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      The PlcR Virulence Regulon of Bacillus cereus

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          Abstract

          PlcR is a Bacillus cereus transcriptional regulator, which activates gene expression by binding to a nucleotidic sequence called the ‘PlcR box’. To build a list of all genes included in the PlcR regulon, a consensus sequence was identified by directed mutagenesis. The reference strain ATCC14579 sequenced genome was searched for occurrences of this consensus sequence to produce a virtual regulon. PlcR control of these genes was confirmed by comparing gene expression in the reference strain and its isogenic Δ- plcR strain using DNA microarrays, lacZ fusions and proteomics methods. The resulting list included 45 genes controlled by 28 PlcR boxes. Forty of the PlcR controlled proteins were exported, of which 22 were secreted in the extracellular medium and 18 were bound or attached to cell wall structures (membrane or peptidoglycan layer). The functions of these proteins were related to food supply (phospholipases, proteases, toxins), cell protection (bacteriocins, toxins, transporters, cell wall biogenesis) and environment-sensing (two-component sensors, chemotaxis proteins, GGDEF family regulators). Four genes coded for cytoplasmic regulators. The PlcR regulon appears to integrate a large range of environmental signals, including food deprivation and self cell-density, and regulate the transcription of genes designed to overcome obstacles that hinder B. cereus growth within the host: food supply, host barriers, host immune defenses, and competition with other bacterial species. PlcR appears to be a key component in the efficient adaptation of B. cereus to its host environment.

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          R: A Language and Environment for Statistical Computing.

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            Normalization of cDNA microarray data.

            Normalization means to adjust microarray data for effects which arise from variation in the technology rather than from biological differences between the RNA samples or between the printed probes. This paper describes normalization methods based on the fact that dye balance typically varies with spot intensity and with spatial position on the array. Print-tip loess normalization provides a well-tested general purpose normalization method which has given good results on a wide range of arrays. The method may be refined by using quality weights for individual spots. The method is best combined with diagnostic plots of the data which display the spatial and intensity trends. When diagnostic plots show that biases still remain in the data after normalization, further normalization steps such as plate-order normalization or scale-normalization between the arrays may be undertaken. Composite normalization may be used when control spots are available which are known to be not differentially expressed. Variations on loess normalization include global loess normalization and two-dimensional normalization. Detailed commands are given to implement the normalization techniques using freely available software.
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              Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.

              Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes. It is closely related to the animal and human pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the former being used as a biological weapon and the latter as a pesticide. B. anthracis and B. thuringiensis are readily distinguished from B. cereus by the presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But phylogenetic studies based on the analysis of chromosomal genes bring controversial results, and it is unclear whether B. cereus, B. anthracis and B. thuringiensis are varieties of the same species or different species. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables us to perform comparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2008
                30 July 2008
                : 3
                : 7
                : e2793
                Affiliations
                [1 ]INRA, Génétique microbienne et Environnement, Guyancourt, France
                [2 ]INRA, Microbiologie et Génétique Moléculaire, Thiverval-Grignon, France
                [3 ]Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
                [4 ]Institut Pasteur, Paris, France
                University of Wisconsin-Milwaukee, United States of America
                Author notes

                Conceived and designed the experiments: MG ABK DL. Performed the experiments: MG KF SP MG. Analyzed the data: MG KF SP SR OA MG ABK DL. Contributed reagents/materials/analysis tools: KF. Wrote the paper: MG.

                Article
                08-PONE-RA-04256R1
                10.1371/journal.pone.0002793
                2464732
                18665214
                b6c8a233-7c45-4e62-86df-02aad1b6ba77
                Gohar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 9 April 2008
                : 23 June 2008
                Page count
                Pages: 9
                Categories
                Research Article
                Genetics and Genomics/Disease Models
                Genetics and Genomics/Functional Genomics
                Genetics and Genomics/Gene Expression
                Microbiology/Cellular Microbiology and Pathogenesis
                Molecular Biology/Translational Regulation
                Infectious Diseases/Bacterial Infections

                Uncategorized
                Uncategorized

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