Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Transcriptional analysis of Bacillus cereus ATCC 14579 and its ccpA deletion strain grown with and without glucose
    Wijman, Janneke ; Abee, Tjakko ; Voort, M. van der - \ 2015
    Wageningen UR
    GSE20057 - Bacillus cereus ATCC 14579 - GSE20057 - Bacillus cereus - PRJNA124327
    The influence of the presence of glucose in the Y1 growth medium of Bacillus cereus strain ATCC 14579 was studied by transcriptional analysis. Furthermore, the role of CcpA in glucose induction or repression of gene expression was assessed by use of a ccpA deletion strain. In total, 300 genes were glucose repressed and 173 genes glucose activated. For 212 genes the glucose repression was clearly CcpA dependent, whereas for 116 genes CcpA dependent glucose induction was observed. Functional analysis of the glucose regulated genes showed these genes mainly to be involve in energy production and conversion and in metabolism. Furthermore, genes that were glucose repressed were shown to be involved in cell motility.
    Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 14579
    Wijman, Janneke ; Mols, M. ; Tempelaars, Marcel ; Abee, Tjakko - \ 2015
    Wageningen UR
    GSE24619 - Bacillus cereus - PRJNA133577 - GSE24619 - Bacillus cereus ATCC 14579 - PRJNA133577
    Planktonic and biofilm cells of Bacillus cereus ATCC 14579 and ATCC 10987 were studied using microscopy and transcriptome analysis. By microscopy, clear differences could be observed between biofilm and planktonic cells as well as between the two strains. By using hierarchical clustering of the transcriptome data, little difference was observed between the biofilm cells of B. cereus ATCC 14579 and ATCC 10987. Different responses between biofilm and planktonic cells could be identified using transcriptome analysis. Biofilm formation seemed to cause a shift in metabolism with up- or down-regulation of genes involved in different metabolic pathways. Genes involved in motility were down-regulated. No clear up-regulation related to capsular or extracellular polysaccharides was observed. Sporulation was observed in biofilm cells using microscopy, which was corroborated with up-regulation of genes involved in sporulation in biofilm cells. The results obtained in this study provide insight in general and strain specific behavior of B. cereus cells in multicellular communities.
    Phylogenetic footprinting and transcriptome profiling reveal new roles for two Bacillus cereus two-component systems
    Been, M. de; Brillard, J. ; Brousolle, V. ; Abee, Tjakko - \ 2014
    Wageningen UR
    GSE18523 - Bacillus cereus - PRJNA120197 - GSE18523 - Bacillus cereus ATCC 14579 - PRJNA120197
    Members of the Bacillus cereus group can adapt to a wide range of environmental challenges. In bacteria, these challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). We have previously developed a phylogenetic footprinting approach that was successfully implemented to predict specific binding sites (operators) and target genes for the RRs of B. cereus and related species. In this study, this footprinting approach was integrated with transcriptome analyses of two B. cereus TCS deletion mutants, involving the TCSs YvrHG and YufLM. Comparison of mutant versus wild-type transcriptomes revealed that the respective TCSs were significantly active during the exponential growth phase in rich medium and that the footprinting-based predictions were accurate for the two TCSs. Moreover, the predicted specific operators were used in combination with the transcriptome data to guide the identification of more extended TCS regulons. This revealed new roles for the respective TCSs, including the participation in an intricate transcriptional network involved in antibiotic resistance, including the confirmed resistance to oxolinic acid (YvrHG) and the confirmed uptake and metabolism of fumarate and the repression of fermentative pathways (YufLM).
    Analysis of germination and outgrowth of sorbic acid-stressed Bacillus cereus ATCC 14579 spores.
    Melis, Clint van; Nierop Groot, Masja ; Tempelaars, Marcel ; Moezelaar, Roy ; Abee, Tjakko - \ 2010
    GSE19186 - Bacillus cereus - PRJNA120671 - Bacillus cereus ATCC 14579
    Sorbic acid (SA) is widely used as a preservative, but the effect of SA on spore germination and outgrowth has gained limited attention up to now. Therefore, the effect of sorbic acid on germination of spores of B. cereus strain ATCC 14579 was analyzed both at phenotype and transcriptome level. Spore germination and outgrowth was assessed at pH 5.5 without and with 0.75, 1.5 and 3.0mM (final concentrations) undissociated sorbic acid (HSA). This resulted in distinct HSA concentration-dependent phenotypes, varying from delays in germination and outgrowth to complete blockage of germination at 3.0mM HSA. The phenotypes reflecting different stages in the germination process could be confirmed using flow cytometry and could be recognized at transcriptome level by distinct expression profiles. In the absence and presence of 0.75 and 1.5mM HSA, similar cellular ATP levels were found up to the initial stage of outgrowth, suggesting that HSA-induced inhibition of outgrowth is not caused by depletion of ATP. Transcriptome analysis revealed the presence of a limited number of transcripts in dormant spores, outgrowth related expression, and genes specifically associated with sorbic acid stress, including alterations in cell envelope and multi-drug resistance. The potential role of these HSA-stress associated genes in spore outgrowth is discussed.
    Comparative transcriptome and phenotype analysis of Bacillus cereus in response to disinfectant treatments
    Ceragioli, Mara ; Mols, J.M. ; Moezelaar, Roy ; Ghelardi, Emilia ; Senesi, Sonia ; Abee, Tjakko - \ 2010
    GSE18807 - Bacillus cereus - PRJNA121223 - GSE18807 - Bacillus cereus ATCC 14579 - PRJNA121223
    Antimicrobial chemicals are widely applied to clean and disinfect food-contacting surfaces. However, the cellular response of bacteria, such as Bacillus cereus, to various disinfectants is unclear. In this study, the physiological and genome-wide transcriptional responses of B. cereus ATCC 14579 exposed to four different disinfectants (i.e., benzalkonium chloride, sodium hypochlorite, hydrogen peroxide, and peracetic acid) were analyzed. The physiological response of B. cereus to different concentrations of the disinfectants used was investigated. For each disinfectant, concentrations leading to the attenuation of growth, growth arrest, and cell death were studied in more detail. The simultaneous analysis of the transcriptional responses of B. cereus upon exposure to the different concentrations of disinfectants revealed common responses induced by the four disinfectants. Notably, genes involved in the general and oxidative stress responses were commonly up-regulated. Furthermore, the obtained results indicate that all the disinfectants also induce specific responses. Exposure to benzalkonium chloride, a disinfectant known to induce membrane damage, specifically induced genes involved in the fatty acid metabolism. Benzalkonium chloride induced-membrane damage was confirmed by fluorescence microscopy and fatty acid analysis confirmed that fatty acid composition of cell membrane was affected upon exposure to benzalkonium chloride. Sodium hypochlorite induced genes involved in sulfur and sulfur-containing amino acids metabolism, which correlated with the observed sodium hypochlorite-specific induction of oxidation of sulphydryl groups. Hydrogen peroxide and peracetic acid exposures induced genes involved in DNA damage and the SOS response. Notably, hydrogen peroxide and peracetic acid-treated cells exhibited higher mutation rates corroborating with the induced SOS response. Understanding the mechanisms displayed by microorganisms coping with disinfectants-induced stress may allow for design of more efficient sequential and/or disinfectant combination treatments in food processing environments.
    A novel hybrid kinase is essential for regulating the σB-mediated stress response of Bacillus cereus.
    Been, M.W.H.J. de; Tempelaars, Marcel ; Schaik, W. van; Moezelaar, Roy ; Siezen, R.J. ; Abee, Tjakko - \ 2009
    Wageningen UR
    GSE14589 - Bacillus cereus - PRJNA111709 - GSE14589 - Bacillus cereus ATCC 14579 - PRJNA111709
    A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor σB is activated by the RR RsbY. Here we present strong indications that the PP2C-type phosphatase RsbY receives its input from the multi-sensor hybrid kinase BC1008 (renamed RsbK). Genome analyses revealed that, across bacilli, rsbY and rsbK are located in a conserved gene cluster. A B. cereus rsbK deletion strain was shown to be incapable of inducing σB upon stress conditions and was impaired in its heat adaptive response. Comparison of the wild-type and rsbK mutant transcriptomes upon heat shock revealed that RsbK was primarily involved in the activation of the σB-mediated stress response. Truncation of the RsbK RR receiver domain demonstrated the importance of
    Assessment of CcpA-mediated catabolite control of metabolism and enterotoxin production in Bacillus cereus ATCC 14579
    Voort, M. van der; Kuipers, O.P. ; Buist, G. ; Vos, Willem de; Abee, Tjakko - \ 2008
    Wageningen UR
    GSE7843 - Bacillus cereus ATCC 14579 - GSE7843 - Bacillus cereus - PRJNA99971
    In Bacillus cereus the catabolite control protein CcpA was shown to be involved in optimizing the efficiency of glucose catabolism by activating genes encoding glycolytic enzymes including a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase that mediates conversion of D-glyceraldehyde 3-phosphate to 3-phospho-D-glycerate in one single step, and by repressing genes encoding the citric acid cycle and gluconeogenic enzymes. Two B. cereus-specific CcpA-regulated operons were identified, encoding enzymes involved in the catabolism of fuculose/arabinose and aspartate. In addition, a genome search using the CRE-site consensus predicted the B. cereus CcpA regulon to include 10 PTS-system gene clusters as well as genes coding for overflow metabolic enzymes leading to acetoin and acetate. Notably, catabolite repression of the genes encoding non-hemolytic enterotoxin (Nhe) and hemolytic (Hbl) enterotoxin appeared CcpA-dependent, and for the corresponding enterotoxin operons, putative CRE-sites were identified. This points to metabolic control of enterotoxin gene expression and suggests that CcpA-mediated glucose sensing provides an additional mode of control to PlcR activated expression of nhe and hbl genes in B. cereus.
    Overexpression analysis of sigZ of B. cereus ATCC 14579.
    Voort, M. van der - \ 2008
    Wageningen UR
    GSE9860 - Bacillus cereus - PRJNA103843 - GSE9860 - Bacillus cereus ATCC 14579 - PRJNA103843
    The Bacillus cereus ATCC 14579 alternative σ factor σZ and its putative regulon have been characterized. σZ shows overall similarity with ECF σ factors and sigZ constitutes an operon together with asfZ encoding its putative anti-σ factor. Expression analysis revealed sigZ to be induced by an array of stresses, including exposure to ethanol, alkaline pH and heat shock, and a typical promoter binding site for the sigZ-operon was identified by 5’RACE. Phenotypic characterization of B. cereus ATCC 14579 and its sigZ-deletion strain revealed diminished growth performance and sporulation capacity. The σZ-regulon was successfully established by transcriptome analysis of a nisin inducible sigZ-overexpression strain. Overexpression of sigZ was shown to affect expression of 42 genes, including 33 genes encoding proteins located in the extracytoplasm. The identified σZ regulon contained genes encoding proteins situated in the extracytoplasm involved in cell surface modifications and transport. The regulation of genes encoding cell surface modification proteins implies σZ to be involved in the regulation of interaction of B. cereus ATCC 14579 with its environments, which includes human intestinal cells, possibly influencing its virulence status.
    Monitoring the ethanol stress response of a sigZ deletion strain of B. cereus ATCC 14579.
    Voort, M. van der - \ 2008
    Wageningen UR
    GSE9858 - Bacillus cereus - PRJNA103839 - GSE9858 - Bacillus cereus ATCC 14579 - PRJNA103839
    The stress response of as sigZ deletion strain of B. cereus ATCC 14579 is monitored true time by use of microarrays. The sigZ regulon in ethanol stress response was determined and compared with the regulon determined by micorarray analysis of overexpression of sigZ.
    Monitoring the ethanol stress response of a sigM deletion strain of B. cereus ATCC 14579.
    Voort, M. van der - \ 2008
    Wageningen UR
    GSE9856 - Bacillus cereus - PRJNA103835 - GSE9856 - Bacillus cereus ATCC 14579 - PRJNA103835
    Here, the role of σM and its regulon in stress response and survival of B. cereus ATCC 14579 was assessed by comparative transciptome and phenotypic analysis of this strain and its sigM deletion strain. Exposure of B. cereus ATCC 14579 to a wide range of stresses revealed expression of sigM, encoding σM, to be up-regulated mainly in the presence of ethanol and after alkaline pH-shock. Next to this, disc diffusion tests showed the sigM deletion strain to be more sensitive to oxidizing agents and to be more resistant to cell-wall targeting antibiotics than the wild-type strain. The σM regulon was subsequently determined by comparative transcriptional analyses of the wild-type and its sigM-deletion strain after exposure to ethanol. The putative σM-regulon was shown to consist of 29 genes, several of these genes are predicted to be involved in counteracting oxidative stress, such as an NADH oxidase, a ferredoxin, and a lysine decarboxylase or could encode enzymes involved in methionine metabolism, leading toward L-cysteine production, including luxS. Screening of promoter upstream regions allowed for the assessment of a B. cereus consensus promoter binding site for σM. Since the consensus promoter binding site for B. cereus ATCC 14579 σM, its regulon and the predicted functionalities are different from the corresponding features in B. subtilis, it can be concluded that σM plays a unique role in B. cereus stress response and survival.
    Gene induction by ethanol stress in B. cereus ATCC 14579
    Voort, M. van der - \ 2008
    Wageningen UR
    GSE9855 - Bacillus cereus ATCC 14579 - GSE9855 - Bacillus cereus - PRJNA103833
    The stress response of B. cereus ATCC 14579 is monitored true time, showing an enormous response in gene expression.
    Anaerobic induction in B. cereus ATCC 14579
    Voort, M. van der; Abee, Tjakko - \ 2008
    Wageningen UR
    GSE9846 - Bacillus cereus ATCC 14579 - GSE9846 - Bacillus cereus - PRJNA103821
    A comparative transcriptome approach was used to assess genes involved in metabolism and pathogenesis that are specifically activated during anaerobic growth of the spore-forming food-borne human pathogen Bacillus cereus ATCC 14579. Growth under anaerobic conditions in Brain Heart Infusion broth revealed a reduced growth rate and a lower yield as compared to that under aerobic conditions. Comparative transcriptome analysis of cells harvested at early- and mid-exponential growth phase, transition phase and stationary phase, subsequently showed hundreds of genes to be induced under anaerobic condition. These included novel genes identified for anaerobic growth of B. cereus, encoding metabolic pathways, such as the arginine deiminase pathway (ArcABDC), a formate dehydrogenase (FdhF) and a pyruvate fomate lyase (Pfl), and alternative respiratory proteins, such as arsenate reductases. Furthermore, the nitrosative stress response was induced in the anaerobic transition phase of growth, conceivably due to the production of nitric oxide as a by-product of nitrite and nitrate respiration. Notably, both hemolytic enzyme and enterotoxin encoding genes were activated in different oxygen limiting conditions, i.e. hemolytic enzyme encoding genes were induced during anaerobic growth, whereas enterotoxin encoding genes were induced in the transition and stationary phase of aerobic cultures reaching a high cell density. These data point to metabolic rearrangements, stress adaptation and activation of the virulent status of B. cereus under anaerobic conditions, such as encountered in the human GI-tract.
    The sigmaB regulon of B. cereus ATCC14579
    Schaik, W. van; Voort, M. van der; Vos, Willem de; Abee, Tjakko - \ 2007
    Wageningen UR
    GSE6005 - Bacillus cereus - PRJNA97797 - GSE6005 - Bacillus cereus ATCC 14579 - PRJNA97797
    The alternative sigma factor sigmaB has an important role in the acquisition of stress-resistance in many gram-positive bacteria. In the foodborne pathogen Bacillus cereus sigmaB is activated strongly upon a heat shock and other stress conditions. Here we describe the identification of the set of sigmaB-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. A total of 24 genes could be identified as being sigmaB-dependent as witnessed by (i) significantly lower expression-levels of these genes in mutants deleted for sigB and rsbY (encoding the alternative sigma factor sigmaB and a PP2C phosphatase that acts as a crucial positive regulator of sigmaB-activity, respectively) than in the parental strain B. cereus ATCC 14579, and (ii) increased expression of these genes upon a heat shock. Newly identified members of the sigmaB-regulon of B. cereus include an ECF-sigma factor (sigmaZ), a histidine kinase and two genes that have predicted functions in spore germination. Our data indicate that the sigmaB-regulon of B. cereus is considerably smaller than that of other gram-positive bacteria. This appears to be in line with phylogenetic analyses of sigmaB in which sigmaB in the B. cereus group was suggested to be close to the ancestral form of sigmaB in gram-positive bacteria.
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