BibSonomy publications for /user/mikromolbio/Molecular_Sequence_DataWed May 07 15:52:44 CEST 2008Journal of bacteriologyMayPMID: 173510373784-92Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: regulatory functions of OxyR1892007Regulon Molecular_Sequence_Data Bacterial Transcription Gene_Expression_Regulation Transcription_Factors Consensus_Sequence Mutation Base_Sequence Oxidants Rhodobacter_sphaeroides Hydrogen_Peroxide IFZ Genetic 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.Wed May 07 15:52:44 CEST 2008The Journal of biological chemistryMayPMID: 1736925213966-76An archaeal protein with homology to the eukaryotic translation initiation factor 5A shows ribonucleolytic activity2822007Nucleic_Acid Peptide_Initiation_Factors Nucleic_Acid_Conformation Base_Sequence Amino_Acid_Sequence Genetic_Vectors Ribonucleases Archaeal Messenger Protein_Processing Halobacterium Archaeal_Proteins Post-Translational Eukaryotic_Cells IFZ Cells Lysine RNA-Binding_Proteins RNA Sequence_Homology Molecular_Sequence_Data Ligands Cultured To identify proteins that are involved in RNA degradation and processing in Halobacterium sp. NRC-1, we purified proteins with RNA-degrading activity by classical biochemical techniques. One of these proteins showed strong homology to the eukaryotic initiation factor 5A (eIF-5A) and was accordingly named archaeal initiation factor 5A (aIF-5A). Eukaryotic IF-5A is known to be involved in mRNA turnover and to bind RNA. Hypusination of eIF-5A is required for sequence-specific binding of RNA. This unique post-translational modification is restricted to Eukarya and Archaea. The exact function of eIF-5A in RNA turnover remained obscure. Here we show for the first time that aIF-5A from Halobacterium sp. NRC-1 exhibits RNA cleavage activity, preferentially cleaving adjacent to A nucleotides. Detectable RNA binding could be shown for aIF-5A purified from Halobacterium sp. NRC-1 but not from Escherichia coli, while both proteins possess RNA cleavage activity, indicating that hypusination of aIF-5A is required for RNA binding but not for its RNA cleavage activity. Furthermore, we show that the hypusinated form of eIF-5A also shows RNase activity while the unmodified protein does not. Charged amino acids in the N-terminal domain of aIF-5A as well as in the C-terminal domain, which is highly similar to the cold shock protein A (CspA), an RNA chaperone of E. coli, are important for RNA cleavage activity. Moreover our results reveal that activity of aIF-5A depends on its oligomeric state.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 sphaeroides642007Recombinant_Proteins Bacterial_Proteins Protein_Structure Sequence_Alignment Signal_Transduction Gene_Expression_Regulation DNA-Binding_Proteins Escherichia_coli Molecular_Sequence_Data Tertiary IFZ Sequence_Deletion Rhodobacter_sphaeroides Electrophoretic_Mobility_Shift_Assay Bacterial Biological Coenzymes Hemin Amino_Acid_Sequence Heme Models Spectrum_Analysis Protein_Binding Repressor_Proteins Flavoproteins Oxidation-Reduction Light 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.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 manner1532007Peroxides Up-Regulation Bacterial_Proteins Rhodobacter_sphaeroides Sigma_Factor Singlet_Oxygen Light Anti-Bacterial_Agents Molecular_Sequence_Data Sequence_Alignment Gene_Expression_Regulation Deoxyribodipyrimidine_Photo-Lyase Microbial_Viability Artificial_Gene_Fusion Transcription_Factors beta-Galactosidase IFZ Bacterial Genes Reporter Superoxides Amino_Acid_Sequence 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.