Ralf Rabus

Summary

Affiliation: Max Planck Institute for Marine Microbiology
Country: Germany

Publications

  1. ncbi request reprint Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Appl Microbiol Biotechnol 68:580-7. 2005
  2. doi request reprint An overview of 2D DIGE analysis of marine (environmental) bacteria
    Ralf Rabus
    Institute of Biology and Chemistry of the Marine Environment ICBM, University Oldenburg, Oldenburg, Germany
    Methods Mol Biol 854:355-72. 2012
  3. pmc Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade
    Tobias Fürch
    Institute of Biochemical Engineering, Technische Universitat Braunschweig, Gaussstrasse 17, D 38106 Braunschweig, Germany
    BMC Microbiol 9:209. 2009
  4. pmc Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism
    R Rabus
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    J Bacteriol 183:1707-15. 2001
  5. ncbi request reprint Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the beta-subclass of Proteobacteria
    R Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Environ Microbiol 1:145-57. 1999
  6. ncbi request reprint Analysis of N-acetylglucosamine metabolism in the marine bacterium Pirellula sp. strain 1 by a proteomic approach
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Proteomics 2:649-55. 2002
  7. ncbi request reprint Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany
    Arch Microbiol 178:506-16. 2002
  8. ncbi request reprint The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359, Bremen, Germany
    Arch Microbiol 183:27-36. 2005
  9. doi request reprint Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395
    Hajo Zech
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 13:2869-85. 2013
  10. doi request reprint Anaerobic degradation of 4-methylbenzoate via a specific 4-methylbenzoyl-CoA pathway
    Sven Lahme
    Institute for Chemistry and Biology of the Marine Environment ICBM, University of Oldenburg, Carl von Ossietzky Strasse 9 11, Oldenburg, Germany
    Environ Microbiol 14:1118-32. 2012

Collaborators

Detail Information

Publications43

  1. ncbi request reprint Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Appl Microbiol Biotechnol 68:580-7. 2005
    ..J Bacteriol 187:1493-1503] indicated coordinated vs sequential modes of regulation for the toluene and ethylbenzene pathways, respectively...
  2. doi request reprint An overview of 2D DIGE analysis of marine (environmental) bacteria
    Ralf Rabus
    Institute of Biology and Chemistry of the Marine Environment ICBM, University Oldenburg, Oldenburg, Germany
    Methods Mol Biol 854:355-72. 2012
    ....
  3. pmc Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade
    Tobias Fürch
    Institute of Biochemical Engineering, Technische Universitat Braunschweig, Gaussstrasse 17, D 38106 Braunschweig, Germany
    BMC Microbiol 9:209. 2009
    ..Based on information from recently sequenced genomes, a rich repertoire of pathways has been identified in the carbon core metabolism of these organisms, but little is known about the actual contribution of the various reactions in vivo...
  4. pmc Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism
    R Rabus
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    J Bacteriol 183:1707-15. 2001
    ..When 2,3-d(2)-fumarate was added to cultures growing on unlabeled n-hexane, 3-d(1)-MPS rather than 2,3-d(2)-MPS was detected, indicating loss of one deuterium atom by an as yet unknown mechanism...
  5. ncbi request reprint Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the beta-subclass of Proteobacteria
    R Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Environ Microbiol 1:145-57. 1999
    ....
  6. ncbi request reprint Analysis of N-acetylglucosamine metabolism in the marine bacterium Pirellula sp. strain 1 by a proteomic approach
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Bremen, Germany
    Proteomics 2:649-55. 2002
    ..Thus the coding genes of three proteins expressed during growth of Pirellula sp. strain 1 on carbohydrates were identified and related by sequence similarity to carbohydrate metabolism...
  7. ncbi request reprint Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany
    Arch Microbiol 178:506-16. 2002
    ..The DNA fragment also included genes for regulatory systems; these were two sets of two-component systems, two LysR homologs, and a TetR homolog. Some of these proteins may be involved in ethylbenzene-dependent gene expression...
  8. ncbi request reprint The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1
    Ralf Rabus
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359, Bremen, Germany
    Arch Microbiol 183:27-36. 2005
    ..Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/...
  9. doi request reprint Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395
    Hajo Zech
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 13:2869-85. 2013
    ..In contrast, metabolites of the Entner-Doudoroff pathway and gluconeogenesis as well as cellular fatty acids increased markedly in abundance in early stationary growth phase. ..
  10. doi request reprint Anaerobic degradation of 4-methylbenzoate via a specific 4-methylbenzoyl-CoA pathway
    Sven Lahme
    Institute for Chemistry and Biology of the Marine Environment ICBM, University of Oldenburg, Carl von Ossietzky Strasse 9 11, Oldenburg, Germany
    Environ Microbiol 14:1118-32. 2012
    ....
  11. pmc Physiological and proteomic adaptation of "Aromatoleum aromaticum" EbN1 to low growth rates in benzoate-limited, anoxic chemostats
    Kathleen Trautwein
    Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
    J Bacteriol 194:2165-80. 2012
    ..This potential catabolic versatility and stress defense during slow growth may be interpreted as preparation for future needs...
  12. doi request reprint Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria
    Florin Musat
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 11:209-19. 2009
    ..The inability to utilize 1-naphthol or 2-naphthol also excludes these compounds as free intermediates. Results leave open the possibility of naphthalene carboxylation, another previously suggested activation mechanism...
  13. ncbi request reprint Genes encoding the candidate enzyme for anaerobic activation of n-alkanes in the denitrifying bacterium, strain HxN1
    Olav Grundmann
    Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 10:376-85. 2008
    ..n-Hexane-induced co-transcription of the mas genes and additional genes of an apparent operon was demonstrated by Northern hybridization experiments...
  14. pmc Anaerobic degradation of p-ethylphenol by "Aromatoleum aromaticum" strain EbN1: pathway, regulation, and involved proteins
    Lars Wöhlbrand
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    J Bacteriol 190:5699-709. 2008
    ..Coregulated proteins of currently unknown function (e.g., EbA329) are possibly involved in p-ethylphenol- and p-hydroxyacetophenone-specific solvent stress responses and related to other aromatic solvent-induced proteins of strain EbN1...
  15. doi request reprint Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium
    Lars Wöhlbrand
    Institute for Chemistry and Biology of Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse 9 11, 26111, Oldenburg, Germany
    Environ Microbiol 15:1334-55. 2013
    ..The multiple heterodisulfide reductase-like proteins (more than described for Desulfobacterium autotrophicum HRM2) may constitute a multifaceted cytoplasmic electron transfer network...
  16. ncbi request reprint Functional proteomic view of metabolic regulation in "Aromatoleum aromaticum" strain EbN1
    Lars Wöhlbrand
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Proteomics 7:2222-39. 2007
    ..g. o-aminobenzoate, anoxic). Comparing all identified regulated and nonregulated proteins provided first insights into regulatory hierarchies of special degradation pathways versus general metabolism in strain EbN1...
  17. pmc Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1
    Simon Kühner
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, 28359 Bremen, Germany
    J Bacteriol 187:1493-503. 2005
    ....
  18. doi request reprint Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395
    Sebastian Koßmehl
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 13:2743-60. 2013
    ..From a proteogenomic perspective, functional prediction of 74 genes (including 17 coding for proteins of hitherto unknown function) could be refined. ..
  19. doi request reprint Biological versus technical variability in 2-D DIGE experiments with environmental bacteria
    Hajo Zech
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 11:3380-9. 2011
    ..Furthermore, comparison of different treatment groups (different substrate conditions) demonstrated that variability within groups is significantly smaller than differences caused by treatment...
  20. doi request reprint Substrate-dependent regulation of carbon catabolism in marine sulfate-reducing Desulfobacterium autotrophicum HRM2
    Judith Amann
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    J Mol Microbiol Biotechnol 18:74-84. 2010
    ..In summary, the different regulatory patterns displayed by Db. autotrophicum HRM2 at the tested metabolic levels point to a multi-layered regulatory network...
  21. ncbi request reprint Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)
    Katharina Drüppel
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Environ Microbiol 16:218-38. 2014
    ..Comparison of genes for the reconstructed amino acid degradation network in Ph. inhibens DSM 17395 across 27 other complete genomes of Roseobacter clade members revealed most of them to be widespread among roseobacters...
  22. pmc Benzoate mediates repression of C(4)-dicarboxylate utilization in "Aromatoleum aromaticum" EbN1
    Kathleen Trautwein
    Institute of Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
    J Bacteriol 194:518-28. 2012
    ..The increased dctP (respectively, dctPQM) transcript and DctP protein abundance following benzoate depletion suggests that repression of C(4)-dicarboxylate uptake seems to be a main determinant for the observed diauxie...
  23. ncbi request reprint Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins
    Dörte Gade
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Proteomics 5:3654-71. 2005
    ..The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization...
  24. ncbi request reprint Growth phase dependent regulation of protein composition in Rhodopirellula baltica
    Dörte Gade
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Environ Microbiol 7:1074-84. 2005
    ..These proteins could possibly be involved in the development of the different R. baltica morphotypes, i.e. motile swarmer cells and sessile cell aggregates (so-called rosettes)...
  25. doi request reprint Proteogenomic evidence for β-oxidation of plant-derived 3-phenylpropanoids in "Aromatoleum aromaticum" EbN1
    Kathleen Trautwein
    Carl von Ossietzky University, Oldenburg, Germany Max Planck Institute for Marine Microbiology, Carl von Ossietzky Strasse 9 11, Bremen, Germany
    Proteomics 12:1402-13. 2012
    ..The low amount of metabolites attributable to cometabolic transformation of nongrowth supporting 3-phenylpropanoids (e.g. o-coumarate, ferulate) may be indicative for a high substrate specificity of the involved enzymes...
  26. doi request reprint Adaptation of Phaeobacter inhibens DSM 17395 to growth with complex nutrients
    Hajo Zech
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 13:2851-68. 2013
    ..Apparently, P. inhibens DSM 17395 modulated its metabolism to simultaneously utilize diverse substrates from the complex nutrient supply. ..
  27. ncbi request reprint Evaluation of two-dimensional difference gel electrophoresis for protein profiling. Soluble proteins of the marine bacterium Pirellula sp. strain 1
    Dörte Gade
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    J Mol Microbiol Biotechnol 5:240-51. 2003
    ..Labeling with CyDyes allowed detection of almost as many protein spots as staining with silver or SYPRO Ruby...
  28. ncbi request reprint Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1
    Peter Hufnagel
    Bruker Daltonik GmbH, Bremen, Germany
    J Mol Microbiol Biotechnol 11:53-81. 2006
    ..In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research...
  29. doi request reprint Proteomic tools for environmental microbiology--a roadmap from sample preparation to protein identification and quantification
    Lars Wöhlbrand
    Institute for Chemistry and Biology of the Marine Environment ICBM, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
    Proteomics 13:2700-30. 2013
    ....
  30. pmc Anaerobic degradation of 4-methylbenzoate by a newly isolated denitrifying bacterium, strain pMbN1
    Sven Lahme
    Carl von Ossietzky University, Oldenburg, Germany
    Appl Environ Microbiol 78:1606-10. 2012
    ..Based on 16S rRNA gene sequence analysis, strain pMbN1 is affiliated with the genus Magnetospirillum...
  31. doi request reprint Development of a genetic system for the denitrifying bacterium 'Aromatoleum aromaticum' strain EbN1
    Lars Wöhlbrand
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    J Mol Microbiol Biotechnol 17:41-52. 2009
    ..The effectiveness of the genetic system was demonstrated by unmarked in-frame deletion of ebdC2, encoding the gamma-subunit of a paralogous ethylbenzene dehydrogenase...
  32. ncbi request reprint Towards habitat-oriented systems biology of "Aromatoleum aromaticum" EbN1: chemical sensing, catabolic network modulation and growth control in anaerobic aromatic compound degradation
    Ralf Rabus
    Institut für Chemie und Biologie des Meeres ICBM, AG Allgemeine und Molekulare Mikrobiologie, Carl von Ossietzky Universitat Oldenburg, Carl von Ossietzky Str 9 11, 26111, Oldenburg, Germany
    Appl Microbiol Biotechnol 98:3371-88. 2014
    ..aromaticum" EbN1...
  33. ncbi request reprint Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica
    Dörte Gade
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Proteomics 5:3672-83. 2005
    ..e.g., a ribose-induced alcohol dehydrogenase is encoded within an operon-like structure together with genes coding for a ribose-specific ABC-transporter. However, most of the regulated genes are randomly distributed across the genome...
  34. ncbi request reprint Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea
    Marc Mussmann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, D 28359 Bremen, Germany
    Environ Microbiol 7:405-18. 2005
    ..This group accounted for up to 6% of total cell numbers and even exceeded SRB numbers in upper sediment layers. These bacteria might substantially contribute to carbon mineralization via dissimilatory reduction of, e.g. Fe(III)...
  35. ncbi request reprint Anaerobic degradation of n-hexane in a denitrifying bacterium: further degradation of the initial intermediate (1-methylpentyl)succinate via C-skeleton rearrangement
    Heinz Wilkes
    Institut für Erdöl und Organische Geochemie, Forschungszentrum Julich GmbH, 52425 Julich, Germany
    Arch Microbiol 177:235-43. 2002
    ..Such a pathway would also allow regeneration of fumarate (for n-hexane activation) from propionyl-CoA formed as intermediate and hence present a cyclic process...
  36. ncbi request reprint Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1
    Michael Kube
    Max Planck Institut fur Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
    Arch Microbiol 181:182-94. 2004
    ..The genes between the bss and bbs operons and in the flanking regions differ between strain EbN1 and the other strains...
  37. pmc Polyhydroxyalkanoate (PHA) accumulation in sulfate-reducing bacteria and identification of a class III PHA synthase (PhaEC) in Desulfococcus multivorans
    Tran Hai
    Institut fur Molekulare Mikrobiologie und Biotechnologie, Westfalische Wilhelms Universitat Munster, Corrensstrasse 3, D 48149 Munster, Germany
    Appl Environ Microbiol 70:4440-8. 2004
    ..Hybrid synthases consisting of PhaC(Dm) and PhaE of Thiococcus pfennigii or Synechocystis sp. strain PCC 6308 were also constructed and were shown to be functionally active...
  38. pmc Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase
    Shelley A Haveman
    Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
    J Bacteriol 185:4345-53. 2003
    ....
  39. ncbi request reprint A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats
    Michael Kube
    Max Planck Institut fir Molekulare Genetik, Ihnestr 73, D 14129 Berlin, Germany
    Syst Appl Microbiol 28:287-94. 2005
    ....
  40. ncbi request reprint Analyses of the vrl gene cluster in Desulfococcus multivorans: homologous to the virulence-associated locus of the ovine footrot pathogen Dichelobacter nodosus strain A198
    Florian Knaust
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    J Mol Microbiol Biotechnol 13:156-64. 2007
    ..The latter is supported by the evidence for expression of the vrl genes in D. multivorans, which has not been described as pathogen or to be associated to any disease pattern before...
  41. pmc Solvent stress response of the denitrifying bacterium "Aromatoleum aromaticum" strain EbN1
    Kathleen Trautwein
    Institute of Chemistry and Biology of the Marine Environment ICBM, University of Oldenburg, Carl von Ossietzky Str 9 11, D 26111 Oldenburg, Germany
    Appl Environ Microbiol 74:2267-74. 2008
    ..g., up-regulation of PHB granule-associated phasins, cytochrome cd(1) nitrite reductase of denitrification, and several proteins involved in oxidative (e.g., SodB) and general (e.g., ClpB) stress responses...
  42. ncbi request reprint Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. an
    Heinz Schlesner
    Institut fur Allgemeine Mikrobiologie, Christian Albrechts Universitat, Am Botanischen Garten 1 9, D 24118 Kiel, Germany
    Int J Syst Evol Microbiol 54:1567-80. 2004
    ..Differentiation between R. baltica, B. marina and Pirellula staleyi was achieved by the integration of morphological, physiological, chemotaxonomic and genetic characteristics...
  43. ncbi request reprint Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1
    H Wolfgang Höffken
    BASF AG, Physical Chemistry and Informatics, 67056 Ludwigshafen, Germany
    Biochemistry 45:82-93. 2006
    ..These elements may transmit the substrate-induced conformational change of the substrate binding loop from one subunit to the others in the tetrameric complex and thus mediate the cooperative behavior of PED...