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pmoA-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment. Michael Pester, 2004.Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene . Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment . T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and the inactive community in an anoxic sediment layer at a 10-cm depth . There were also no major changes in community structure between littoral sediment cores sampled in summer and winter . By contrast, the fingerprint patterns showed substantial differences between the methanotrophic communities of littoral and profundal sediments . Overexpression of the PepF Oligopeptidase Inhibits Sporulation Initiation in Bacillus subtilis. Kyoko Kanamaru, 2002.The yjbG gene encoding the homologue of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis (Monnet et al., J . Biol . Chem . 269:32070–32076, 1994; Nardi et al., J . Bacteriol . 179:4164–4171, 1997) has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when present in the cells on a multicopy plasmid . Genetic analysis suggested that the inhibitory effect is due to hydrolysis of the PhrA peptide in a form as small as the pentapeptide (ARNQT) . Inactivation of PhrA results in deregulation of the RapA phosphatase and thus dephosphorylation of the Spo0F  P response regulator component of the phosphorelay for sporulation initiation . When overexpressed, the B . subtilis PepF is most likely hydrolyzing additional peptides of the Phr family, as is the case for PhrC involved in control of competence development . Chromosomal inactivation of the yjbG/pepF gene did not give rise to any detectable phenotype . The function of PepF in B . subtilis remains unknown . Limited experiments with a yjbG paralogue called yusX indicated that a frameshift is present, making the corresponding gene product inactive .
FlhD/FlhC Is a Regulator of Anaerobic Respiration and the Entner-Doudoroff Pathway through Induction of the Methyl-Accepting Chemotaxis Protein Aer. Birgit M. Prüß, 2003.The regulation by two transcriptional activators of flagellar expression (FlhD and FlhC) and the chemotaxis methyl-accepting protein Aer was studied with glass slide DNA microarrays . An flhD::Kan insertion and an aer deletion were independently introduced into two Escherichia coli K-12 strains, and the effects upon gene regulation were investigated . Altogether, the flhD::Kan insertion altered the expression of 29 operons of known function . Among them was Aer, which in turn regulated a subset of these operons, namely, the ones involved in anaerobic respiration and the Entner-Doudoroff pathway . In addition, FlhD/FlhC repressed enzymes involved in aerobic respiration and regulated many other metabolic enzymes and transporters in an Aer-independent manner . Expression of 12 genes of uncharacterized function was also affected . FlhD increased gltBD, gcvTHP, and ompT expression . The regulation of half of these genes was subsequently confirmed with reporter gene fusions, enzyme assays, and real-time PCR . Growth phenotypes of flhD and flhC mutants were determined with Phenotype MicroArrays and correlated with gene expression . Localization of rRNA Synthesis in Bacillus subtilis: Characterization of Loci Involved in Transcription Focus Formation. Karen M. Davies, 2003.In Bacillus subtilis, RNA polymerase becomes concentrated into regions of the nucleoid called transcription foci . With green fluorescent protein-tagged RNA polymerase, these structures are only observed at higher growth rates and have been shown to represent the sites of rRNA synthesis . There are 10 rRNA (rrn) operons distributed around nearly half of the chromosome . In this study we analyzed the rrn composition of transcription foci with fluorescently tagged loci and showed that they comprise the origin-proximal operon rrnO but not the more dispersed rrnE or rrnD . This suggests that transcription foci comprise only the seven origin-proximal operons rrnO, rrnA, rrnJ, rrnW, rrnI, rrnH, and rrnG . These results have important implications for our understanding of microbial chromosome structure .
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