@article{zeller_regulation_2007, title = {Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: regulatory functions of OxyR}, author = {Tanja Zeller and Mobarak A Mraheil and Oleg V Moskvin and Kuanyu Li and Mark Gomelsky and Gabriele Klug}, journal = {Journal of bacteriology}, month = {May}, note = {PMID: 17351037}, pages = {3784-92}, volume = 189, year = 2007, issn = {00219193}, abstract = {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.}, biburl = {http://www.bibsonomy.org/bibtex/28f70cb140c45721ef0acab94f03009d2/mikromolbio}, keywords = {Bacterial Base_Sequence Mutation Gene_Expression_Regulation Rhodobacter_sphaeroides Hydrogen_Peroxide Regulon Consensus_Sequence Oxidants Transcription_Factors Molecular_Sequence_Data Genetic Transcription IFZ} } @article{wagner_archaeal_2007, title = {An archaeal protein with homology to the eukaryotic translation initiation factor 5A shows ribonucleolytic activity}, author = {Steffen Wagner and Gabriele Klug}, journal = {The Journal of biological chemistry}, month = {May}, note = {PMID: 17369252}, pages = {13966-76}, volume = 282, year = 2007, issn = {00219258}, abstract = {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.}, biburl = {http://www.bibsonomy.org/bibtex/2dca52bc2607846f74bf0d7984035d738/mikromolbio}, keywords = {IFZ Molecular_Sequence_Data Post-Translational Archaeal Cultured Cells Peptide_Initiation_Factors RNA Nucleic_Acid Archaeal_Proteins Sequence_Homology Amino_Acid_Sequence Nucleic_Acid_Conformation Messenger Base_Sequence Lysine Halobacterium Ligands RNA-Binding_Proteins Ribonucleases Genetic_Vectors Eukaryotic_Cells Protein_Processing} } @article{han_haem_2007, title = {A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides}, author = {Yuchen Han and Martin H F Meyer and Michael Keusgen and Gabriele Klug}, journal = {Molecular microbiology}, month = {May}, note = {PMID: 17501930}, pages = {1090-104}, volume = 64, year = 2007, issn = {0950382}, abstract = {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.}, biburl = {http://www.bibsonomy.org/bibtex/24ac18fa9640073e4d8ca4eaa9746a5a4/mikromolbio}, keywords = {Tertiary Spectrum_Analysis Electrophoretic_Mobility_Shift_Assay Repressor_Proteins Signal_Transduction Recombinant_Proteins Gene_Expression_Regulation Escherichia_coli Rhodobacter_sphaeroides Flavoproteins Bacterial DNA-Binding_Proteins Bacterial_Proteins Models Sequence_Deletion Coenzymes Light Sequence_Alignment Oxidation-Reduction Biological Molecular_Sequence_Data Protein_Binding Amino_Acid_Sequence Protein_Structure IFZ Heme Hemin} } @article{hendrischk_phra_2007, title = {The phrA gene of Rhodobacter sphaeroides encodes a photolyase and is regulated by singlet oxygen and peroxide in a sigma(E)-dependent manner}, author = {Anne-Kathrin Hendrischk and Stephan Braatsch and Jens Glaeser and Gabriele Klug}, journal = {Microbiology (Reading, England)}, month = {June}, note = {PMID: 17526841}, pages = {1842-51}, volume = 153, year = 2007, issn = {13500872}, abstract = {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.}, biburl = {http://www.bibsonomy.org/bibtex/2f1831a18a9ee9dba81778273d45463ab/mikromolbio}, keywords = {Reporter Bacterial_Proteins Light Rhodobacter_sphaeroides Bacterial beta-Galactosidase Up-Regulation Superoxides Amino_Acid_Sequence Microbial_Viability Gene_Expression_Regulation Peroxides Deoxyribodipyrimidine_Photo-Lyase Sequence_Alignment Anti-Bacterial_Agents Transcription_Factors Molecular_Sequence_Data IFZ Singlet_Oxygen Artificial_Gene_Fusion Genes Sigma_Factor} }