• Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).

      Fiebig, Anne; Pradella, Silke; Petersen, Jörn; Päuker, Orsola; Michael, Victoria; Lünsdorf, Heinrich; Göker, Markus; Klenk, Hans-Peter; Wagner-Döbler, Irene (2013)
      Labrenzia alexandrii Biebl et al. 2007 is a marine member of the family Rhodobacteraceae in the order Rhodobacterales, which has thus far only partially been characterized at the genome level. The bacterium is of interest because it lives in close association with the toxic dinoflagellate Alexandrium lusitanicum. Ultrastructural analysis reveals R-bodies within the bacterial cells, which are primarily known from obligate endosymbionts that trigger "killing traits" in ciliates (Paramecium spp.). Genomic traits of L. alexandrii DFL-11(T) are in accordance with these findings, as they include the reb genes putatively involved in R-body synthesis. Analysis of the two extrachromosomal elements suggests a role in heavy-metal resistance and exopolysaccharide formation, respectively. The 5,461,856 bp long genome with its 5,071 protein-coding and 73 RNA genes consists of one chromosome and two plasmids, and has been sequenced in the context of the Marine Microbial Initiative.
    • Genome Organization and Localization of the pufLM Genes of the Photosynthesis Reaction Center in Phylogenetically Diverse Marine Alphaproteobacteria

      Pradella, Silke; Allgaier, Martin; Hoch, Christa; Päuker, Orsola; Stackebrandt, Erko; Wagner-Döbler, Irene (American Society for Microbiology, 2004-06)
    • Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684T), a member of the Roseobacter clade

      Fiebig, Anne; Riedel, Thomas; Gronow, Sabine; Petersen, Jörn; Klenk, Hans-Peter; Göker, Markus; reseach group microbial communication, Helmholtz Centre for infection research, D-38124 Braunschweig, Germany (2014-05-15)
    • A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains

      Song, Lifu; Sudhakar, Padhmanand; Wang, Wei; Conrads, Georg; Brock, Anke; Sun, Jibin; Wagner-Döbler, Irene; Zeng, An-Ping (2012-04-04)
      Abstract Background Mutans streptococci are a group of gram-positive bacteria including the primary cariogenic dental pathogen Streptococcus mutans and closely related species. Two component systems (TCSs) composed of a signal sensing histidine kinase (HK) and a response regulator (RR) play key roles in pathogenicity, but have not been comparatively studied for these oral bacterial pathogens. Results HKs and RRs of 8 newly sequenced mutans streptococci strains, including S. sobrinus DSM20742, S. ratti DSM20564 and six S. mutans strains, were identified and compared to the TCSs of S. mutans UA159 and NN2025, two previously genome sequenced S. mutans strains. Ortholog analysis revealed 18 TCS clusters (HK-RR pairs), 2 orphan HKs and 2 orphan RRs, of which 8 TCS clusters were common to all 10 strains, 6 were absent in one or more strains, and the other 4 were exclusive to individual strains. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. While TCS complements were comparable within the six S. mutans strains, S. sobrinus DSM20742 lacked TCSs possibly involved in acid tolerance and fructan catabolism, and S. ratti DSM20564 possessed 3 unique TCSs but lacked the quorum-sensing related TCS (ComDE). Selected computational predictions were verified by PCR experiments. Conclusions Differences in the TCS repertoires of mutans streptococci strains, especially those of S. sobrinus and S. ratti in comparison to S. mutans, imply differences in their response mechanisms for survival in the dynamic oral environment. This genomic level study of TCSs should help in understanding the pathogenicity of these mutans streptococci strains.
    • A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains.

      Song, Lifu; Sudhakar, Padhmanand; Wang, Wei; Conrads, Georg; Brock, Anke; Sun, Jibin; Wagner-Döbler, Irene; Zeng, An-Ping; Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. (2012)
      Mutans streptococci are a group of gram-positive bacteria including the primary cariogenic dental pathogen Streptococcus mutans and closely related species. Two component systems (TCSs) composed of a signal sensing histidine kinase (HK) and a response regulator (RR) play key roles in pathogenicity, but have not been comparatively studied for these oral bacterial pathogens.
    • Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales.

      Kopejtka, Karel; Tomasch, Jürgen; Zeng, Yonghui; Tichý, Martin; Sorokin, Dimitry Y; Koblížek, Michal; Helmholtz Centre for infection research, Inhoffenstr.7,38124 Braunschweig, Germany. (2017-07-01)
      A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.
    • Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.

      Riedel, Thomas; Gómez-Consarnau, Laura; Tomasch, Jürgen; Martin, Madeleine; Jarek, Michael; González, José M; Spring, Stefan; Rohlfs, Meike; Brinkhoff, Thorsten; Cypionka, Heribert; et al. (2013)
      Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.
    • The global impact of the delta subunit RpoE of the RNA polymerase on the proteome of Streptococcus mutans.

      Xue, Xiaoli; Li, Jinshan; Wang, Wei; Sztajer, Helena; Wagner-Döbler, Irene; Research Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. Xiaoli.Xue@helmholtz-hzi.de (2012-01)
      Transcriptional specificity in low-G+C Gram-positive bacteria is maintained by RpoE, the delta subunit of the RNA polymerase. Here, we studied the effect of RpoE at the proteome level in the human dental pathogen Streptococcus mutans by comparing the ΔrpoE mutant with the wild-type under five conditions: (0) exponential growth, (1) early stationary phase, (2) acid stress, (3) oxidative stress, and (4) combined acid and oxidative stress. A total of 280 cellular protein spots were reproducibly detected, of which 97 differentially expressed protein spots were identified by MALDI-TOF MS. Lack of RpoE caused downregulation of proteins for carbohydrate metabolism and energy production, including phosphoglucomutase (PGM), the phosphopentomutase DeoB and the pyruvate formate-lyase Pfl. The ΔrpoE mutant had extensive changes in the abundance of proteins involved in acid and oxidative tolerance and protein turnover, and of chaperones, at exponential phase in the absence of stress, suggesting a potential internal stress. In addition, the mutant had reduced amounts of proteins for adaptation responses, e.g. the multiple sugar transport and metabolism enzymes required for entering early stationary phase, and the proteins for stress-defence mechanisms and glycolysis under oxidative stress. Comparison of the proteome data with the corresponding transcriptome data suggested that the effects were the result of altered transcriptional and post-transcriptional regulation. The data are consistent with the reduced transcriptional specificity of the RNA polymerase in the ΔrpoE mutant, and suggest a general impact, but not a specific regulatory role, of RpoE in stress adaptation.
    • High-resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis.

      Szafranski, Szymon P; Wos-Oxley, Melissa L; Vilchez-Vargas, Ramiro; Jáuregui, Ruy; Plumeier, Iris; Klawonn, Frank; Tomasch, Jürgen; Meisinger, Christa; Kühnisch, Jan; Sztajer, Helena; et al. (2015-02)
      The oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis.
    • Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a.

      Biebl, Hanno; Tindall, Brian J; Pukall, Rüdiger; Lünsdorf, Heinrich; Allgaier, Martin; Wagner-Döbler, Irene (2006-04-01)
      Within a collection of marine strains that were shown to contain the photosynthesis reaction-centre genes pufL and pufM, a novel group of alphaproteobacteria was found and was characterized phenotypically. The 16S rRNA gene sequence data suggested that the strains belonged to the order Rhizobiales and were closest (98.5 % sequence similarity) to the recently described species Hoeflea marina. The cells contained bacteriochlorophyll a and a carotenoid, presumably spheroidenone, in small to medium amounts. Cells of the novel strains were small rods and were motile by means of single polarly inserted flagella. Good growth occurred in complex media with 0.5-7.0 % sea salts, at 25-33 degrees C (optimum, 31 degrees C) and at pH values in the range 6-9. With the exception of acetate and malate, organic carbon sources tested supported poor growth or no growth at all. Growth factors were required; these were provided by small amounts of yeast extract, but not by standard vitamin solutions. Growth occurred under aerobic to microaerobic conditions, but not under anaerobic conditions, either in the dark or light. Nitrate was not reduced. Photosynthetic pigments were formed at low to medium salt concentrations, but not at the salt concentration of sea water (3.5 %). On the basis of smaller cell size, different substrate utilization profile and photosynthetic pigment content, the novel strains can be classified as representatives of a second species of Hoeflea, for which the name Hoeflea phototrophica sp. nov. is proposed. The type strain of Hoeflea phototrophica sp. nov. is DFL-43T (=DSM 17068T = NCIMB 14078T).
    • Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae

      Brinkmann, Henner; Göker, Markus; Koblížek, Michal; Wagner-Döbler, Irene; Petersen, Jörn; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
    • Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum.

      Wang, Hui; Tomasch, Jürgen; Michael, Victoria; Bhuju, Sabin; Jarek, Michael; Petersen, Jörn; Wagner-Döbler, Irene; Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. (2015)
      The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the "Jekyll-and-Hyde" interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.
    • Identification, synthesis, and conformation of tri- and tetrathiacycloalkanes from marine bacteria.

      Sobik, Paul; Grunenberg, Jörg; Böröczky, Katalin; Laatsch, Hartmut; Wagner-Döbler, Irene; Schulz, Stefan (2007-05-11)
      Seven new cyclic natural polysulfides 1-7 were identified in extracts of two bacterial Cytophaga strains (CFB-phylum) isolated from biofilms from the North Sea. Their structures are based on mono- and dimeric-cyclization products of 2-methylpropane-1,2-dithiol 8, which was also present in the extract in trace amounts. The structures were deduced by analysis of their mass spectra and confirmed by synthesis. The 1H NMR spectra of some these compounds suggested a high flexibility of the trithiepane and tetrathiocane systems. Therefore, their conformation was further analyzed by DFT calculations and dynamic NMR spectroscopy. While thiepane 4 possesses a twist-chair lowest energy conformation, its isomers 2 and 3 adopt a chairlike conformation, as does the tetrathiocane 5. In contrast, tetrathiocane 6 favors again a twisted chair conformation.
    • Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol.

      Beckers, Veronique; Poblete-Castro, Ignacio; Tomasch, Jürgen; Wittmann, Christoph; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016)
      Given its high surplus and low cost, glycerol has emerged as interesting carbon substrate for the synthesis of value-added chemicals. The soil bacterium Pseudomonas putida KT2440 can use glycerol to synthesize medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA), a class of biopolymers of industrial interest. Here, glycerol metabolism in P. putida KT2440 was studied on the level of gene expression (transcriptome) and metabolic fluxes (fluxome), using precisely adjusted chemostat cultures, growth kinetics and stoichiometry, to gain a systematic understanding of the underlying metabolic and regulatory network.
    • Iromycins from Streptomyces sp. and from synthesis: new inhibitors of the mitochondrial electron transport chain.

      Surup, Frank; Shojaei, Heydar; von Zezschwitz, Paultheo; Kunze, Brigitte; Grond, Stephanie; Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany. (2008-02-15)
      Two new alpha-pyridone metabolites, iromycins E and F, were isolated from cultures of strain Streptomyces sp. Dra 17, thus expanding the recently discovered iromycin family. The inhibitory potential on the mitochondrial respiratory chain was examined and revealed that iromycin metabolites block NADH oxidation in beef heart submitochondrial particles with different efficacy, yet remarkably show only very low cytotoxicity. Difference spectroscopic studies indicated that iromycins inhibit the electron transport at the site of complex I (NADH-ubiquinone oxidoreductase). Derivatives of the natural products were semisynthetically prepared and provided detailed insights into structure-activity relationships. Drawn from these results, there are strong similarities with the piericidins, which are among the most potent complex I inhibitors of the mitochondrial electron transport chain. Furthermore, total synthesis afforded new analogues, and the non-natural iromycin S (IC50 = 58 ng/mL) emerged as the most active compound, thus opening avenues of future studies with the iromycins as new valuable biochemical tools.
    • Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria.

      Brock, Nelson L; Citron, Christian A; Zell, Claudia; Berger, Martine; Wagner-Döbler, Irene; Petersen, Jörn; Brinkhoff, Thorsten; Simon, Meinhard; Dickschat, Jeroen S; Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany. (2013)
      Members of the marine Roseobacter clade can degrade dimethylsulfoniopropionate (DMSP) via competing pathways releasing either methanethiol (MeSH) or dimethyl sulfide (DMS). Deuterium-labeled [(2)H6]DMSP and the synthetic DMSP analogue dimethyltelluriopropionate (DMTeP) were used in feeding experiments with the Roseobacter clade members Phaeobacter gallaeciensis DSM 17395 and Ruegeria pomeroyi DSS-3, and their volatile metabolites were analyzed by closed-loop stripping and solid-phase microextraction coupled to GC-MS. Feeding experiments with [(2)H6]DMSP resulted in the incorporation of a deuterium label into MeSH and DMS. Knockout of relevant genes from the known DMSP demethylation pathway to MeSH showed in both species a residual production of [(2)H3]MeSH, suggesting that a second demethylation pathway is active. The role of DMSP degradation pathways for MeSH and DMS formation was further investigated by using the synthetic analogue DMTeP as a probe in feeding experiments with the wild-type strain and knockout mutants. Feeding of DMTeP to the R. pomeroyi knockout mutant resulted in a diminished, but not abolished production of demethylation pathway products. These results further corroborated the proposed second demethylation activity in R. pomeroyi. Isotopically labeled [(2)H3]methionine and (34)SO4 (2-), synthesized from elemental (34)S8, were tested to identify alternative sulfur sources besides DMSP for the MeSH production in P. gallaeciensis. Methionine proved to be a viable sulfur source for the MeSH volatiles, whereas incorporation of labeling from sulfate was not observed. Moreover, the utilization of selenite and selenate salts by marine alphaproteobacteria for the production of methylated selenium volatiles was explored and resulted in the production of numerous methaneselenol-derived volatiles via reduction and methylation. The pathway of selenate/selenite reduction, however, proved to be strictly separated from sulfate reduction.
    • Lack of the delta subunit of RNA polymerase increases virulence related traits of Streptococcus mutans.

      Xue, Xiaoli; Sztajer, Helena; Buddruhs, Nora; Petersen, Jörn; Rohde, Manfred; Talay, Susanne R; Wagner-Döbler, Irene; Research Group Microbial Communication, Division of Cell Biology, Helmholtz Centre for Infection Research GmbH, Braunschweig, Germany. (2011)
      The delta subunit of the RNA polymerase, RpoE, maintains the transcriptional specificity in gram-positive bacteria. Lack of RpoE results in massive changes in the transcriptome of the human dental caries pathogen Streptococcus mutans. In this study, we analyzed traits of the ΔrpoE mutant which are important for biofilm formation and interaction with oral microorganisms and human cells and performed a global phenotypic analysis of its physiological functions. The ΔrpoE mutant showed higher self-aggregation compared to the wild type and coaggregated with other oral bacteria and Candida albicans. It formed a biofilm with a different matrix structure and an altered surface attachment. The amount of the cell surface antigens I/II SpaP and the glucosyltransferase GtfB was reduced. The ΔrpoE mutant displayed significantly stronger adhesion to human extracellular matrix components, especially to fibronectin, than the wild type. Its adhesion to human epithelial cells HEp-2 was reduced, probably due to the highly aggregated cell mass. The analysis of 1248 physiological traits using phenotype microarrays showed that the ΔrpoE mutant metabolized a wider spectrum of carbon sources than the wild type and had acquired resistance to antibiotics and inhibitory compounds with various modes of action. The reduced antigenicity, increased aggregation, adherence to fibronection, broader substrate spectrum and increased resistance to antibiotics of the ΔrpoE mutant reveal the physiological potential of S. mutans and show that some of its virulence related traits are increased.
    • Low diversity of planktonic bacteria in the tropical ocean.

      Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L; Wang, Hui; Jáuregui, Ruy; Camarinha-Silva, Amelia; Deng, Zhi-Luo; Plumeier, Iris; Giebel, Helge-Ansgar; Wurst, Mascha; et al. (2016)
      The diversity of macro-organisms increases towards the equator, with almost no exceptions. It is the most conserved biogeographical pattern on earth and is thought to be related to the increase of temperature and productivity in the tropics. The extent and orientation of a latitudinal gradient of marine bacterioplankton diversity is controversial. Here we studied the euphotic zone of the Atlantic Ocean based on a transect covering ~12.000 km from 51°S to 47 °N. Water samples were collected at 26 stations at five depths between 20 and 200 m and sequentially filtered through 8 μm, 3 μm and 0,22 μm filters, resulting in a total of 359 samples. Illumina sequencing of the V5-V6 region of the 16S rRNA gene revealed a clear biogeographic pattern with a double inverted latitudinal gradient. Diversity was higher in mid-latitudinal regions of the Atlantic Ocean and decreased towards the equator. This pattern was conserved for bacteria from all three planktonic size fractions. Diversity showed a non-linear relationship with temperature and was negatively correlated with bacterial cell numbers in the upper depth layers (<100 m). The latitudinal gradients of marine bacterial diversity and the mechanisms that govern them are distinct from those found in macro-organisms.