The project area C "Systems Biology" focuses on the two model organisms D. shibae and P. gallaeciensis.
The final goal here is the generation of bioinformatics models which allow for the prediction of metabolic and gene regulatory adaptation processes. In order to generate the necessary data for model building a strictly coordinated experimental effort is conducted. Highly standardized and reproducible growth conditions in a chemostat provide the basis for the integrated analysis of transcriptome, proteome, metabolome and the dynamic fluxome in response to defined growth changes or genetic variations.
Obtained data are used to generate and iteratively optimize genome based metabolic and gene regulatory models. Data from closely related B area projects will be integrated. The long-term goal is the integration of the various models in complex systems biology models for the prediction of multi-level adaptation processes. Based on the genome information of other Roseobacter clade bacteria the established bioinformatics models will be used to predict and understand their strain specific adaptation strategies to their habitats. These systems biology analyses of roseobacters in their environment closes the circuit to project area A.
Adaptation of metabolic and cellular networks to changing nutrient conditions in Phaeobacter gallaeciensis and Dinoroseobacter shibae
Principal investigator: Prof. Dr. Ralf Rabus
PhD Students: K. Drüppel, S. Koßmehl
Project
The main goal of this project is to elucidate the metabolic strategies and molecular mechanisms enabling the habitat success of roseobacters from a systems biology perspective. To this end, Phaeobacter inhibens DSM 17395 was selected as representative of nutritional versatile Roseobacter clade members. During the first funding period, we mainly focus on elucidating the catabolic network of amino acids and carbohydrates and on advancing proteomics approaches for investigations with P. inhibens DSM 17395. Moreover, we perform extensive proteomic analysis of D. shibae DFL12T studied in Braunschweig with respect to light/dark and oxic/anoxic shifts.
Amino acid catabolism of P. inhibens DSM 17395: Roseobacters, as abundant members of the marine bakterioplankton, contribute substantially to organic matter (OM) turnover in ocean waters. Since OM consists to a large part of proteins and since P. inhibens DSM 17395 grows best with amino acids, their utilization was investigated in close collaboration with AG Schomburg on 3 different levels. (i) To study the adaptive strategies to availability of complex and excess nutrients, as typically encountered in the course of collapsing algal blooms, Marine Broth (MB) and process-controlled fermenters were used to mimic such a nutritional scenario (Zech et al. 2013a). (ii) To resolve preferential utilization of certain amino acids from a complex while analytically traceable mixture of amino acids, casamino acids were used (Zech et al. 2013b). (iii) Despite the growing number of genome sequences from the Roseobacter clade, amino acid degradation remains in parts unclear or ambiguous. This was studied for nine selected individual amino acids. In all three topics, physiology was combined with enzymatic, proteomic and metabolomic analysis.
Proteomics approaches: At the beginning of the first funding period we assessed the influence of biological versus technical variation in 2D DIGE experiments of P. inhibens DSM 17395 on the basis of raw data. This led to the decision to only use biological replicates and to apply a conservative threshold of significance of -1.5 and 1.5 (Zech et al. 2011). Subcellular fractionation of P. inhibens DSM 17395, followed by gel- or nanoLC-based separation of proteins and peptides yielded MS-based identification of 1,187 proteins. From these, the functionalities of the cell envelope compartments were reconstructed, e.g. protein secretion/sorting and direct effector molecule transit. Notably, the functional prediction of 74 genes (including 17 coding for proteins of hitherto unknown function) could be refined (Koßmehl et al. 2013).
Methods
Physiology:
Proteomics:
Figure 1.
Publikationen
2017
Ruppersberg HS, Goebel MR, Kleinert SI, Wünsch D, Trautwein K, Rabus R (2017) Photometric determination of ammonium and phosphate in seawater medium using a microplate reader. J Mol Microbiol Biotechnol 27:73-80
Trautwein K, Feenders C, Hulsch R, Ruppersberg HS, Strijkstra A, Kant M, Vagts J, Wünsch D, Michalke B, Maczka M, Schulz S, Hillebrand H, Blasius B, Rabus R (2017) Non-Redfield, nutrient synergy, and flexible internal elemental stoichiometry in a marine bacterium. FEMS Microbiol Ecol doi: 10.1093/femsec/fix059
Wöhlbrand L, Rabus R, Blasius B, Feenders C (2017b) Influence of nanoLC column- and gradient-length as well as MS/MS frequency and sample complexity on shotgun protein identification of marine bacteria. J Mol Microbiol Biotechnol accepted
Wöhlbrand L, Wemheuer B, Feenders C, Ruppersberg HS, Hinrichs C, Blasius B, Daniel R, Rabus R (2017a) Complementary metaproteomic approaches to assess the bacterioplankton response toward a phytoplankton spring bloom in the Southern North Sea. Front Microbiol 8:442
2016
Trautwein K, Will SE, Hulsch R, Maschmann U, Wiegmann K, Hensler M, Michael V, Ruppersberg H, Wünsch D, Feenders C, Neumann-Schaal M, Kaltenhäuser S, Ulbrich M, Schmidt-Hohagen K, Blasius B, Petersen J, Schomburg D, Rabus R (2016) Native plasmids restrict growth of Phaeobacter inhibens DSM 17395. Energetic costs of plasmids assessed by quantitative physiological analyses. Environ Microbiol 18: 4817-4829.
2014
Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, Schomburg D, Rabus R (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol 16: 218–238. doi:10.1111/1462-2920.12276.
Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D (2014) Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 289: 13219–13231. doi:10.1074/jbc.M113.545004.
Wiegmann K, Hensler M, Wöhlbrand L, Ulbrich M, Schomburg D, Rabus R (2014) Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, member of the marine Roseobacter clade. Appl Environ Microbiol 80:4725-4737
2013
Ebert M, Laaß S, Burghartz M, Petersen J, Rabus R, Wöhlbrand L, Tielen P, Jahn D. (2013) Chromosomal and plasmid encoded genes are essential for the anaerobic growth of the marine bacterium Dinoroseobacter shibae. J.Bacteriol, 195/20: 4769-4777.
Koßmehl S, Wöhlbrand L, Drüppel K, Feenders C, Blasius B, Rabus R (2013) Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395. Proteomics 13/18-19 SI: 2743-2760.
Rabus R (2013) Environmental Microbial Proteomics: New avenues for a molecular understanding of the functional role of microorganisms in the natural environment. Proeomics 13/18-19 SI: 2697-2699.
Wöhlbrand L, Trautwein K, Rabus R (2013) Proteomic tools for environmental microbiology – a roadmap from sample preparation to protein identification and quantification. Proteomics 13/18-19 SI: 2700-2730.
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013b) Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395. Proteomics doi:10.1002/pmic.201200560.
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Hulsch R, Maschmann U, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013a) Adaptation of Phaeobacter gallaeciensis DSM 17395 to growth with complex nutrients. Proteomics doi:10.1002/pmic.201200513.
2011
Zech H, Echtermeyer C, Wöhlbrand L, Blasius B, Rabus R (2011) Biological versus technical variability in 2D DIGE experiments with environmental bacteria. Proteomics 11: 3380-3399.
2010
Wagner-Döbler, I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al.. 2010. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.
2009
Zech, H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R. 2009. Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade.. Proteomics. 9(14):3677-97.
Fürch, T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C. 2009. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.
Bachelor and Master theses
TRINKLER, Mirjam (Bachelor thesis, 2011) „Analysis of nitrogen and phosphate requirement by Phaeobacter gallaeciensis”
JONGMANS, Elanor (Bachelor thesis, 2011) „Growth condition-dependent morphotypes of Phaeobacter gallaeciensis”
BERGEN, Nils (Bachelor thesis, 2010) „Enzymaktivitäten im Zentralstoffwechsel von Phaeobacter gallaeciensis bei Wachstum im Minimalmedium“
VOCKE, Farina (Bachelor thesis, 2010) „Enzymaktivitäten im Zentralstoffwechsel von Phaeobacter gallaeciensis bei Wachstum im Vollmedium“
LEISKE, Maike Nicole (Bachelor thesis, 2012) „Enzymatik des Abbaus verzweigtkettiger Aminosäuren in Phaeobacter gallaeciensis”
RUPPERSBERG, Hanna Sibyll (Bachelor thesis, 2012) „Metaproteomic analysis of marine environmental samples”
NIEHAUS, Nils (Bachelor thesis, 2012) „Quantitative image analysis in proteomic research”
STOLTENBERG, Philip (Bachelor thesis, 2012) „Stoichiometry of amino acids (L-threonine, L-valine, L-leucine, L-isoleucine) utilization by Phaeobacter gallaeciensis DSM 17395 during growth in process-controlled fermenters”
LEHMANN, Jochen (Bachelor thesis, 2012) „Stoichiometry of amino acids (lysine, methionine, phenylalanine, tryptophane) utilization by Phaeobacter gallaeciensis DSM 17395 during growth in process-controlled fermenters”
BOOSMANN, Inka (Master thesis, 2011) „Cultivation and membrane proteome analysis of Phaeobacter gallaeciensis DSM 17395”
SCHWAB, Julia (Master thesis, 2011) „Cultivation and membrane proteome analysis of Phaeobacter gallaeciensis DSM 17395”
STRIJKSTRA, Annemieke (Master thesis, 2012) „Phaeobacter gallaeciensis DSM 17395 growth control by nitrogen and phosphorous: a physiological and proteomic perspective”
Metabolic profiling and extracellular signaling compounds of Dinoroseobacter shibae and other members of the Roseobacter clade
Principal investigator: Prof. Dr. Stefan Schulz
PhD Students: H. Bruns, L. Ziesche, T. Harig, M. Maczka
Objective
The secondary metabolites of different Roseobacter strains will be analyzed, including the model strains Dinoroseobacter shibae and Phaeobacter gallaeciensis but also other strains of potential interest. The identification of their function and their contribution to the success of the Roseobacter clade will be the main focus. Aiming at identifying as many secondary metabolites as possible, extracellular metabolite profiles will be established including compounds of a wide polarity spectrum. The compositional change of these profiles depending on different conditions, metabolites and micro- and macroorganisms will be explored in close cooperation with partners of the C‑ and B-area.
Methods
To elucidate the structure of volatile organic compounds (VOCs) emitted by bacteria the "Closed loop stripping apparatus" (CLSA) is used.[1,2] A cell culture of the bacterium grown in liquid media or on agar plates is placed into a closed air circuit. Volatiles emitted by the bacteria are collected on an activated charcoal filter which is extracted with an organic solvent after 24 hrs and analyzed by means of GC/MS. Identification of the compounds is carried out by comparison of the mass spectra with mass spectral data of libraries. If this doesn´t lead to identification of the compound a mass spectrum based structural proposal is made which is verified by synthesis of the compound in our workgroup.
Figure 1. Schematic diagram of a "closed-loop stripping apparatus", CLSA.
For the investigation of extracellular metabolites of higher polarity porous, hydrophobe polymers like XAD are used. The polymer is directly added to the liquid cell culture. After some time the XAD is filtered off and extracted with an organic solvent. The extract is investigated by means of HPLC/MS, which is especially suited for the examination of polar substances. The structural elucidation is based upon various data like molecular weight, MSn fragmentation pattern and the chemical formular derived from high resolution mass spectrometry. If these data are not sufficient for resolving the structure the compound is isolated by preparative HPLC and examined with nuclear magnetic resonance (NMR) spectroscopy. This is followed by synthesis of the compound and data comparison with the natural product.
Other methods used in our workgroup as needed comprise OASIS, liquid-liquid extraction, solid phase micro extraction (SPME) and analysis of gases with gas sampling tubes.
[1] W. Boland, P. Ney, L. Jaenicke, G. Gassmann in Analysis of Volatiles, (Ed.: P. Schreier), de Gruyter, Berlin, 1984, pp. 371-380.
[2] S. Schulz, J. Fuhlendorff, H. Reichenbach, Identification and synthesis of volatiles released by the myxobacterium Chondromyces crocatus, Tetrahedron 2004, 60, 3863-3872.
Publications
2017
Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N(2017) Function-related Pathway Replacement of Bacterial Siderophores. ISME J., in press (2017).
Celik E, Maczka M, Bergen N, Brinkhoff T, Schulz S, Dickschat JS (2017) Metabolism of 2,3-dihydroxypropane-1-sulfonate by marine bacteria. Org Biomol Chem 15: 2919-2922.
Trautwein K, Feenders C, Hulsch R, Ruppersberg HS, Strijkstra A, Kant M, Vagts J, Wünsch D, Michalke B, Maczka M, Schulz S, Hillebrand H, Blasius B, Rabus R (2017) Non-Redfield, nutrient synergy, and flexible internal elemental stoichiometry in a marine bacterium. FEMS Microbiol Ecol doi: 10.1093/femsec/fix059.
2015
Schulz S, Hötling S (2015) The use of the lactone motif in chemical communication. Nat Prod Rep 32:1042–1066.
Voget S, Bruns H, Wagner-Döbler I, Schulz S, Daniel R (2015) Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones. Genome Announcement 3(5):15.
Ziesche L, Bruns H, Dogs M, Wolter L, Mann F, Wagner-Döbler I, Brinkhoff T, Schulz S (2015) Homoserine lactones, methyl oligohydroxybutyrates and other extracellular metabolites of macroalgae associated bacteria of the Roseobacter clade: Identification and function. ChemBioChem. 16: 2094-2107.
2014
Wang H, Ziesche L, Frank O, Michael V, Martin M, Petersen J, Schulz S, Wagner-Döbler I, Tomasch J (2014) The CtrA phosphorelay integrates differentiation and communication in the marine alphaproteobacterium Dinoroseobacter shibae. BMC Genomics 15: 130.
2013
Bruns H, Thiel V, Voget S, Patzelt H, Daniel R, Wagner-Döbler I, Schulz S (2013) N-Acylated Alanine Methyl Esters from Roseovarius tolerans, Structural Analogs of Quorum-Sensing Autoinducers, N-Acylhomoserine Lactones. Chem Biodiversity: 10/9: 1559-1573.
Neumann A, Patzelt, D, Wagner-Döbler I, Schulz, S. (2013). Identification of New N-Acylhomoserine Lactone Signalling Compounds of Dinoroseobacter Shibae DFL-12 by Overexpression of LuxI Genes. Chembiochem 14/17: 2355-2361.
Groenhagen U, Baumgartner R, Bailly A, Gardiner A, Eberl L, Schulz S, Weisskopf L (2013) Production of bioactive volatiles by various Burkholderia ambifaria strains. J. Chem. Ecol: 39/10: 1343-1345.
Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench R, Jahn D, Wagner-Döbler I, Tomasch J (2013). You Are What You Talk: Quorum Sensing Induces Individual Morphologies and Cell Division Modes in Dinoroseobacter Shibae. ISME J 7/12: 2274-2286.
2011
Berger M, Neumann A, Schulz S, Simon M, Brinkhoff T (2011) Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J. Bacteriol. 193: 6576–6585.
2010
Thiel V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S (2010) Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46. Abstract
Schulz S, Dickschat JS, Kunze B, Wagner-Dobler I, Diestel R, Sasse F (2010) Biological activity of volatiles from marine and terrestrial bacteria.. Marine drugs. 8(12):2976-87.
2009
Thiel V, Kunze B, Verma P, Wagner-Döbler I, Schulz S (2009) New structural variants of homoserine lactones in bacteria.. Chembiochem : a European journal of chemical biology. 10(11):1861-8.
Thiel V, Vilchez R, Sztajer H, Wagner-Döbler I, Schulz S (2009) Identification, quantification, and determination of the absolute configuration of the bacterial quorum-sensing signal autoinducer-2 by gas chromatography-mass spectrometry.. Chembiochem : a European journal of chemical biology. 10(3):479-85.
2008
Bodor A, Elxnat B, Thiel V, Schulz S, Wagner-Döbler I (2008) Potential for luxS related signalling in marine bacteria and production of autoinducer-2 in the genus Shewanella.. BMC microbiology. 8:13.
2007
Vilchez R, Lemme A, Thiel V, Schulz S, Sztajer H, Wagner-Döbler I (2007) Analysing traces of autoinducer-2 requires standardization of the Vibrio harveyi bioassay.. Analytical and bioanalytical chemistry. 387(2):489-96.
2005
Bruhn J B, Nielsen K F, Hjelm M, Hansen M, Bresciani J, Schulz S, Gram L (2005) Ecology, inhibitory activity, and morphogenesis of a marine antagonistic bacterium belonging to the Roseobacter clade.. Applied and environmental microbiology. 71(11):7263-70.
Wagner-Döbler I, Thiel V, Eberl L, Allgaier M, Bodor A, Meyer S, Ebner S, Hennig A, Pukall R, Schulz S (2005) Discovery of complex mixtures of novel long-chain quorum sensing signals in free-living and host-associated marine alphaproteobacteria.. Chembiochem : a European journal of chemical biology. 6(12):2195-206.
Dickschat JS, Wagner-Döbler I, Schulz S (2005) The chafer pheromone buibuilactone and ant pyrazines are also produced by marine bacteria.. Journal of chemical ecology. 31(4):925-47.
Contributions to conferences
S. Schulz, Chemical Diversity of Microbial Volatiles, 32. ISCE meeting Foz de Iguazu, Juli 2016.
S. Schulz, Volatiles from Marine Bacteria , Gordon conference on Marine Natural Products, Ventura, March 2016
L. Ziesche, H. Bruns, M. Dogs, L. Wolter, T. Brinkhoff, S. Schulz, 07.04.2016, N-Acylhomoserine lactones of macroalgae associated Roseobacter bacteria, 7th Braunschweiger Jungchemiker Tagung, Haus der Wissenchaft, Braunschweig, Germany. Poster presentation.
L. Ziesche, H. Bruns, M. Dogs, L. Wolter, T. Brinkhoff, S. Schulz, 29.06-03.07.2015, N-Acylhomoserine lactones of macroalgae associated Roseobacter bacteria, International Society of Chemical Ecology Conference, Stockholm University, Stockholm, Sweden. Poster presentation.
S. Schulz, Bacterial volatiles - New compounds and functions , 2. European Conference on Natural Products and Bioflavour 2015, Frankfurt, September 2015
S. Schulz, Bacterial volatiles - Structures, biosynthesis and function 17. Challenges in Chemical Biology ISACS 16, Zürich, Juni 2015
L. Ziesche, H. Bruns, M. Maczka, N. Kahkin Taniwal, S. Schulz, 09.11.2015, C2 secondary metabolites of Roseobacter and their biological activity, 11th Status Seminar of the Transregio 51, Helmholtz-Center for Infection Research, Braunschweig, Germany. Poster presentation.
H. Bruns, S. Schulz, 05.03.2015, N Acylated Alanine Methyl Esters (NAMEs) from Roseovarius tolerans, Seminar Prof. Bradley Moore, Scripps Institute of Oceanography, University of California San Diego (UCSD), La Jolla, USA. Oral presentation.
L. Ziesche, H. Bruns, M. Maczka, 07.-08.05.2015, C2 secondary metabolites of Roseobacter and their biological activity, 10th Status Seminar of the Transregio 51, Alter Landtag zu Oldenburg, Oldenburg, Germany. Oral presentation.
S. Schulz, Analysis of Microbial Volatiles by Orthogonal Methods, 30. ISCE meeting Urbana, Juli 2014
S. Schulz, The Chemical Structure Space of Microbial Volatiles, 30. ISCE meeting Urbana, Juli 2014
H. Bruns, L. Ziesche, N. Khakin Taniwal, S. Schulz, 20.11.2014, Progress report and future perspectives (Algicidal activities and new N acylated amino acids), 9th Status Seminar the Transregio 51, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany. Oral presentation.
L. Ziesche, M. Dogs, T. Brinkhoff, S. Schulz, 15.04.2014, N-Acylhomoserine lactones: signal molecules produced by macroalgae associated Roseobacter bacteria, 5th Braunschweiger Jungchemiker Tagung, Haus der Wissenchaft, Braunschweig, Germany. Poster presentation.
L. Ziesche, S. Schulz, 08.-09.05.2014, C2 Chemistry of secondary metabolite mediated interactions between bacteria of the Roseobacter clade an other organisms, 8th Status Seminar of the Transregio 51, Alter Landtag zu Oldenburg, Oldenburg, Germany. Oral presentation.
H. Bruns, S. Schulz, 21.01.2014, Progress report (N Acylated Alanine Methyl Esters (NAMEs) from Roseovarius tolerans), 2nd Meeting of the graduate school Microbial Natural Products (MINAS), Leibnizhaus, Hannover, Germany. Oral presentation.
S. Schulz, Chemical communication by volatiles in animals and bacteria - Are there common themes? , Flavor and Fragrances, Leipzig, September 2013
H. Bruns, A. Neumann, S. Schulz, 24.-26. 6. 2013, major outcome of 1st phase (Acylhomoserine lactones and other compounds from Roseobacter clade organisms), International Symposium of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.
H. Bruns, S. Schulz, 15-16.10.2012, Progress report and future perspectives, 7th Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.
H. Bruns, V. Thiel, S. Schulz, 27-29.09.2012, Acylated Alanine Methyl Esters from Roseovarius, VAAM, Braunschweig, Germany. Poster presentation.
A. Neumann, S. Schulz, 05.06.2012, Detection of signalling molecules and other metabolites, 6th Status Seminar of the Transregio 51, Helmholtz Centre for Infection Research, Braunschweig, Germany. Oral presentation.
A. Neumann, S. Schulz, 16-17.05.2011, Metabolic profiling and extracellular signaling compounds of Dinoroseobacter shibae and other members of the Roseobacter clade, 3rd Status Seminar of the Transregio 51, Hanse Wissenschaftskolleg, Delmenhorst, Germany. Oral presentation.
A. Neumann, S. Schulz, 23-25.02.2011, Metabolites of marine bacteria of the Roseobacter clade, 23rd Irseer Naturstofftage der Gesellschaft für Chemische Technik und Biotechnologie e.V. (DECHEMA), Irsee. Poster presentation.
H. Bruns, N. Brock, J. Dickschat, S. Schulz, 10.02.2011, Biosynthetic pathways to secondary metabolites of the Roseobacter clade, 2nd Status Seminar of the Transregio 51, University of Oldenburg, Oldenburg, Germany. Oral presentation.
Metabolome analysis and modelling of the metabolisms of Dinoroseobacter shibae and Phaeobacter inhibens DSM 17395
Principal investigators: D. Schomburg, K. Schmidt-Hohagen (née Schreiber)
PhD students: S. Will, E. Majer
Objective:
The overall goal of this project is to analyse and model the metabolome of Dinoroseobacter shibae and Phaeobacter inhibens DSM 17395 (formerly deposited as Phaeobacter gallaeciensis DSM 17395, Buddruhs et al. unpublished), serving as model organisms of the Roseobacter clade. This will be done using a closely integrated theoretical/experimental approach. Based on experimental data obtained from metabolome analyses and from the collaborating partners under various growth conditions, a model of the metabolic network will be constructed to deduce hypotheses. They will be tested experimentally to optimise the model.
Methods:
Bild1
Fig. 1: Chemostat with tunable light source for cultivation of bacteria designed by us
Bild2
Fig. 2: GC-MS chromatogram
Bild 3
Fig. 3: Network construction
Invited talks / Contributions to conferences:
Schomburg D (2013) Metabolic networks and models – creation, application and experiment. 6th June 2013, Uni Luxemburg (Talk)
Hensler M, Zech H, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Schmidt-Hohagen K, Rabus R, Schomburg D (2013) Dynamics of amino acid utilization by Phaeobacter inhibens DSM 17395. VAAM 10th - 13th March 2013, Bremen (Poster)
Schreiber K, Schomburg D (2012) C3: Progress report and future perspectives. 7th Status Seminar of the Transregio 51, 12th - 13th October 2012, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Rex R, Schomburg D (2012) Predicting concentration, enzyme capacity and flux distribution changes from integrated systems biology data using Boolean algebra. German Conference on Bioinformatics (Workshop Computational Proteomics and Metabolomics) 19th - 22nd September 2012, Jena (Talk)
Schomburg D (2011) Von Bioinformatik und Metabolom zur Systembiologie. 10th November 2011, Uni Freiberg/Sachsen (Talk)
Schomburg D (2011) Theoretical and experimental aspects of genome-sized models. 5th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations (ESCEC), 12th - 16th September 2011, Rüdesheim (Talk)
Schomburg D (2011) The creation and application of genome-scale metabolic models - theoretical and experimental steps. Dechema (Trends in Metabolomics – Analytics and Applications), 19th - 20th May 2011, Frankfurt (Talk)
Hensler, Bill N, Rex R, Schreiber K, Schomburg D (2011) Metabolome analysis and modelling of the metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis. 3rd Status Seminar of the Transregio 51, 16th - 17th May 2011, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Schomburg D (2011) From genome to genome-scale metabolic models – theoretical and experimental steps. Dechema (System Biology: Between Science and Application), 18th - 19th January 2011, Frankfurt (Talk)
Rex R, Schomburg D (2010) Automated creation of simulation-ready metabolic models. German Conference on Bioinformatics, 20th - 22nd September 2010, Braunschweig (Poster)
Schreiber K, Rex R, Schomburg D (2010) Metabolome analysis and modelling of the metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis. Kick-off Symposium of the Transregio 51, 13th - 15th June 2010, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Schomburg D (2010) From Metabolism to Systems Biology. EMBO (Catalytic Mechanisms by Biological Systems: at the interface between Chemistry and Biology), 5th - 7th May 2010, EMBL Hamburg (Talk)
Publications:
2017
Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D (2017) Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol doi:10.1111/1462-2920.13746.
Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R, Schomburg D (2017) Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae. Environ Microbiol 19: 894–908. doi:10.1111/1462-2920.13266.
Will SE, Neumann-Schaal M, Heydorn RL, Bartling P, Petersen J, Schomburg D (2017) The limits to growth – energetic burden of the endogenous tropodithietic acid in Phaeobacter inhibens DSM 17395. PLoS ONE 12(5): e0177295. https://doi.org/10.1371/journal.pone.0177295.
2016
Trautwein K, Will SE, Hulsch R, Maschmann U, Wiegmann K, Hensler M, Michael V, Ruppersberg H, Wünsch D, Feenders C, Neumann-Schaal M, Kaltenhäuser S, Ulbrich M, Schmidt-Hohagen K, Blasius B, Petersen J, Schomburg D, Rabus R (2016) Native plasmids restrict growth of Phaeobacter inhibens DSM 17395. Energetic costs of plasmids assessed by quantitative physiological analyses. Environ Microbiol 18: 4817-4829.
Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R and Schomburg D (2016) Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium Dinoroseobacter shibae. Environ. Microbiol.
2014
Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D (2014) Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 289: 13219–13231. doi:10.1074/jbc.M113.545004.
Wiegmann K, Hensler M, Wöhlbrand L, Ulbrich M, Schomburg D, Rabus R (2014) Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, member of the marine Roseobacter clade. Appl Environ Microbiol 80:4725-4737.
Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, Schomburg D, Rabus R (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Environ Microbiol 16: 218–238. doi:10.1111/1462-2920.12276.
2013
Rex R, Bill N, Schmidt-Hohagen K, Schomburg D (2013) Swimming in light: A large-scale computational analysis of the metabolism of Dinoroseobacter shibae.PLOS Comp Biol, 9/10 Article e1003224.
Riemer SA, Rex R, Schomburg D (2013) A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol 7: 33.
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013b) Dynamics of amino acid utilization by Phaeobacter inhibens DSM 17395. Proteomics, in press (doi: 10.1002/pmic.201200560).
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Hulsch R, Maschmann U, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R (2013a) Adaption of Phaeobacter inhibens DSM 17395 to growth with complex nutrients. Proteomics, in press (doi: 10.1002/pmic.201200513).
2009
Zech H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon S, Schomburg D, Rabus R (2009) Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 9: 3677–3697.
PhD dissertations:
René Rex (2012) Towards a new view on metabolic networks: automated reconstruction and large-scale computational analysis applied to Dinoroseobacter shibae. 19.12.2012.
Sarah Alessandra Kleist (2016) Metabolic adaptation processes of the marine bacterium Dinoroseobacter shibae DFL12T to changing environmental conditions
Metabolic network analysis of the Roseobacter clade: Pathways and pathways fluxes in Dinoroseobacter shibae, Phaeobacter gallaeciensis and other members
Principal investigators: Prof. Dr. C. Wittmann, Dr. Judith Becker
PhD students: A. Bartsch und A. Klingner
Aims
The goal of this project is the investigation of the metabolic flexibility, adaptation and robustness of the two model strains Dinoroseobacter shibae and Phaeobacter inhibens (former P. gallaeciensis) by quantitative 13C metabolic flux analysis. Despite the obvious ecological success of the Roseobacter clade, only little is known about their metabolic pathways. Most interestingly, the planned analysis will provide detailed insights into the metabolic response of the model strains to nutritional supply and other environmental parameters that are relevant for a marine life style. The study will be complemented with model-independent flux-profiling of novel isolates to unravel eco-specific flux signatures. This will be an initial step towards metafluxome studies, i.e. investigations of microbial communities, which will be carried out in close cooperation with subproject A.
Objectives/Methods
Publications
2015
Klingner A, Bartsch A, Dogs M, Wagner-Döbler I, Jahn D, Simon M, Brinkhoff T, Becker J, Wittmann C (2015) Large-scale 13C flux profiling reveals conservation of the Entner-Doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose. Appl Environ Microbiol 81/7: 2408-2422.
2014
Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D (2014) Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 289: 13219–13231. doi:10.1074/jbc.M113.545004.
2013
Ebert, M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D. 2013. Transposon mutagenesis identified chromosomal and plasmid encoded genes essential for the adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions.. Journal of bacteriology.
2011
Bartsch A, Bunk B, Haddad I, Klein J, Münch R, Johl T, Kärst U, Jänsch L, Jahn D, & Retter I (2011) GeneReporter-sequence-based document retrieval and annotation. Bioinformatics 27:1034-1035.
2009
Fürch, T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C. 2009. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.
Contribution to conferences
Bartsch AK, Klingner A, Becker J, Wittmann C (2013) Functional contribution of central metabolic pathway to carbon dioxide assimilation in the marine bacterium Dinoroseobacter shibae. PhD Seminar of the Transregio 51, 8 May, TU Braunschweig (Talk)
Klingner A, Bartsch AK, Becker J, Wittmann C (2012) Fluxomics of selected marine bacteria and first results of a mesocosm experiment on metafluxomics. 5th Status Seminar of the Transregio 51, 6 February, HZI, Braunschweig (Talk).
Klingner A, Bartsch AK, Becker J, Wittmann C (2012) Large-scale 13C flux profiling of the Roseobacter clade. 7th Status Seminar of the Transregio 51, 15-16 October, Hanse Wissenschaftskolleg, Delmenhorst (Talk).
Bartsch AK, Klingner A Becker J, Wittmann C (2012) Functional contribution of central metabolic pathway to carbon dioxide assimilation in the marine bacterium Dinoroseobacter shibae. 7th Status Seminar of the Transregio 51, 15-16 October, Hanse Wissenschaftskolleg, Delmenhorst (Talk).
Bartsch AK, Klingner A, Becker J, Wittmann C (2012) Systems-wide metabolic flux analysis of Dinoroseobacter shibae. PhD Seminar of the Transregio 51, 2 July, TU Braunschweig (Talk)
Klingner A, Bartsch AK, Becker J, Wittmann C (2012) 13C metabolic flux profiling of P. gallaeciensis and novel isolates of the Roseobacter clade. PhD Seminar of the Transregio 51, 5 December, TU Braunschweig (Talk)
Bartsch AK, Klingner A, Becker J, Wittmann C (2012) Metabolic flux response of Dinoroseobacter shibae to genetic and environmental burdens. PhD Seminar of the Transregio 51, 5 December, TU Braunschweig (Talk)
Bartsch A, Klingner A, Becker J, Wittmann C (2012) Metabolic pathway fluxes of the marine model bacterium Dinoroseobacter shibae under changing environmental conditions. VAAM Annual Conference, 18-21 March, Tübingen (Vortrag).
Klingner A, Bartsch A, Becker J, Wittmann C (2012) Systems biology of the marine antibiotic producer Phaeobacter gallaeciensis. VAAM Annual Conference, March 18-21, Tübingen (Talk).
Wittmann C (2012) Systems biology and systems metabolic engineering, International Course on Microbial Physiology, 20 Januar, Delft, Holland (Talk).
Klingner A, Bartsch AK, Becker J, Wittmann C (2011) Metabolic network analysis of the Roseobacter clade: Pathways and pathway fluxes in Dinoroseobacter shibae, Phaeobacter gallaeciensis and other members. 3rd Status Seminar of the Transregio 51, 16-17 May, (Talk).
Becker J, Wittmann C (2011) Systems metabolic engineering of tailor-made cell factories,International Union of Microbiological Societies Congress, 6.September, Sapporo, Japan (Talk).
Wittmann C (2011) Systems biology and synthetic metabolic engineering, Research Colloquium, INSA Toulouse, 22. July, Toulouse, Frankreich (Talk).
Wittmann C (2011) From knowledge to improvement – analysis and engineering of microbial metabolism, Nestle Research Colloquium, 15 March, Lausanne, Schweiz (Talk).
Wittmann C (2010) Systembiologie. Deutsch-Japanisches Life Science Symposium. 31 August, Technische Universität Braunschweig (Talk).
Bolten C, Fürch T, Preusse M, Wittmann C (2010) Metabolic network analysis of the Roseobacter clade: Pathways and pathway fluxes in Dinoroseobacter shibae and Phaeobacter gallaeciensis. Kick-off Symposium of the Transregio 51, 13-15 June, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Bachelor- and Mastertheses
Samuel Hauf (2012) Marine Systembiologie: Untersuchung von Wachstum und Zentralstoffwechsel des Modellorganismus Dinoroseobacter shibae und verschiedener Mutanten
Systems biology of interaction between roseobacters and algae
Supervisors: Prof. Dr. Wagner-Döbler, Prof. Dr. R. Rabus
Scientists: Dr. Jürgen Tomasch (Phd/Postdoc), Dr. Thomas Riedel (Phd/Postdoc)
PhD Students: Steffi Heyber
Bachelor- and master students: Meike Rohlfs, Regina Gohl
Aim
Two special types of generating energy through light play an important role In the world´s oceans : Aerobic anoxygenic photosynthesis and the light powered proton pump proteorhodopsin. We study the first one using Dinoroseobacter shibae, a symbiont of algae which is a model organism for the Roseobacter group, and the second one in Dokdonia donghaensis PRO95, one of the few published bacteria which carries a proteorhodopsin.
Fig. 1. Bacteriochlorophyll a in D. shibae during a day-night shift on the single cell level (time-lapse microscopy using an infrarot sensor, Münch, unpublished).
Methods
The adaptation of aerobic anoxygenic photosynthesis to the daily day-night rhythm is modelled using a systems biology approach. Data from all cellular levels are being integrated. Hypotheses derived from theoretical models are tested experimentally and optimized in an iterative process. The role of proteorhodopsin is investigated using physiological experiments, comparative genome analyses and studies of gene expression.
Publications
List of publications (AG Wagner Döbler):
2017
Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D (2017) Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol doi:10.1111/1462-2920.13746.
Milici M, Vital M, Tomasch J, Badewien TH, Giebel H-A, Plumeier I, Wang H, Pieper DH, Wagner-Döbler I, Simon M. (2017) Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: evidence of dispersal limitation in the Bransfield strait. Limnol Oceanogr 62: 1080-1095.
2016
Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sanudo-Wilhelmy SA, Fuhrman JA (2016) Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J 10: 1102-1112. ismej2015196 [pii];10.1038/ismej.2015.196 [doi].
Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jauregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton. Front Microbiol 7: 649. 10.3389/fmicb.2016.00649 [doi].
Milici M, Tomasch J, Wos-Oxley M, Decelle J, Jáuregui R, Wang H, Deng ZL, Plumeier I, Giebel HA, Badewien T, Wurst M, Pieper DH, Simon M, Wagner-Doebler I (2016) Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship. Frontiers Microbiol. 7: Article 570.
Milici M, Tomasch J, Wos-Oxley ML, Wang H, Jauregui R, Camarinha-Silva A, Deng ZL, Plumeier I, Giebel HA, Wurst M, Pieper DH, Simon M, Wagner-Döbler I (2016) Low diversity of planktonic bacteria in the tropical ocean. Sci Rep 6: 19054. srep19054 [pii];10.1038/srep19054 [doi].
2015
Soora M, Tomasch J, Wang H, Michael V, Petersen J, Engelen B, Wagner-Döbler I, Cypionka H (2015) Oxidative stress and starvation in Dinoroseobacter shibae: The role of extrachromosomal elements. Front Microbiol 6: 233.
2013
Brock, NL, Citron CA, Zell C, Berger M, Wagner-Döbler I, Petersen J, Brinkhoff T, Simon M, Dickschat JS. 2013. Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria.. Beilstein journal of organic chemistry. 9:942-50.
Bruns, H, Thiel V, Voget S, Patzelt D, Daniel R, Wagner-Döbler I, Schulz S. 2013. N-acylated alanine methyl esters (NAMEs) from Roseovarius tolerans, structural analogs of quorum-sensing autoinducers, N-acylhomoserine lactones.. Chemistry & biodiversity. 10(9):1559-73.
Neumann, A, Patzelt D, Wagner-Döbler I, Schulz S. 2013. Identification of new N-acylhomoserine lactone signalling compounds of Dinoroseobacter shibae DFL-12(T) by overexpression of luxI genes.. Chembiochem : a European journal of chemical biology. 14(17):2355-61.
Riedel, T, Rohlfs M, Buchholz I, Wagner-Döbler I, Reck M. 2013. Complete sequence of the suicide vector pJP5603.. Plasmid. 69(1):104-7.
Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench R, Jahn D, Wagner-Döbler I, Tomasch J (2013). You Are What You Talk: Quorum Sensing Induces Individual Morphologies and Cell Division Modes in Dinoroseobacter Shibae. ISME J 7/12: 2274-2286.
Fiebig, A, Pradella S, Petersen J, Michael V, Päuker O, Rohde M, Göker M, Klenk H-P, Wagner-Döbler I. 2013. Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).. Standards in genomic sciences. 7(3):440-8.
Fiebig, A, Pradella S, Petersen J, Päuker O, Michael V, Lünsdorf H, Göker M, Klenk H-P, Wagner-Döbler I. 2013. Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).. Standards in genomic sciences. 7(3):413-26.
Riedel T, Gomez-Consarnau L, Tomasch J, Martin M, Jarek M, Gonzalez JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. 2013a. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 8:e57487.
Riedel T, Rohlfs M, Buchholz I, Wagner-Döbler I, Reck M. 2013b. Complete sequence of the suicide vector pJP5603. Plasmid 69:104-107.
Spring S, Riedel T. 2013. Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability. BMC Microbiol. 24;13:117. doi: 10.1186/1471-2180-13-117.
Spring S, Riedel T, Spröer K, Yan S, Harder J, Fuchs BM. 2013. Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: Description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol. 24;13:118. doi: 10.1186/1471-2180-13-118.
2012
Brinkhoff, T, Fischer D, Vollmers J, Voget S, Beardsley C, Thole S, Mussmann M, Kunze B, Wagner-Döbler I, Daniel R et al.. 2012. Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.. The ISME journal. 6(6):1260-72.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012a. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282T). Standards in Genomic Sciences 7:117-119.
Riedel T, … Rohde M, Tindall BJ, Göker M, Klenk HP, and 27 authors. 2012b. Genome sequence of the orange-pigmented sea-water bacterium Owenweeksia hongkongensis type strain (UST20020801 T ). Standards in Genomic Sciences 7:120-130.
2011
Tomasch J, Gohl R, Bunk B, Diez MS, Wagner-Döbler I. 2011. Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. ISME J 5:1957-1968.
2010
Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Döbler I. 2010. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 76:3187-3197.
Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Döbler I. 2010. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea.. Applied and environmental microbiology. 76(10):3187-97.
Thiel, V, Brinkhoff T, Dickschat JS, Wickel S, Grunenberg J, Wagner-Döbler I, Simon M, Schulz S. 2010. Identification and biosynthesis of tropone derivatives and sulfur volatiles produced by bacteria of the marine Roseobacter clade.. Organic & biomolecular chemistry. 8(1):234-46.
Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al.. 2010. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.
2009
Thiel V, Kunze B, Verma P, Wagner-Döbler I, Schulz S. 2009. New structural variants of homoserine lactones in bacteria.. Chembiochem : a European journal of chemical biology. 10(11):1861-8.
Thiel V, Vilchez R, Sztajer H, Wagner-Döbler I, Schulz S. 2009. Identification, quantification, and determination of the absolute configuration of the bacterial quorum-sensing signal autoinducer-2 by gas chromatography-mass spectrometry.. Chembiochem : a European journal of chemical biology. 10(3):479-85.
Fürch T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C. 2009. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade.. BMC microbiology. 9:209.
2008
Bodor A, Elxnat B, Thiel V, Schulz S, Wagner-Döbler I. 2008. Potential for luxS related signalling in marine bacteria and production of autoinducer-2 in the genus Shewanella.. BMC microbiology. 8:13. Abstract
Pommerenke, C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D. 2008. ROSY--a flexible and universal database and bioinformatics tool platform for Roseobacter related species.. In silico biology. 8(2):177-86.
2007
Vilchez R, Lemme A, Thiel V, Schulz S, Sztajer H, Wagner-Döbler I. 2007. Analysing traces of autoinducer-2 requires standardization of the Vibrio harveyi bioassay.. Analytical and bioanalytical chemistry. 387(2):489-96.
2006
Wagner-Döbler I, Biebl H. 2006. Environmental biology of the marine Roseobacter lineage.. Annual review of microbiology. 60:255-80.
2005
Biebl H, Allgaier M, Lünsdorf H, Pukall R, Tindall BJ, Wagner-Döbler I. 2005. Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a.. International journal of systematic and evolutionary microbiology. 55(Pt 6):2377-83.
Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lünsdorf H, Pukall R, Wagner-Döbler I. 2005. Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates.. International journal of systematic and evolutionary microbiology. 55(Pt 3):1089-96.
List of publications (AG Jahn / Münch):
2017
Blasenovic I, Kind T, Torbasinovic H, Obrenovic S, Mehta SS, Tsugawa H, Wermuth T, Schauer N, Jahn M, Biedendieck R, Jahn D (2017) Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy. J Cheminform) 9: 32.
2014
Roselius L, Langemann D, Müller J, Hense B, Filges S, Jahn D & Münch R (2014) Modeling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator. J Theoret Biol., 363:290–299.
2013
Patzelt D, Wang, H, Buchholz, I, Rohde, M, Gröbe, L, Pradella, S, Neumann A, Schulz S, Heyber S, Muench K, Muench R, Jahn D, Wagner-Döbler I, Tomasch J (2013) You Are What You Talk: Quorum Sensing Induces Individual Morphologies and Cell Division Modes in Dinoroseobacter Shibae. ISME J 7/12: 2274-2286.
Ebert M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013) Transposon mutagenesis identified chromosomal and plasmid encoded genes essential for the adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions.. Journal of bacteriology.
2012
Klein J, Leupold S, Biegler I, Biedendieck R, Münch R & Jahn D (2012) TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies. Bioinformatics 28:2276-2277.
Shevchuk O, Roselius L, Günther G, Klein J, Jahn D, Steinert M & Münch R (2012) InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. Bioinformatics 28:306-310.
2010
Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G et al. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.. The ISME journal. 4(1):61-77.
2009
Piekarski T, Buchholz I, Drepper T, Schobert M, Wagner-Doebler I, Tielen P, Jahn D (2009) Genetic tools for the investigation of Roseobacter clade bacteria.. BMC microbiology. 9:265.
2008
Pommerenke C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D (2008) ROSY--a flexible and universal database and bioinformatics tool platform for Roseobacter related species.. In silico biology. 8(2):177-86.
Contributions to conferences
Wagner-Döbler I (2012) C5: Progress report and future perspectives. 7th Status Seminar of the Transregio 51, 12-13. October 2012, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Riedel T, Gómez-Consarnau L, Tomasch J, Jarek M, Martin M, Brinkhoff T, Cypionka H, Fuhrman J and Wagner-Döbler I (2012) A xanthorhodopsin-like second bacterial rhodopsin is expressed in the flavobacterium Dokdonia donghaensis PRO95. ISME 14, 19th – 24th August 2012, Copenhagen (Poster)
Riedel T, Gómez-Consarnau L, Tomasch J, Jarek M, Fuhrman J and Wagner-Döbler I Understanding the role of genomic context onn proteorhodopsin function through analysis of the Dokdonia donghaensis PRO95 genome. SAME 12, 28th August – 2nd September 2011, Rostock, Germany (Poster)
Tomasch J, Gohl R, Bunk B, Diez M-S, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes (2011) BAGECO 11, 29th May – 6th June, Corfu (Talk)
Tomasch J, Gohl R, Bunk B, Diez M-S, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes (2011) Gordon Research Conference „Applied and Environmental Microbiology“, 10th – 15th July, 2011, Mount Holyoke College (Poster)
Tomasch J, Gohl R, Bunk B, Suarez-Diez M, Wagner-Döbler I (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. VAAM 3rd – 6th April, Karlsruhe, 2011 (Poster)
Tomasch J, Wang H, Buchholz I and Wagner-Döbler I (2011) Statistische Analyse der morphologischen Heterogenität bakterieller Kulturen. Biostats – Biologie und Statistik in der Praxis, 22-24. März 2011, Deutsche Sammlung für Mikroorganismen und Zellkulturen, Brauschweig (Talk)
Tomasch J, Gohl R, Bunk B, Suarez-Diez M, Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to light exposure. Workshop on Aerobic Anoxygenic Phototrophs; 22th – 24th September 2010, Institut for Microbiology, Academy of Sciences, Czech Republic, Trebon (Talk)
Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. Gordon Rearch Conference „Marine Microbes“, 4th to 9th July, 2010, Tilton School, NH, USA (Poster)
Tomasch J, Gohl R, Bunk B, Münch R and Wagner-Döbler I (2010) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to light exposure. Kick-off Symposium of the Transregio 51, 13th -15th June 2010, Hanse Wissenschaftskolleg, Delmenhorst (Talk)
Tomasch J, Bunk B, Münch R, Wagner-Döbler I (2010) Transcriptional Response of the Photoheterotrophic Marine Bacterium Dinoroseobacter shibae to Light. VAAM 29th – 31st March 2010, Göttingen (Poster)
Invited talks
Riedel T. (2012) Rhodopsin phototrophy in the oceans. Microbiological Colloquium, 18th April 2012, ICBM, University of Oldenburg, Germany. Wagner-Döbler I. Transcriptional response of the photoheterotrophic bacterium Dinoroseobacter shibae to changing light regimes – sustainable use of energy on a global scale. Invitation by Prof. Jed Fuhrman, University of Southern California, Los Angeles, U.S., 19th July, 2011, Prof. Feng Chen, Institute of Marine and Environmental Technology, Baltimore, U.S., 27th July, 2011, Prof. Farooq Azam, Woods Hole Oceanographic Institute, San Diego, U.S., 21th June, 2012.
Wagner-Döbler I (2011) Global transcriptome analysis of the response to light and quorum sensing signals in a marine Roseobacter strain – sustainable use of energy on a global scale. Mikrobiologisches Kolloquium, Universität Jena, 13th April, 2011, Jena.
Wagner-Döbler I (2010) Global transcriptome analysis of the response to light and quorum sensing signals in a marine Roseobacter strain. Mikrobiologisches Kolloquium, Universität Mainz, 6th December, 2010 (invitation by Prof. Dr. G. Unden)
Phd dissertations
Jürgen Tomasch (2011). Experimentelle und bioinformatische Analyse der aeroben anoxygenen Photosynthese in dem photoheterotrophen Meeresbakterium Dinoroseobacter shibae DFL12. TU Braunschweig, 27.06.2011.
Thomas Riedel (2012). Dokdonia sp. PRO95: A marine flavobacterium with two phylogenetically different rhodopsin genes in its genome. TU Braunschweig, 20.12.2012
Bachelor- und Master theses
Meike Rohlfs (2012) Untersuchung von Knockout-Strategien für Dokdonia donghaensis PRO95. Bachelorarbeit, FH Emden.
Regina Gohl (2009)
Ended
Principal investigators: Prof. Dr. Susanne Engelmann
PhD students:
Project outline:
Scientific questions
Dinoroseobacter shibae is a photoheterotophic bacterium and performs aerobic anoxygenic photosynthesis. As a marine bacterium living in the photic zone environment of marine eco-systems D. shibae is frequently exposed to oxygen and, hence, oxidative stress is one of the challenges the bacterium has to cope with. The aim of the present study is to provide detailed insights into the response of D. shibae to different kinds of oxidative stress. Hydrogen peroxide and paraquat will be used as agents that induce oxidative stress and changes in the protein pattern will be analysed in response to these substances in order to describe the respective stimulons. The proteomic data will be compared with transcriptomic data. One major effect of oxygen radicals in the cell is the oxidation of thiols in proteins also called disulfide stress resulting in reversible and irreversible modifications. Disulfide stress can be specifically induced by diamide which will be used to define the disulfide stress stimulon by proteomics and transcriptomics. The obtained OMICs data will be deposited in a database that can be used to extensively compare expression profiles and to identify marker proteins for the respective stimulus and to decipher regulatory networks involved in the adaptation to these stimuli. In collaboration with projects B5 and C5 the expression profiles will be compared with those generated under iron and oxygen limitation and in response to light. In future the marker proteins/genes will be used to characterize the physiology of the bacterium under more complex in vivo conditions. The genome of D. shibae codes for three OxyR like proteins. In Gram-negative bacteria, the LysR-type regulator OxyR is a major regular for genes involved in oxidative stress response. Consequently, we are interested in the function of the OxyR like proteins of D. shibae in the oxidative stress response.
Aims, work program and methods
Work package 1
To define the peroxide, the superoxide and the diamide stress stimulon in D. shibae we want to employ 2-D PAGE combined with MALDI-TOF MS for spot identification and gel free MS approaches. Moreover, DNA arrays will be used to analyse the transcriptome under these conditions. Marker genes and proteins will be identified whose expression significantly changed in response to the respective stimuli by cross comparisons of expression profiles ob-tained under different growth conditions. Postranslational modifications of thiol groups in cysteine residues in response to oxidative stress will be visualized by a fluorescence based proteomic approach.
Work package 2
To analyse the role of the three OxyR like proteins in oxidative stress response, the impact of these proteins on global gene expression in D. shibae will be analysed using a transcriptomic and proteomic approach. Northern blot experiments will be performed to study the transcrip-tion of the respective genes in response to different stimuli. Gel shifts and foot print analyses with the purified regulator proteins and PCR products will be applied to verify the direct in-teraction of these proteins with regulatory regions of selected genes, probably leading to the identification of possible DNA-binding motifs. A genome wide search using the genome se-quence of D. shibae and the possible binding motive can be used to identify possible targets of the OxyR like proteins. Additional regulatory proteins for oxidative stress induced genes will be identified by aligning upstream regions if these genes to search for conserved binding motifs and by using biotinylated PCR products of the respective regulatory regions, immobi-lized to strepatividin coated magnetic beads. These beads will be incubated with protein ex-tracts of D. shibae. Proteins that have bound can be identified by mass spectrometry.
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