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Whole-Genome Expression Profiling of Thermotoga maritima in Response to Growth on Sugars in a Chemostat. Tu N. Nguyen, 2004.To provide data necessary to study catabolite-linked transcriptional networks in Thermotoga maritima, we used full-genome DNA microarray analysis of global transcriptional responses to growth on glucose, lactose, and maltose in a chemostat . A much larger number of genes changed expression in cells grown on lactose than on maltose, each relative to genes expressed in cells grown on glucose . Genes encoding putative oligopeptide transporters were often coregulated with adjacent glycosidase-encoding genes . Genes encoding enzymes catalyzing NADH oxidation were up-regulated on both lactose and maltose . Genes involved in iron and sulfur metabolism were differentially expressed in response to lactose . These data help define the sets of coregulated genes and suggest possible functions for their encoded products . Comparison of Coliforms and Coliphages as Tools for Assessment of Viral Contamination in River Water. S. Skraber, 2004.The aim of the study was to evaluate the presence of pathogenic viruses in the Moselle River and to compare the usefulness of thermotolerant coliforms and somatic coliphages as tools for river water quality assessment in terms of viral contamination . Thermotolerant coliforms and somatic coliphages were enumerated by standardized methods in 170 samples of river water drawn from five sampling sites along the Moselle River (eastern France) . BGM cell culture and integrated cell culture-reverse transcription-PCR DNA enzyme immunoassay were used to determine the presence of pathogenic viral genome (Enterovirus and Norovirus genogroup II [GGII]) and infectious Enterovirus spp . in 90 1-liter samples . No infectious Enterovirus spp . were isolated, but Enterovirus and Norovirus GGII genomes were detected in 38% of the samples . Norovirus GGII genome was mostly detected in winter, whereas Enterovirus genome was mostly detected in summer and fall . Somatic coliphages appeared to be less sensitive to higher river water temperature than thermotolerant coliforms . Furthermore, the number of river water samples positive for pathogenic viral genome increased with increasing concentration of somatic coliphages, whereas coliform concentration was unrelated to viral genome contamination . Consequently somatic coliphages, which are less sensitive to environmental factors than thermotolerant coliforms in river water, would provide a promising tool for assessment of river water quality in terms of fecal and viral pollution . CcaR Is an Autoregulatory Protein That Binds to the ccaR and cefD-cmcI Promoters of the Cephamycin C-Clavulanic Acid Cluster in Streptomyces clavuligerus. Irene Santamarta, 2002.The putative regulatory CcaR protein, which is encoded in the ß-lactam supercluster of Streptomyces clavuligerus, has been partially purified by ammonium sulfate precipitation and heparin affinity chromatography . In addition, it was expressed in Escherichia coli, purified as a His-tagged recombinant protein (rCcaR), and used to raise anti-rCcaR antibodies . The partially purified CcaR protein from S . clavuligerus was able to bind DNA fragments containing the promoter regions of the ccaR gene itself and the bidirectional cefD-cmcI promoter region . In contrast, CcaR did not bind to DNA fragments with the promoter regions of other genes of the cephamycin-clavulanic acid supercluster including lat, blp, claR, car-cyp, and the unlinked argR gene . The DNA shifts obtained with CcaR were prevented by anti-rCcaR immunoglobulin G (IgG) antibodies but not by anti-rabbit IgG antibodies . ccaR and the bidirectional cefD-cmcI promoter region were fused to the xylE reporter gene and expressed in Streptomyces lividans and S . clavuligerus . These constructs produced low catechol dioxygenase activity in the absence of CcaR; activity was increased 1.7- to 4.6-fold in cultures expressing CcaR . Amplification of the ccaR promoter region lacking its coding sequence in a high-copy-number plasmid in S . clavuligerus ATCC 27064 resulted in a reduced production of cephamycin C and clavulanic acid, by 12 to 20% and 40 to 60%, respectively, due to titration of the CcaR regulator . These findings confirm that CcaR is a positively acting autoregulatory protein able to bind to its own promoter as well as to the cefD-cmcI bidirectional promoter region . Hydroxylamine Reductase Activity of the Hybrid Cluster Protein from Escherichia coli. Marcus T. Wolfe, 2002.The hybrid cluster protein (HCP; formerly termed the prismane protein) has been extensively studied due to its unique spectroscopic properties . Although the structural and spectroscopic characteristics are well defined, its enzymatic function, up to this point, has remained unidentified . While it was proposed that HCP acts in some step of nitrogen metabolism, a specific role for this enzyme remained unknown . Recent studies of HCP purified from Escherichia coli have identified a novel hydroxylamine reductase activity . These data reveal the ability of HCP to reduce hydroxylamine in vitro to form NH3 and H2O . Further biochemical analyses were completed in order to determine the effects of various electron donors, different pH levels, and the presence of CN- on in vitro hydroxylamine reduction . Overexpression of the Escherichia coli sugE Gene Confers Resistance to a Narrow Range of Quaternary Ammonium Compounds. Yong Joon Chung, 2002.SugE of Escherichia coli, first identified as a suppressor of groEL mutations but a member of the small multidrug resistance family, has not previously been shown to confer a drug resistance phenotype . We show that high-level expression of sugE leads to resistance to a subset of toxic quaternary ammonium compounds . Characterization of the Integrase Gene and Attachment Site for the Myxococcus xanthus Bacteriophage Mx9. Bryan Julien, 2003.Bacteriophage Mx9 is a temperate phage that infects Myxococcus xanthus . It lysogenizes the bacteria by integrating into the bacterial chromosome by site-specific recombination at one of two sites, attB1 or attB2 . Integration at attB1 results in deletion of DNA between the two attB sites . The attB2 site lies within the 5' region of the M . xanthus tRNAGly gene . Mx9 integration requires a single protein, Int . Analysis of integration revealed that the phage attachment site (attP) is contained in the int gene and that upon integration, the 3' end of the int gene is altered . Plasmids containing fusions of the pilA or mgl promoter to lacZ integrated at either Mx9 attB site have higher levels of transcription than the same fusions integrated at the Mx8 attB site .
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