Institute of Marine Biotechnology

Greifswald, Germany

Institute of Marine Biotechnology

Greifswald, Germany
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Markert S.,Institute of Marine Biotechnology | Gardebrecht A.,University of Greifswald | Felbeck H.,University of California at San Diego | Sievert S.M.,Woods Hole Oceanographic Institution | And 9 more authors.
Proteomics | Year: 2011

Riftia pachyptila, the giant deep-sea tube worm, inhabits hydrothermal vents in the Eastern Pacific ocean. The worms are nourished by a dense population of chemoautotrophic bacterial endosymbionts. Using the energy derived from sulfide oxidation, the symbionts fix CO 2 and produce organic carbon, which provides the nutrition of the host. Although the endosymbionts have never been cultured, cultivation-independent techniques based on density gradient centrifugation and the sequencing of their (meta-) genome enabled a detailed physiological examination on the proteomic level. In this study, the Riftia symbionts' soluble proteome map was extended to a total of 493 identified proteins, which allowed for an explicit description of vital metabolic processes such as the energy-generating sulfide oxidation pathway or the Calvin cycle, which seems to involve a reversible pyrophosphate-dependent phosphofructokinase. Furthermore, the proteomic view supports the hypothesis that the symbiont uses nitrate as an alternative electron acceptor. Finally, the membrane-associated proteome of the Riftia symbiont was selectively enriched and analyzed. As a result, 275 additional proteins were identified, most of which have putative functions in electron transfer, transport processes, secretion, signal transduction and other cell surface-related functions. Integrating this information into complex pathway models a comprehensive survey of the symbiotic physiology was established. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gardebrecht A.,University of Greifswald | Markert S.,University of Greifswald | Markert S.,Institute of Marine Biotechnology | Sievert S.M.,Woods Hole Oceanographic Institution | And 15 more authors.
ISME Journal | Year: 2012

The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments. © 2012 International Society for Microbial Ecology All rights reserved.

Kabisch A.,University of Greifswald | Otto A.,University of Greifswald | Konig S.,University of Greifswald | Konig S.,University Pierre and Marie Curie | And 7 more authors.
ISME Journal | Year: 2014

Members of the phylum Bacteroidetes are abundant in many marine ecosystems and are known to have a pivotal role in the mineralization of complex organic substrates such as polysaccharides and proteins. We studied the decomposition of the algal glycans laminarin and alginate by 'Gramella forsetii' KT0803, a bacteroidetal isolate from North Sea surface waters. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed two large polysaccharide utilization loci (PULs) that were specifically induced, one by alginate and the other by laminarin. These regulons comprised genes of surface-exposed proteins such as oligomer transporters, substrate-binding proteins, carbohydrate-active enzymes and hypothetical proteins. Besides, several glycan-specific TonB-dependent receptors and SusD-like substrate-binding proteins were expressed also in the absence of polysaccharide substrates, suggesting an anticipatory sensing function. Genes for the utilization of the beta-1,3-glucan laminarin were found to be co-regulated with genes for glucose and alpha-1,4-glucan utilization, which was not the case for the non-glucan alginate. Strong syntenies of the PULs of 'G. forsetii' with similar loci in other Bacteroidetes indicate that the specific response mechanisms of 'G. forsetii' to changes in polysaccharide availability likely apply to other Bacteroidetes. Our results can thus contribute to an improved understanding of the ecological niches of marine Bacteroidetes and their roles in the polysaccharide decomposition part of carbon cycling in marine ecosystems. © 2014 International Society for Microbial Ecology All rights reserved.

Kabisch J.,University of Greifswald | Thurmer A.,University of Gottingen | Hubel T.,Miltenyi Biotec GmbH | Popper L.,Stern Enzym GmbH and Co. KG | And 3 more authors.
Journal of Biotechnology | Year: 2013

The genome sequence of Bacillus subtilis ATCC 6051 and its suitability as an expression host for recombinant protein production was determined. The comparison of this undomesticated wild type with the widely used laboratory strain B. subtilis 168 reveals a high degree of congruency between the two strains. Differences could only be detected on the level of point mutations or small insertions. B. subtilis ATCC 6051 shows none of the auxotrophies known for B. subtilis 168 and is able to produce polyketides. It exhibits better use of complex media and higher genomic stability through reduced natural competence. Consequently, B. subtilis ATCC 6051 was genetically modified to yield an optimized strain for the production of heterologously expressed proteins under control of an acetoin-inducible promoter. © 2012 Elsevier B.V.

Petasch J.,Max Planck Institute for Marine Microbiology | Disch E.-M.,Max Planck Institute for Marine Microbiology | Markert S.,Institute of Marine Biotechnology | Markert S.,University of Greifswald | And 7 more authors.
BMC Microbiology | Year: 2014

Background: The facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen utilizes acyclic, monocyclic and bicyclic monoterpenes as sole carbon source under oxic as well as anoxic conditions. A biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. An in-frame deletion mutant did not use myrcene, but was able to grow on monocyclic monoterpenes. The genome sequence and a comparative proteome analysis together with a random transposon mutagenesis were conducted to identify genes involved in the monocyclic monoterpene metabolism. Metabolites accumulating in cultures of transposon and in-frame deletion mutants disclosed the degradation pathway. Results: Castellaniella defragrans 65Phen oxidizes the monocyclic monoterpene limonene at the primary methyl group forming perillyl alcohol. The genome of 3.95 Mb contained a 70 kb genome island coding for over 50 proteins involved in the monoterpene metabolism. This island showed higher homology to genes of another monoterpene-mineralizing betaproteobacterium, Thauera terpenica 58Eu T, than to genomes of the family Alcaligenaceae, which harbors the genus Castellaniella. A collection of 72 transposon mutants unable to grow on limonene contained 17 inactivated genes, with 46 mutants located in the two genes ctmAB (cyclic terpene metabolism). CtmA and ctmB were annotated as FAD-dependent oxidoreductases and clustered together with ctmE, a 2Fe-2S ferredoxin gene, and ctmF, coding for a NADH:ferredoxin oxidoreductase. Transposon mutants of ctmA, B or E did not grow aerobically or anaerobically on limonene, but on perillyl alcohol. The next steps in the pathway are catalyzed by the geraniol dehydrogenase GeoA and the geranial dehydrogenase GeoB, yielding perillic acid. Two transposon mutants had inactivated genes of the monoterpene ring cleavage (mrc) pathway. 2-Methylcitrate synthase and 2-methylcitrate dehydratase were also essential for the monoterpene metabolism but not for growth on acetate. Conclusions: The genome of Castellaniella defragrans 65Phen is related to other genomes of Alcaligenaceae, but contains a genomic island with genes of the monoterpene metabolism. Castellaniella defragrans 65Phen degrades limonene via a limonene dehydrogenase and the oxidation of perillyl alcohol. The initial oxidation at the primary methyl group is independent of molecular oxygen. © 2014 Petasch et al.; licensee BioMed Central Ltd.

PubMed | Okinawa Institute of Science and Technology, Leibniz Institute of Marine Science, Genoscope Center National Of Sequencage, Institute of Clinical Molecular Biology and 3 more.
Type: | Journal: eLife | Year: 2015

Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable arsenal of TRGs.

Welsch N.,University of Greifswald | Homuth G.,University of Greifswald | Schweder T.,University of Greifswald | Schweder T.,Institute of Marine Biotechnology
Applied Microbiology and Biotechnology | Year: 2015

In order to improve the overproduction of “difficult to express” proteins, a low-temperature expression system for Bacillus subtilis based on the cold-inducible promoter of the desaturase-encoding des gene was constructed. Selected regulatory DNA sequence elements from B. subtilis genes known to be cold-inducible were fused to different model genes. It could be demonstrated that these regulatory elements are able to mediate increased heterologous gene expression, either by improved translation efficiency or by higher messenger RNA (mRNA) stability. In case of a cold-adapted β-galactosidase from Pseudoalteromonas haloplanktis TAE79A serving as the model, significantly higher expression was achieved by fusing its coding sequence to the so-called “downstream box” sequence of cspB encoding the major B. subtilis cold-shock protein. The combination of this fusion with a cspB 5′-UTR stem-loop structure resulted in further enhancement of the β-galactosidase expression. In addition, integration of the transcription terminator of the B. subtilis cold-inducible bkd operon downstream of the target genes caused a higher mRNA stability and enabled thus a further significant increase in expression. Finally, the fully optimized expression system was validated by overproducing a B. subtilis xylanase as well as an α-glucosidase from Saccharomyces cerevisiae, the latter known for tending to form inclusion bodies. These analyses verified the applicability of the engineered expression system for extracellular and intracellular protein synthesis in B. subtilis, thereby confirming the suitability of this host organism for the overproduction of critical, poorly soluble proteins. © 2015, Springer-Verlag Berlin Heidelberg.

Finke B.,Leibniz Institute for Plasma Science and Technology | Polak M.,Leibniz Institute for Plasma Science and Technology | Hempel F.,Leibniz Institute for Plasma Science and Technology | Rebl H.,University of Rostock | And 8 more authors.
Advanced Engineering Materials | Year: 2012

The application of antimicrobial surfaces to titanium alloy (Ti) implants would be beneficial to prevent implant-associated infections of joint endoprostheses and osteosyntheses. Copper (Cu) could be advantageously applied for this purpose, since it exhibits a well-known antimicrobial activity and is a trace element in the human body, i.e., it is non-toxic in small concentrations. This approach was evaluated with two plasma-based surface modification procedures: Implantation of Cu ions into Ti by means of plasma immersion ion implantation (PIII) and Coating of Ti surfaces with Cu-Ti films by means of dual high power impulse magnetron sputtering (dual HiPIMS). In this manner, the surfaces could be equipped with various amounts of Cu, as it was analyzed by X-ray photoelectron spectroscopy (XPS). The surfaces released up to 8 mmol · L -1 of Cu within 24 h, measured with atomic absorption spectroscopy (AAS). Hence, the surfaces possessed an antimicrobial potential against typical infect-associated bacteria (Staphylococcus aureus). Surfaces with a higher Cu release prepared by HiPIMS technique revealed a higher antimicrobial effect, while surfaces implanted by PIII were less cytotoxic to osteoblasts (MG-63 cells). These results show that Cu doped and coated implants could be useful for prevention and therapy of implant-associated infections. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Welsch N.,University of Greifswald | Homuth G.,University of Greifswald | Schweder T.,University of Greifswald | Schweder T.,Institute of Marine Biotechnology
Applied Microbiology and Biotechnology | Year: 2012

The suitability of three β-galactosidases as reporter enzymes for promoter expression analyses was investigated in Bacillus subtilis with respect to various temperature conditions during cultivation and assay procedures. Starting from the hypothesis that proteins derived from diverse habitats have different advantages as reporters at different growth temperatures, the beta-galactosidases from the thermophilic organism Bacillus stearothermophilus, from the mesophilic bacterium Escherichia coli and from the psychrophilic organism Pseudoalteromonas haloplanktis TAE79 were analysed under control of the constitutive B. subtilis lepA promoter. Subsequent expression of the β-galactosidase genes and determination of specific activities was performed at different cultivation and assay temperatures using B. subtilis as host. Surprisingly, the obtained results demonstrated that the highest activities over a broad cultivation temperature range were obtained using the β-galactosidase from the mesophilic bacterium E. coli whereas the enzymes from the thermophilic and psychrophilic bacteria revealed a more restricted usability in terms of cultivation temperature. © 2011 Springer-Verlag.

Voigt B.,University of Greifswald | Voigt B.,Institute of Marine Biotechnology | Hieu C.X.,University of Greifswald | Hieu C.X.,Leibniz Institute of Plant Genetics and Crop Plant Research | And 10 more authors.
Proteomics | Year: 2012

The surface proteome (surfaceome) of the marine planctomycete Rhodopirellula baltica SH1T was studied using a biotinylation and a proteinase K approach combined with SDS-PAGE and mass spectrometry. 52 of the proteins identified in both approaches could be assigned to the group of potential surface proteins. Among them are some high molecular weight proteins, potentially involved in cell-cell attachment, that contain domains shown before to be typical for surface proteins like cadherin/dockerin domains, a bacterial adhesion domain or the fasciclin domain. The identification of proteins with enzymatic functions in the R. baltica surfaceome provides further clues for the suggestion that some degradative enzymes may be anchored onto the cell surface. YTV proteins, which have been earlier supposed to be components of the proteinaceous cell wall of R. baltica, were detected in the surface proteome. Additionally, 8 proteins with a novel protein structure combining a conserved type IV pilin/N-methylation domain and a planctomycete-typical DUF1559 domain were identified. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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