http://www.bibsonomy.org/burst/user/mikromolbio/Gene_Expression_RegulationBibSonomy BuRST Feed for /user/mikromolbio/Gene_Expression_Regulation2008-09-07T19:41:45+02:00http://www.bibsonomy.org/bibtex/27ffd100e93e552721654848a86efd795/mikromolbiomikromolbio2008-05-07T15:52:44+02:00RNA Divalent Gel Gene_Expression_Regulation IFZ Bacterial Catalase Singlet_Oxygen Reactive_Oxygen_Species Proteome Protein_Biosynthesis Sigma_Factor Hydrogen_Peroxide Host_Factor_1_Protein Two-Dimensional Light Rhodobacter_sphaeroides Mutation Bacterial_Proteins Cations Messenger Transcription_Factors Electrophoresis <span style="color:#555555;">Jens <a href="http://www.bibsonomy.org/author/Glaeser">Glaeser</a> und Monica <a href="http://www.bibsonomy.org/author/Zobawa">Zobawa</a> und Friedrich <a href="http://www.bibsonomy.org/author/Lottspeich">Lottspeich</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Journal of proteome research</em><em>July2007. </em><em>PMID: 17536848 . </em>Wed May 07 15:52:44 CEST 2008Journal of proteome researchJulyPMID: 175368482460-71Protein synthesis patterns reveal a complex regulatory response to singlet oxygen in Rhodobacter62007RNA Divalent Gel Gene_Expression_Regulation IFZ Bacterial Catalase Singlet_Oxygen Reactive_Oxygen_Species Proteome Protein_Biosynthesis Sigma_Factor Hydrogen_Peroxide Host_Factor_1_Protein Two-Dimensional Light Rhodobacter_sphaeroides Mutation Bacterial_Proteins Cations Messenger Transcription_Factors Electrophoresis Singlet oxygen (1O2) is a stress factor and signal in the facultative phototrophic bacterium Rhodobacter sphaeroides. In vivo protein labeling with L-[35S]-methionine and analysis by two-dimensional gel electrophoresis revealed that the synthesis of 61 proteins was changed in response to 1O2. After 1O2 treatment, protein synthesis patterns were distinct from those after H2O2 treatment but similar to those after high light exposure. This indicates regulatory mechanisms selective for different reactive oxygen species (ROS) and a response to light partly mediated by 1O2. Analysis of mutant strains support that the response to 1O2 is regulated mainly by rpoE (sigma E), but also a modulation of the sigma E dependent response by other factors and the existence of sigma E independent responses. The involvement of the RNA chaperon Hfq in the 1O2 response implies a role of small regulatory RNAs.http://www.bibsonomy.org/bibtex/2192438d916f82e78d51d7cfdd8031f65/mikromolbiomikromolbio2008-05-07T15:52:44+02:00Polyacrylamide_Gel Oxidation-Reduction Bacterial Two-Hybrid_System_Techniques Electrophoretic_Mobility_Shift_Assay Protein_Binding Deoxyribonuclease_I Northern Trans-Activators Luciferases Bacterial_Proteins Electrophoresis IFZ Rhodobacter_capsulatus Blotting Gene_Expression_Regulation <span style="color:#555555;">Jutta <a href="http://www.bibsonomy.org/author/Gregor">Gregor</a> und Tanja <a href="http://www.bibsonomy.org/author/Zeller">Zeller</a> und Angelika <a href="http://www.bibsonomy.org/author/Balzer">Balzer</a> und Kerstin <a href="http://www.bibsonomy.org/author/Haberzettl">Haberzettl</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Journal of molecular microbiology and biotechnology</em>(<em>2007</em>) <em>PMID: 17693720 . </em>Wed May 07 15:52:44 CEST 2008Journal of molecular microbiology and biotechnologyPMID: 17693720126-39Bacterial regulatory networks include direct contact of response regulator proteins: interaction of RegA and NtrX in Rhodobacter capsulatus132007Polyacrylamide_Gel Oxidation-Reduction Bacterial Two-Hybrid_System_Techniques Electrophoretic_Mobility_Shift_Assay Protein_Binding Deoxyribonuclease_I Northern Trans-Activators Luciferases Bacterial_Proteins Electrophoresis IFZ Rhodobacter_capsulatus Blotting Gene_Expression_Regulation The formation of photosynthetic complexes in facultatively photosynthetic bacteria is controlled by the oxygen tension in the environment. In Rhodobacter capsulatus the two-component system RegB/RegA plays a major role in the redox control of photosynthesis genes but also controls other redox-dependent systems. The response regulator RegA is phosphorylated under low oxygen tension and activates the puf and puc operons, which encode pigment binding proteins, by binding to their promoter regions. Data from a yeast two-hybrid analysis as well as an in vitroanalysis indicate that RegA interacts with the NtrX protein, the response regulator of the NtrY/NtrX two-component system which is believed to be involved in regulation of nitrogen fixation genes. Our further analysis revealed that NtrX is indeed involved in the regulation of the puf and puc operons. Furthermore, we showed that an altered NtrX protein, which is predicted to adopt the conformation of phosphorylated NtrX protein, binds within the puf promoter region close to the RegA binding sites. We conclude that a direct interaction of two response regulators connects the regulatory systems for redox control and nitrogen control.http://www.bibsonomy.org/bibtex/28f70cb140c45721ef0acab94f03009d2/mikromolbiomikromolbio2008-05-07T15:52:44+02:00Regulon Bacterial Transcription Rhodobacter_sphaeroides Genetic Hydrogen_Peroxide Molecular_Sequence_Data Oxidants IFZ Base_Sequence Consensus_Sequence Transcription_Factors Gene_Expression_Regulation Mutation <span style="color:#555555;">Tanja <a href="http://www.bibsonomy.org/author/Zeller">Zeller</a> und Mobarak A <a href="http://www.bibsonomy.org/author/Mraheil">Mraheil</a> und Oleg V <a href="http://www.bibsonomy.org/author/Moskvin">Moskvin</a> und Kuanyu <a href="http://www.bibsonomy.org/author/Li">Li</a> und Mark <a href="http://www.bibsonomy.org/author/Gomelsky">Gomelsky</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Journal of bacteriology</em><em>May2007. </em><em>PMID: 17351037 . </em>Wed May 07 15:52:44 CEST 2008Journal of bacteriologyMayPMID: 173510373784-92Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: regulatory functions of OxyR1892007Regulon Bacterial Transcription Rhodobacter_sphaeroides Genetic Hydrogen_Peroxide Molecular_Sequence_Data Oxidants IFZ Base_Sequence Consensus_Sequence Transcription_Factors Gene_Expression_Regulation Mutation Genome-wide transcriptome profiling was used to reveal hydrogen peroxide (H(2)O(2))-dependent regulatory mechanisms in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. In this study we focused on the role of the OxyR protein, a known regulator of the H(2)O(2) response in bacteria. The transcriptome profiles of R. sphaeroides wild-type and oxyR mutant strains that were exposed to 1 mM H(2)O(2) for 7 min or were not exposed to H(2)O(2) were analyzed. Three classes of OxyR-dependent genes were identified based on their expression patterns in the wild type of oxyR mutant strains with differing predicted roles of oxidized and reduced OxyR as activators of transcription. DNA binding studies revealed that OxyR binds upstream of class I genes, which are induced by H(2)O(2) and exhibit similar basal levels of expression in the wild-type and oxyR mutant strains. The effect of OxyR on class II genes, which are also induced by H(2)O(2) but exhibit significantly lower basal levels of expression in the wild-type strain than in the mutant, is indirect. Interestingly, reduced OxyR also activates expression of few genes (class III). The role of reduced OxyR as an activator is shown for the first time. Our data reveal that the OxyR-mediated response is fast and transient. In addition, we found that additional regulatory pathways are involved in the H(2)O(2) response.http://www.bibsonomy.org/bibtex/24ac18fa9640073e4d8ca4eaa9746a5a4/mikromolbiomikromolbio2008-05-07T15:52:44+02:00Coenzymes Sequence_Deletion Protein_Binding Heme Models Recombinant_Proteins Rhodobacter_sphaeroides Light Repressor_Proteins Hemin IFZ Bacterial_Proteins Biological Electrophoretic_Mobility_Shift_Assay Amino_Acid_Sequence Sequence_Alignment Gene_Expression_Regulation Molecular_Sequence_Data Spectrum_Analysis Oxidation-Reduction Signal_Transduction Escherichia_coli Protein_Structure Flavoproteins Bacterial DNA-Binding_Proteins Tertiary <span style="color:#555555;">Yuchen <a href="http://www.bibsonomy.org/author/Han">Han</a> und Martin H F <a href="http://www.bibsonomy.org/author/Meyer">Meyer</a> und Michael <a href="http://www.bibsonomy.org/author/Keusgen">Keusgen</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Molecular microbiology</em><em>May2007. </em><em>PMID: 17501930 . </em>Wed May 07 15:52:44 CEST 2008Molecular microbiologyMayPMID: 175019301090-104A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides642007Coenzymes Sequence_Deletion Protein_Binding Heme Models Recombinant_Proteins Rhodobacter_sphaeroides Light Repressor_Proteins Hemin IFZ Bacterial_Proteins Biological Electrophoretic_Mobility_Shift_Assay Amino_Acid_Sequence Sequence_Alignment Gene_Expression_Regulation Molecular_Sequence_Data Spectrum_Analysis Oxidation-Reduction Signal_Transduction Escherichia_coli Protein_Structure Flavoproteins Bacterial DNA-Binding_Proteins Tertiary The AppA protein of Rhodobacter sphaeroides is unique in its ability to sense and transmit redox signals as well as light signals. By functioning as antagonist to the PpsR transcriptional repressor, it regulates the expression of photosynthesis genes in response to these environmental stimuli. Here we show binding of the cofactor haem to a domain in the C-terminal part of AppA and redox activity of bound haem. This is supported by the findings that: (i) the C-terminal domain of AppA (AppADeltaN) binds to haemin agarose, (ii) AppADeltaN isolated from Escherichia coli shows absorbance at 411 nm and absorbances at 424 nm and 556 nm after reduction with dithionite and (iii) AppADeltaN can be reconstituted with haem in vitro. Expression of AppA variants in R. sphaeroides reveals that the haem binding domain is important for normal expression levels of photosynthesis genes and for normal light regulation in the presence of oxygen. The haem cofactor affects the interaction of the C-terminal part of AppA to PpsR but also its interaction to the N-terminal light sensing AppA-BLUF domain. Based on this we present a model for the transmission of light and redox signals by AppA.http://www.bibsonomy.org/bibtex/2f1831a18a9ee9dba81778273d45463ab/mikromolbiomikromolbio2008-05-07T15:52:44+02:00Sequence_Alignment Singlet_Oxygen Reporter Bacterial Light Bacterial_Proteins Gene_Expression_Regulation IFZ Sigma_Factor Up-Regulation Amino_Acid_Sequence Peroxides Transcription_Factors Genes beta-Galactosidase Rhodobacter_sphaeroides Microbial_Viability Molecular_Sequence_Data Deoxyribodipyrimidine_Photo-Lyase Anti-Bacterial_Agents Superoxides Artificial_Gene_Fusion <span style="color:#555555;">Anne-Kathrin <a href="http://www.bibsonomy.org/author/Hendrischk">Hendrischk</a> und Stephan <a href="http://www.bibsonomy.org/author/Braatsch">Braatsch</a> und Jens <a href="http://www.bibsonomy.org/author/Glaeser">Glaeser</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Microbiology (Reading, England)</em><em>June2007. </em><em>PMID: 17526841 . </em>Wed May 07 15:52:44 CEST 2008Microbiology (Reading, England)JunePMID: 175268411842-51The phrA gene of Rhodobacter sphaeroides encodes a photolyase and is regulated by singlet oxygen and peroxide in a sigma(E)-dependent manner1532007Sequence_Alignment Singlet_Oxygen Reporter Bacterial Light Bacterial_Proteins Gene_Expression_Regulation IFZ Sigma_Factor Up-Regulation Amino_Acid_Sequence Peroxides Transcription_Factors Genes beta-Galactosidase Rhodobacter_sphaeroides Microbial_Viability Molecular_Sequence_Data Deoxyribodipyrimidine_Photo-Lyase Anti-Bacterial_Agents Superoxides Artificial_Gene_Fusion The genome of the facultatively photosynthetic bacterium Rhodobacter sphaeroides encodes three proteins of the photolyase/cryptochrome family. This paper shows that phrA (RSP2143) encodes a functional photolyase, which is an enzyme that repairs UV radiation-induced DNA damage in a blue light dependent manner. Expression of phrA is upregulated in response to light, with no photoreceptor or the photosynthetic electron transport being involved. The results reveal that singlet oxygen and hydrogen peroxide dependent signals are transmitted by the sigma(E) factor and the anti-sigma(E) factor ChrR affecting phrA expression, while superoxide anions do not stimulate phrA expression. Thus, the sigma(E) regulon is involved not only in the response to singlet oxygen but also in the hydrogen peroxide response.http://www.bibsonomy.org/bibtex/2d09486188bc04d8a07c7ef5a470fbac6/mikromolbiomikromolbio2008-05-07T15:52:44+02:00Oxygen Paracoccus_denitrificans Signal_Transduction Microbial Photoreceptors Repressor_Proteins IFZ Escherichia_coli Rhodobacter_capsulatus DNA-Binding_Proteins Trans-Activators Flavoproteins Bacterial_Proteins Light Photosynthesis Gene_Expression_Regulation Bacterial Rhodobacter_sphaeroides Oxidation-Reduction <span style="color:#555555;">Andreas <a href="http://www.bibsonomy.org/author/Jäger">J&#228;ger</a> und Stephan <a href="http://www.bibsonomy.org/author/Braatsch">Braatsch</a> und Kerstin <a href="http://www.bibsonomy.org/author/Haberzettl">Haberzettl</a> und Sebastian <a href="http://www.bibsonomy.org/author/Metz">Metz</a> und Lisa <a href="http://www.bibsonomy.org/author/Osterloh">Osterloh</a> und Yuchen <a href="http://www.bibsonomy.org/author/Han">Han</a> und Gabriele <a href="http://www.bibsonomy.org/author/Klug">Klug</a> </span><em>Journal of bacteriology</em><em>March2007. </em><em>PMID: 17209035 . </em>Wed May 07 15:52:44 CEST 2008Journal of bacteriologyMarchPMID: 172090352274-82The AppA and PpsR proteins from Rhodobacter sphaeroides can establish a redox-dependent signal chain but fail to transmit blue-light signals in other bacteria1892007Oxygen Paracoccus_denitrificans Signal_Transduction Microbial Photoreceptors Repressor_Proteins IFZ Escherichia_coli Rhodobacter_capsulatus DNA-Binding_Proteins Trans-Activators Flavoproteins Bacterial_Proteins Light Photosynthesis Gene_Expression_Regulation Bacterial Rhodobacter_sphaeroides Oxidation-Reduction The AppA protein of Rhodobacter sphaeroides has the unique ability to sense and transmit redox and light signals. In response to decreasing oxygen tension, AppA antagonizes the transcriptional regulator PpsR, which represses the expression of photosynthesis genes, including the puc operon. This mechanism, which is based on direct protein-protein interaction, is prevented by blue-light absorption of the BLUF domain located in the N-terminal part of AppA. In order to test whether AppA and PpsR are sufficient to transmit redox and light signals, we expressed these proteins in three different bacterial species and monitored oxygen- and blue-light-dependent puc expression either directly or by using a luciferase-based reporter construct. The AppA/PpsR system could mediate redox-dependent gene expression in the alphaproteobacteria Rhodobacter capsulatus and Paracoccus denitrificans but not in the gammaproteobacterium Escherichia coli. Analysis of a prrA mutant strain of R. sphaeroides strongly suggests that light-dependent gene expression requires a balanced interplay of the AppA/PpsR system with the PrrA response regulator. Therefore, the AppA/PpsR system was unable to establish light signaling in other bacteria. Based on our data, we present a model for the interdependence of AppA/PpsR signaling and the PrrA transcriptional activator.