Helicobacter pylori
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA93753 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Growth phase-dependent response of Helicobacter pylori to iron starvation.
| PRJNA94129 | ENA
Project description:Gram negative bacteria release outer membrane vesicles (OMVs) as part of their natural growth. These OMVs take part in a biological functions including bacterial communication, exchange of genetic material and bacterial pathogenesis. However, the relationship between bacterial growth stage and OMV protein composition has not been explored before nor how their proteome is different to their parent bacterium. In this study, we examined the proteome of Helicobacter pylori and its OMVs from early log, late log or stationary phase of growth and found that globally, the protein content of OMVs over time is vastly different to one another as well as to their parent bacterium. OMVs purified from early log phase of growth contained the greatest number of unique proteins and a significant upregulation of virulence and pathogenic proteins. However, when compared back to their parent bacterium, OMVs from later stages of growth contained more unique proteins than those from earlier stages of growth. We show for the first time the regulation of OMV protein composition by H. pylori that is dependent on bacterial growth stage. Our results have expanded our understanding of the fundamental production of OMVs and the selective packaging of cargo in OMVs that result in specific functions.
2021-03-23 | PXD024918 | Pride
Project description:This data set was used to determine genes that are regulated by iron availability and to access the growth phase dependence on that regulation. Stationary (Stat Chelate and Stat.iron.survival)and exponential (Log Chelate and Log.iron.survival)were subjected to chelation using DPP. Growth status of the cultures was confirmed by determing the correlation coefficient of the Stat chelate T=0/control and Log Chelate T=0/control vs data generated in the TC Motility series. Arrays used for iron addback experiments are listed as FeAddBack-1-time or FeAddBack-2-time. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-12-22 | GSE3888 | GEO
Project description:This data set was used to determine genes that are regulated by iron availability and to access the growth phase dependence on that regulation. Stationary (Stat Chelate and Stat.iron.survival)and exponential (Log Chelate and Log.iron.survival)were subjected to chelation using DPP. Growth status of the cultures was confirmed by determing the correlation coefficient of the Stat chelate T=0/control and Log Chelate T=0/control vs data generated in the TC Motility series. Arrays used for iron addback experiments are listed as FeAddBack-1-time or FeAddBack-2-time. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-12-21 | E-GEOD-3888 | biostudies-arrayexpress
Project description:The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-11-22 | GSE3636 | GEO
Project description:Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are subject to phase-variable expression (high-frequency reversible ON/OFF switching of gene expression). In Haemophilus influenzae, Neissera Meningtidis and Neisseria Gonorrhoeae, the random switching of the modA gene, associated with a phase variable type III restriction modification (R-M) system, controls expression of a phase-variable regulon of genes (a “phasevarion”), via differential methylation of the genome in the modA ON and OFF states. Phase variable type III R-M systems are also found in Helicobacter pylori, suggesting that phasevarions may also exist in this intriguing pathogen. Phylogenetic studies on the phase-variable type III modC gene revealed that there are 12 distinct alleles in H. pylori, which differ only in their DNA recognition domain, with the majority containing the C5 allele. Microarray analysis comparing the H. pylori wild-type P12modC5 ON strain to the P12(delta)modC5 mutant revealed that six genes were either up-regulated or down-regulated, some of which were virulence-associated. For example flaA, which encodes a flagella protein important in motility and hopG, which encodes an important outer membrane protein. This study, in conjunction with our previous work, indicates that phasevarions may be a common strategy used by host-adapted bacterial pathogens to randomly switch between “differentiated” cell types.
2012-01-16 | GSE26759 | GEO
Project description:Helicobacter pylori infection reprograms host gene expression and influences various cellular processes, which have been investigated by cDNA microarray in vitro culture cells and in vivo patients of the chronic abdominal complaint. In this study，the effects of H. pylori infection on host gene expression in the gastric antral mucosa of patients with chronic gastritis were examined.
2012-04-30 | GSE30042 | GEO
Project description:The genome of the gastric pathogen Helicobacter pylori harbors a remarkably low number of regulatory genes, including three and five open reading frames encoding two-component histidine kinases and response regulators, respectively, which are putatively involved in transcriptional regulation. Inactivation of the response regulator gene hp1021 resulted in a severe growth defect, as indicated by a small-colony phenotype. Recently we found that phosphorylation of the receiver domain HP1021 is not needed for its response regulator function and may not occur at all. No target genes have been identified so far. In this study we define the HP1021-dependent regulon consisting of 79 genes (51 activated, 28 repressed) by global transcriptional profiling of an HP1021-deficient H. pylori mutant. Keywords: Identification of an HP1021-Regulon
2007-04-01 | GSE5971 | GEO
Project description:The microarrays for the three time course experiments described in the publication titled "Gene expression profiling of Helicobacter pylori reveals a growth phase dependent switch in virulence gene expression". TC1 refers to the first time course investigating gene expression changes over the time course of growth while TC2 refers to the second time course. TC Motility_broth refers to the third time course described in the manuscript used to investigate the concurrent changes in motility and the expression of the genes in the flagellar regulon. Detailed description of the growth of H. pylori for these 3 time courses can be found in the Materials and Methods section of the manuscript along with the exact filtering criteria used to download the data from these arrays. Note that in all three time courses the data for each array were transformed after download such that the abundance of each gene's transcript represented by a given spot was relative to the level of that transcript at the 6 h time point. Also duplicate spots for each ORF on the microarray were averaged for analysis after transformation. Groups of assays that are related as part of a time series. Computed
2005-11-21 | E-GEOD-3636 | biostudies-arrayexpress
Project description:Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are subject to phase-variable expression (high-frequency reversible ON/OFF switching of gene expression). In Haemophilus influenzae, Neissera Meningtidis and Neisseria Gonorrhoeae, the random switching of the modA gene, associated with a phase variable type III restriction modification (R-M) system, controls expression of a phase-variable regulon of genes (a M-bM-^@M-^\phasevarionM-bM-^@M-^]), via differential methylation of the genome in the modA ON and OFF states. Phase variable type III R-M systems are also found in Helicobacter pylori, suggesting that phasevarions may also exist in this intriguing pathogen. Phylogenetic studies on the phase-variable type III modC gene revealed that there are 12 distinct alleles in H. pylori, which differ only in their DNA recognition domain, with the majority containing the C5 allele. Microarray analysis comparing the H. pylori wild-type P12modC5 ON strain to the P12(delta)modC5 mutant revealed that six genes were either up-regulated or down-regulated, some of which were virulence-associated. For example flaA, which encodes a flagella protein important in motility and hopG, which encodes an important outer membrane protein. This study, in conjunction with our previous work, indicates that phasevarions may be a common strategy used by host-adapted bacterial pathogens to randomly switch between M-bM-^@M-^\differentiatedM-bM-^@M-^] cell types. Direct comparison of biological triplicates of wild type and mutant strains
2012-01-16 | E-GEOD-26759 | biostudies-arrayexpress