Protein translation as major target for gene expression control of O. tsutsugamushi
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PROVIDER: PRJNA117253 | ENA |
REPOSITORIES: ENA
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Project description:Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The bacterium can replicate both in its arthropod host and in mammals, including humans. The control mechanisms for bacterial gene expression within eukaryotic host cells are largely unknown. Previously, we reported that the O. tsutsugamushi genome has the highest repeat density of any sequenced bacterial genome due to the extraordinary proliferation of mobile genetic elements (MGEs), suggesting a unique genomic evolution in intracellular niches. In this study, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches. These approaches identified 643 genes, corresponding to approximately 30% of genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the genomes of different O. tsutsugamushi strains to identify gene blocks impermeable to proliferating MGEs. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs with sizes ranging from 1 kbp to 29 kbp, covering 48% of the genome, were identified. When combining the data of the CSBs and global gene expression, CSBs in the O. tsutsugamushi genomes correlates well with the location of expressed genes, especially in protein level, suggesting the functional conservation between gene expression and genomic location. Finally, we compared global gene expression of the bacteria infecting fibroblasts and macrophages using microarray analysis. Major changes in the expression of genes with known functions were the downregulation of genes involved in translation, protein processing and secretion, which resulted in significant reduction in bacterial translation rates and growth within macrophages. These results suggest that the replication of O. tsutsgamushi is controlled primarily by the expression of genes involved in bacterial translation and subsequent protein processing/secretion.
2010-03-31 | GSE16966 | GEO
Project description:Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The bacterium can replicate both in its arthropod host and in mammals, including humans. The control mechanisms for bacterial gene expression within eukaryotic host cells are largely unknown. Previously, we reported that the O. tsutsugamushi genome has the highest repeat density of any sequenced bacterial genome due to the extraordinary proliferation of mobile genetic elements (MGEs), suggesting a unique genomic evolution in intracellular niches. In this study, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches. These approaches identified 643 genes, corresponding to approximately 30% of genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the genomes of different O. tsutsugamushi strains to identify gene blocks impermeable to proliferating MGEs. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs with sizes ranging from 1 kbp to 29 kbp, covering 48% of the genome, were identified. When combining the data of the CSBs and global gene expression, CSBs in the O. tsutsugamushi genomes correlates well with the location of expressed genes, especially in protein level, suggesting the functional conservation between gene expression and genomic location. Finally, we compared global gene expression of the bacteria infecting fibroblasts and macrophages using microarray analysis. Major changes in the expression of genes with known functions were the downregulation of genes involved in translation, protein processing and secretion, which resulted in significant reduction in bacterial translation rates and growth within macrophages. These results suggest that the replication of O. tsutsgamushi is controlled primarily by the expression of genes involved in bacterial translation and subsequent protein processing/secretion. Microarray analysis using the Combimatrix CustomArrayTM 4X2 microarray (CombiMatrix) was performed according to the standard CombiMatrix protocol described in detail at http://www.combimatrix.com/ products_custom4x2.htm (PTL005). Oligonucleotide probes (27 to 40-mers, 1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array. A local background subtraction method was used and the background-subtracted signal values were imported into the Avadis Prophetic software (ver. 3.3, Strand Genomics) or Expander (ver. 4.1, http://acgt.cs.tau.ac.il/expander/) for data analysis. . Global normalization of gene expression data was performed using the quantile normalization method embedded in the Expander software. The standard deviations of log data and the p-values were calculated using default settings in the Avadis software. Transcriptome analysis was carried out using three biological replicates for uninfected samples (uninfected L929 cells) and five biological replicates for infected samples (L929 cells infected with O. tsutsugamushi for 48 h). For comparison of the O. tsutsugamushi transcriptome from fibroblasts (L929 cells) and macrophages (J774A.1 cells), two biological replicates from each cell line were used.
2010-06-05 | E-GEOD-16966 | biostudies-arrayexpress
Project description:Scrub typhus is a life-threatening disease caused by Orientia tsutsugamushi, a bacterium that mainly infects endothelial cells in vitro and in vivo. Evidence suggests that the interaction of O. tsutsugamushi with myeloid cells may play a pivotal role in O. tsutsugamushi infection. We showed here that O. tsutsugamushi intensively replicated within human monocyte-derived macrophages. Bacterial organisms stimulated the expression of a large panel of genes including type I interferon, interferon-stimulated, inflammatory, apoptosis-related genes and induced an M1-type gene response in macrophages. This transcriptional signature was accompanied by functional consequences such as the release of inflammatory cytokines such as Tumor Necrosis Factor and interleukin-gamma. Live O. tsutsugamushi organisms were necessary for type I interferon response and, to a lesser degree, to inflammatory response. As interferon-gamma is known to elicit M1 polarization, we assessed the effect of interferon-gamma on O. tsutsugamushi fate in macrophages. Exogenous interferon-gamma partly inhibited O. tsutsugamushi replication within macrophages. Our results suggest that the inflammatory response induced by O. tsutsugamushi may account for the local and systemic inflammation observed in scrub typhus and that interferon-gamma may be useful as an adjuvant treatment of patients with scrub typhus.
2013-01-29 | GSE38194 | GEO
Project description:Scrub typhus is a life-threatening disease caused by Orientia tsutsugamushi, a bacterium that mainly infects endothelial cells in vitro and in vivo. Evidence suggests that the interaction of O. tsutsugamushi with myeloid cells may play a pivotal role in O. tsutsugamushi infection. We showed here that O. tsutsugamushi intensively replicated within human monocyte-derived macrophages. Bacterial organisms stimulated the expression of a large panel of genes including type I interferon, interferon-stimulated, inflammatory, apoptosis-related genes and induced an M1-type gene response in macrophages. This transcriptional signature was accompanied by functional consequences such as the release of inflammatory cytokines such as Tumor Necrosis Factor and interleukin-gamma. Live O. tsutsugamushi organisms were necessary for type I interferon response and, to a lesser degree, to inflammatory response. As interferon-gamma is known to elicit M1 polarization, we assessed the effect of interferon-gamma on O. tsutsugamushi fate in macrophages. Exogenous interferon-gamma partly inhibited O. tsutsugamushi replication within macrophages. Our results suggest that the inflammatory response induced by O. tsutsugamushi may account for the local and systemic inflammation observed in scrub typhus and that interferon-gamma may be useful as an adjuvant treatment of patients with scrub typhus. Macrophages (4 M-CM-^W 10.5 cells per assay) were incubated with O. tsutsugamushi at a bacterium-to-cell ratio of 20:1 for 8 hours. RNA samples (four samples per experimental condition) were processed for microarray analysis.
2013-01-29 | E-GEOD-38194 | biostudies-arrayexpress
Project description:Orientia tsutsugamushi Raw Sequencing Reads
| PRJNA316643 | ENA
Project description:We performed RNAseq on total RNA extracted from splenic B cells isolated from mice infected with Orientia tsutsugamushi to investigate the dynamic transcriptomic signature of these cells throughout infection. We then performed differential expression analysis, meta-analysis, and gene set enrichment anaylsis using data obtained by RNA-seq of mock infected (D0) and O. tsutsugamushi-infected mice (D4 and D8).
2023-01-16 | GSE222692 | GEO
Project description:Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of scrub typhus. As O. tsutsugamushi is detected in circulating monocytes during acute phase of scrub typhus, we wondered if this organism was able to infect monocytes. We showed here that O. tsutsugamushi replicated in monocytes from healthy donors. Using human whole genome microarrays, we found that O. tsutsugamushi the expression of genes in which up-regulated and down-modulated genes were equally distributed. , the expression of type I interferon, interferon-stimulated genes and M1-associated genes was significantly up-regulated. Second, O. tsutsugamushi the expression of apoptosis-related genes and induced cell death in monocytes. Live organisms were indispensable to type I interferon response and apoptosis and enhanced the expression of M1 cytokines. These findings were related to the transcriptional changes found in mononuclear cells from patients with scrub typhus. Hence, a microarray study revealed the up-regulation of 613 genes and the down-modulation of 517 genes. Importantly, IFN-related genes were specifically enriched and some features of M1 polarization were observed in patients, as found in O. tsutsugamushi-stimulated cells. Our results provide a comprehensive understanding of scrub typhus pathogenesis in which IFN-mediated activation of monocytes appears as critical.
2010-09-21 | GSE24247 | GEO
Project description:Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of scrub typhus. As O. tsutsugamushi is detected in circulating monocytes during acute phase of scrub typhus, we wondered if this organism was able to infect monocytes. We showed here that O. tsutsugamushi replicated in monocytes from healthy donors. Using human whole genome microarrays, we found that O. tsutsugamushi the expression of genes in which up-regulated and down-modulated genes were equally distributed. , the expression of type I interferon, interferon-stimulated genes and M1-associated genes was significantly up-regulated. Second, O. tsutsugamushi the expression of apoptosis-related genes and induced cell death in monocytes. Live organisms were indispensable to type I interferon response and apoptosis and enhanced the expression of M1 cytokines. These findings were related to the transcriptional changes found in mononuclear cells from patients with scrub typhus. Hence, a microarray study revealed the up-regulation of 613 genes and the down-modulation of 517 genes. Importantly, IFN-related genes were specifically enriched and some features of M1 polarization were observed in patients, as found in O. tsutsugamushi-stimulated cells. Our results provide a comprehensive understanding of scrub typhus pathogenesis in which IFN-mediated activation of monocytes appears as critical. Monocytes (1.5 x 105 per assay) were incubated with or without 3 x 105 O. tsutsugamushi organisms in RPMI 1640 containing 10% FBS, 20 mM HEPES and 2 mM L-glutamine (Invitrogen) for 2 hours. The raw data, from the Agilent feature extraction software, were preprocessed with background subtraction and quantile normalization. This pretreatment was performed by using a bioconductor limma package, called Agi4x44PreProcess (http://www.bioconductor.org/packages/2.3/bioc/html/ Agi4x44PreProcess.html)
2010-09-21 | E-GEOD-24247 | biostudies-arrayexpress
Project description:We performed RNAseq on total RNA extracted from brains of mice infected with Orientia tsutsugamushi to investigate the transcriptomic signature of this tissue throughout infection.
2023-05-04 | GSE227525 | GEO
Project description:We performed NanoString analysis on total RNA extracted from spleens of mice infected with Orientia tsutsugamushi to investigate the transcriptomic signature of these cells throughout infection.
2023-03-20 | GSE227523 | GEO