Data set for transcriptome analysis of Escherichia coli exposed to nickel

AbstractNi is recognized as an element that is toxic to humans, acting as an allergen and a carcinogenic agent, and it is also toxic to plants. The toxicity of Ni has been understudied in microorganisms. The data presented here were obtained by submitting the model bacterium Escherichia coli K-12 to nickel stress. To identify expressed genes, RNA-Seq was performed. Bacteria were exposed to 50µM NiCl2 during 10min. Exposure to Ni lead to the deregulation of 57% of the E. coli transcripts. Further analysis using DAVID identified most affected biological pathways. The list of differentially expressed genes and physiological consequences of Ni stress are described in “Ni exposure impacts the pool of free Fe and modifies DNA supercoiling via metal-induced oxidative stress in Escherichia coli K-12” (M. Gault, G. Effantin, A. Rodrigue, 2016) [1]

RcnB Is a Periplasmic Protein Essential for Maintaining Intracellular Ni and Co Concentrations in Escherichia coli

International audienceNickel and cobalt are both essential trace elements that are toxic when present in excess. The main resistance mechanism that bacteria use to overcome this toxicity is the efflux of these cations out of the cytoplasm. RND (resistance-nodulation-cell division)- and MFS (major facilitator superfamily)-type efflux systems are known to export either nickel or cobalt. The RcnA efflux pump, which belongs to a unique family, is responsible for the detoxification of Ni and Co in Escherichia coli. In this work, the role of the gene yohN, which is located downstream of rcnA, is investigated. yohN is cotranscribed with rcnA, and its expression is induced by Ni and Co. Surprisingly, in contrast to the effect of deleting rcnA, deletion of yohN conferred enhanced resistance to Ni and Co in E. coli, accompanied by decreased metal accumulation. We show that YohN is localized to the periplasm and does not bind Ni or Co ions directly. Physiological and genetic experiments demonstrate that YohN is not involved in Ni import. YohN is conserved among proteobacteria and belongs to a new family of proteins; consequently, yohN has been renamed rcnB. We show that the enhanced resistance of rcnB mutants to Ni and Co and their decreased Ni and Co intracellular accumulation are linked to the greater efflux of these ions in the absence of rcnB. Taken together, these results suggest that RcnB is required to maintain metal ion homeostasis, in conjunction with the efflux pump RcnA, presumably by modulating RcnA-mediated export of Ni and Co to avoid excess efflux of Ni and Co ions via an unknown novel mechanism

Antioxidative Enzyme Responses to Antimony Stress of Serratia marcescens – an Endophytic Bacteria of Hedysarum pallidum Roots

International audienceStudies on bacterial endophytes resistant to antimony (Sb), a pollutant deemed alarming, are virtually non-existent. An endophytic bacterial strain showing resistance to high antimony concentrations was isolated for the first time from the roots of Hedysarum pallidum Desf., a Sb accumulator Fabacea growing on mining spoils. With the combined use of morphological, biochemical and molecular methods, the isolated strain was identified as Serratia marcescens species. It showed a minimum inhibitory concentration (MIC) to its growth at 450 mM of Sb. In the presence of excessive concentrations of Sb, corresponding to 30 mM of Sb, i.e., 3652.8 mg/L of Sb, the strain maintained important growth compared to the control. The Sb toxicity caused a significant increase (p<0.05) in the hydrogen peroxide (H2O2) amount and malondialdehyde (MDA) content. The oxidative stress induced significant increases (p<0.05) in the strain antioxidant biomarkers such as proline, catalase (CAT), ascorbate peroxidase (APX), peroxidase (POD) and superoxide dismutase (SOD). Significant and positive correlations (p<0.05) were found between oxidative and antioxidant biomarkers and between antioxidant biomarkers, highlighting the interrelationships between them in oxidative stress fighting. Results show an important adaptation of the strain to high Sb levels that can be used in the Sb-contaminated soils bioremediation

Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression

<p>Abstract</p> <p>Background</p> <p>In man, infection by the Gram-negative enteropathogen <it>Yersinia pseudotuberculosis </it>is usually limited to the terminal ileum. However, in immunocompromised patients, the microorganism may disseminate from the digestive tract and thus cause a systemic infection with septicemia.</p> <p>Results</p> <p>To gain insight into the metabolic pathways and virulence factors expressed by the bacterium at the blood stage of pseudotuberculosis, we compared the overall gene transcription patterns (the transcriptome) of bacterial cells cultured in either human plasma or Luria-Bertani medium. The most marked plasma-triggered metabolic consequence in <it>Y. pseudotuberculosis </it>was the switch to high glucose consumption, which is reminiscent of the acetogenic pathway (known as "glucose overflow") in <it>Escherichia coli</it>. However, upregulation of the glyoxylate shunt enzymes suggests that (in contrast to <it>E. coli</it>) acetate may be further metabolized in <it>Y. pseudotuberculosis</it>. Our data also indicate that the bloodstream environment can regulate major virulence genes (positively or negatively); the <it>yadA </it>adhesin gene and most of the transcriptional units of the pYV-encoded type III secretion apparatus were found to be upregulated, whereas transcription of the pH6 antigen locus was strongly repressed.</p> <p>Conclusion</p> <p>Our results suggest that plasma growth of <it>Y. pseudotuberculosis </it>is responsible for major transcriptional regulatory events and prompts key metabolic reorientations within the bacterium, which may in turn have an impact on virulence.</p

Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)

A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies

Biosynthèse de l\u27hydrogénase chez Escherichia coli. Incorporation du nickel, maturation et translocation transmembranaire de l\u27hydrogénase

En conditions de croissance anaérobies, l\u27entérobactérie Escherichia coli synthétise trois isoenzymes hydrogénase (HYD). HYD1 et HYD2 sont des protéines intégralement membranaires, composées chacune d\u27une petite et d\u27une grande sous-unités, tandis que HYD3 est une protéine périphérique de la membrane cytoplasmique. HYD1 et HYD2 catalyse l\u27oxydation de l\u27hydrogène couplée à la réduction d\u27un accepteur terminal d\u27électrons. HYD3 est responsable de la production d\u27hydrogène en liaison avec l\u27oxydation du formiate. Les trois hydrogénase contiennent du nickel. Nous avons démontré que l\u27incorporation du nickel dans les grandes sous-unités des trois hydrogénsases se déroule dans le cytoplasme. Les protèines chaperons GroEL et GroES sont nécessaires à l\u27incorporation du nickel dans HYD3, mais pas dans HYD2. D\u27autre part nos études cellulaire, biochimique te immunologique révèlent que : (1) HYD2 est localisée dans le périplasme, (2) l\u27incorporation du nickel engendre un changement de conformation et une condition préalable de la translocation de HYD2, (3) la translocation de HYD2 est indépendante de la protéine SecY. Enfin, après clonage de l\u27opéron hyb codantHYD2, nous avons montré que les deux sous-unités de HYD2 sont co-transloquées. L\u27ensemble de ces résultats suggère l\u27existence d\u27un nouveau mécanisme pour la translocation de l\u27hydrogénase

Ni exposure impacts the pool of free Fe and modifies DNA supercoiling via metal-induced oxidative stress in Escherichia coli K-12

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