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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Bdellovibrio bacteriovorus attack phase and Host-Independent grown cells

ABSTRACT: Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrioâ??s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a â??predatosomeâ?? of genes specifically upregulated during predation and implicates some of those important in HI growth. 3 replicates of attack phase cells and 3 replicates of Host-Independent grown cells were analysed on individual arrays.

ORGANISM(S): Bdellovibrio bacteriovorus

SUBMITTER: Liz Sockett

PROVIDER: E-GEOD-16034 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio.

Lambert Carey C Chang Chien-Yi CY Capeness Michael J MJ Sockett R Elizabeth RE

PloS one 20100106 1

Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs ...[more]

PMID: 20062540

Similar Datasets

Bdellovibrio bacteriovorus attack phase and Host-Independent grown cells

Project description:Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrio’s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a “predatosome” of genes specifically upregulated during predation and implicates some of those important in HI growth.

2009-12-09 | GSE16034 | GEO

Bdellovibrio bacteriovorus attack phase and post-infection cells

Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent âHIâ manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis 3 replicates of attack phase cells and 3 replicates of 30 minutes post-infection cells were analysed on individual arrays. Replicate 3 was normalized separately.

2010-05-18 | E-GEOD-9269 | biostudies-arrayexpress

Bdellovibrio bacteriovorus attack phase and post-infection cells

Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis

2009-12-09 | GSE9269 | GEO

Variegated gene expression caused by cell-specific long-range DNA interactions

Project description:Mammalian genomes contain numerous DNA elements with potential transcription regulatory function but unknown target genes. We used transgenic, gain-of-function mice with an ectopic copy of the beta-globin locus control region (LCR) to better understand how regulatory elements dynamically search the genome for target genes. We find that the LCR samples a restricted nuclear sub-volume in which it forms preferential contacts with genes controlled by shared transcription factors. One contacted gene, betah1, located on another chromosome, is upregulated, providing genetic demonstration that mammalian enhancers can function between chromosomes. Upregulation is not pan-cellular but confined to selected ‘jackpot’ cells significantly enriched for inter-chromosomal LCR-betah1 interactions. This implies that long-range DNA contacts are relatively stable and cell-specific and, when functional, cause variegated expression. We refer to this as spatial effect variegation (SEV). The data provide a dynamic and mechanistic framework for enhancer action, important for assigning function to the one- and three-dimensional structure of DNA. A knock-in mouse strain was compared to a wild-type FVB strain. The knock-in mouse strain carries a human beta-globin LCR in the Rad23a locus. We performed 4C for the Rad23a locus in the knock-in and the wild-type strain. Biological replicates were analyzed in a reversed dye orientation. At the RNA level these mice were characterized with Affymetrix expression arrays. We analyzed three biological replicates for the WT and the knock-in.

2011-06-15 | E-GEOD-24614 | biostudies-arrayexpress

Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription.

Project description:A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition binding of RNA polymerase II to gene regulatory elements is severely reduced. However, contacts between regulatory DNA elements and genes in the Î²-globin locus are unaffected and the locus still interacts with the same genomic regions elsewhere on the chromosome. This is a general phenomenon since the great majority of intra- and interchromosomal interactions with the ubiquitously expressed Rad23a gene are also not affected. Our data demonstrate that without transcription the organization and modification of nucleosomes at active loci and the local binding of specific trans-acting factors is unaltered. We propose that these parameters, more than transcription or RNA polymerase II binding, determine the maintenance of long-range DNA interactions. Keywords: transcription inhibition 4C 4C experiments were performed in duplo, dye swap was included. Hybridisation was performed on dedicated micro-arrays. Probes (60-mers) were selected from the sequences 100 bp up âand downstream of HindIII sites. To prevent cross-hybridization, probes that had any similarity with highly abundant repeats (RepBase 10.09) were removed from the probeset. In addition, probes that gave more than two BLAST hits in the genome were also removed from the probeset. Sequence alignments were performed using MegaBLAST using the standard settings. A hit was defined as an alignment of 30 nt or longer.

2010-05-26 | E-GEOD-10170 | biostudies-arrayexpress

Gene Expression analysis of Kc and Mbn2 cell lines from Drosophila melanogaster.

Project description:Comparison of gene expression between Kc and Mbn2 cell lines derived from Drosophila melanogaster. Microarray analysis was performed with two biological replicates for each cell line. Each array contains 15,634 Drosophila genes in duplicate with 12, 60 mer probes per gene.

2010-05-19 | E-GEOD-15660 | biostudies-arrayexpress

Indole Negatively Impacts Predation by Bdellovibrio bacteriovorus HD100 and Its Release from the Bdelloplast

Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic.

2013-11-19 | GSE52455 | GEO

Indole Negatively Impacts Predation by Bdellovibrio bacteriovorus HD100 and Its Release from the Bdelloplast

2013-11-19 | E-GEOD-52455 | biostudies-arrayexpress

Comparison of Invasive TAM sub-population to General TAM population

Project description:The tumor microenvironment modifies the malignancy of tumors. In solid tumors this environment is populated by many macrophages (tumor-associated macrophages; TAMs) that in genetic studies that depleted these cells from mouse models of breast cancer were shown to promote tumor progression to malignancy and increase metastatic potential. Mechanistic studies showed that these effects are through the stimulation of tumor cell migration, invasion, intravasation as well as an enhancement of angiogenesis. Using an in vivo invasion assay it was demonstrated that invasive carcinoma cells are a unique sub-population of tumor cells whose invasion and chemotaxis is dependent upon the co-migration of TAMs with obligate reciprocal signaling through an EGF/CSF-1 paracrine loop. In this study these invasion-promoting macrophages were isolated and subjected to analysis of their transcriptome in comparison to TAMs isolated indiscriminately to function using established macrophage markers by flow cytometry. Five biological replicates for each population (Invasive and General TAM) were used.

2010-05-16 | E-GEOD-18295 | biostudies-arrayexpress

Proteins used by the predatory yeast Saccharomycopsis schoenii as it attacks and kills the prey cell Saccharomyces cerevisiae

Project description:Saccahromycopsis schoenii belongs to a genus of yeasts that have the ability to attack and kill other yeast and fungi. De novo genomic sequencing and genome assembly suggests that S. schoenii might belong to the CTG clade. To examine whether it translated CTG codons to leucine (standard codon usage) or serine (alternative codon usage), we analysed its proteome during growth on full media. To see if translation is changed during nutritional stress or during predation on a prey cell (Saccharomyces cerevisiae), we analysed and quantified its proteome during these conditions compared to its proteomic expression in full media.

2019-03-18 | PXD008453 | Pride

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