@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 = {Mutation Genetic Base_Sequence Transcription Oxidants Regulon Consensus_Sequence Transcription_Factors Hydrogen_Peroxide Gene_Expression_Regulation Bacterial Rhodobacter_sphaeroides Molecular_Sequence_Data IFZ}
}

@article{hundt_global_2007,
        title = {Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays},
        author = {Sonja Hundt and Alexander Zaigler and Christian Lange and Jörg Soppa and Gabriele Klug},
        journal = {Journal of bacteriology},
        month = {October},
        note = {PMID: 17644597},
        pages = {6936-44},
        volume = 189,
        year = 2007,
        issn = {00219193},
	abstract = {RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1,717 open reading frames, 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 min to more than 18 min, with 79\% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min, which is considerably longer than the ones found in the other prokaryotes investigated thus far. As previously observed in Escherichia coli and Saccharomyces cerevisiae, we could not detect a significant correlation between transcript length and transcript stability, but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives. These results provide initial insights into mRNA turnover in a euryarchaeon. Moreover, our model organism, H. salinarum NRC-1, is one of just two archaea sequenced to date that are missing the core subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced thus far.},
	biburl = {http://www.bibsonomy.org/bibtex/2878c84029d2104ff7f5177044c52c670/mikromolbio},
	keywords = {IFZ RNA_Stability RNA Dactinomycin Halobacterium_salinarum Messenger Half-Life Transcription Northern Blotting Archaeal Oligonucleotide_Array_Sequence_Analysis Genome Genetic}
}