiers in Marine Science, Frontiers Media S.A., 6(297), ISSN: 2296-7745
    Details
    Publication Date: 2019-07-25
    Description: Marine sponges (Phylum Porifera) are globally distributed within marine and freshwater ecosystems. In addition, sponges host dense and diverse prokaryotic communities, which are potential sources of novel bioactive metabolites and other complex compounds. Those sponge-derived natural products can span a broad spectrum of bioactivities, from antibacterial and antifungal to antitumor and antiviral compounds. However, most analyses concerning sponge-associated prokaryotes have mainly focused on conveniently accessible relatively shallow sampling locations for sponges. Hence, knowledge of community composition, host-relatedness and biotechnological potential of prokaryotic associations in temperate and cold-water sponges from greater depths (mesophotic to mesopelagic zones) is still scarce. Therefore, we analyzed the prokaryotic community diversity of four phylogenetically divergent sponge taxa from mesophotic to mesopelagic depths of Antarctic shelf at different depths and locations in the region of the South Shetland Islands using 16S rRNA gene amplicon-based sequencing. In addition, we predicted functional profiles applying Tax4Fun from metagenomic 16S rRNA gene data to estimate their biotechnological capability and possible roles as sources of novel bioactive compounds. We found indications that cold and deep-water sponges exhibit host-specific prokaryotic communities, despite different sampling sites and depths. Functional prediction analysis suggests that the associated prokaryotes may enhance the roles of sponges in biodegradation processes of xenobiotics and their involvement in the biosynthesis of secondary metabolites.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 7
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    CAZymes in Maribacter dokdonensis 62–1 from the Patagonian shelf: genomics and physiology compared to related flavobacteria and a co-occurring Alteromonas strain (2021)
    In:  EPIC3Frontiers in Microbiology, 12, pp. 628055, ISSN: 1664-302X
    Details
    Publication Date: 2021-04-19
    Description: Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 8
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    Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans (2015)
    In:  EPIC3Environmental Microbiology, 17(10), pp. 3822-3831, ISSN: 14622912
    Details
    Publication Date: 2021-11-16
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 9
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    Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle (2021)
    In:  EPIC3Systematic and Applied Microbiology, 44, pp. 126166, ISSN: 07232020
    Details
    Publication Date: 2021-11-16
    Description: The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T = LMG 30557T) as a novel species with the name Pseudooceanicola algae.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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    Format: application/zip
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  • 10
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    Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont (2017)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 12 (2017): 50, doi:10.1186/s40793-017-0266-y.
    Description: Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis.
    Description: This study was supported by the EU-funded Marie Curie Initial Training Network “Symbiomics” (project no. 264774). RP was supported by a fellowship of the Institute of Marine Biotechnology, Greifswald. MK was supported by a NSERC Banting Postdoctoral Fellowship. LS was supported by a DAAD scholarship. SMS was supported by US National Science Foundation grant OCE-1136727.
    Keywords: Uncultured endosymbiont ; Hydrothermal vents ; Marine invertebrate symbiosis ; Thiotrophy ; Autotrophy ; Atlantis (Ship : 1996-) Cruise AT26-10
    Repository Name: Woods Hole Open Access Server
    Type: Article
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