Comparative transcriptome analysis of artificially induced rough-type Brucella strain RM57 and its parent strain
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ABSTRACT:
PROVIDER: PRJNA543473 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9079160.fastq.gz | Fastqsanger.gz | |||
| SRR9079161.fastq.gz | Fastqsanger.gz | |||
| SRR9079162.fastq.gz | Fastqsanger.gz | |||
| SRR9079163.fastq.gz | Fastqsanger.gz | |||
| SRR9079164.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To uncover the related mechanisms underlie virulence attenuation of RM57 vaccine candidate. Methods: Three Brucella melitensis M1981 strains and three Brucella melitensis RM57 strains were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.The HiSeq 4000 platform was used to perform the transcriptome sequencing. Results: The results revealed that expressions of 1205 genes were significantly different between RM57 and M1981. Data analysis showed that in the gene ontology term, the different expressed genes involved in energy production and conversion, and translation, ribosomal structure and biogenesis were significantly enriched. Pathway enrichment analysis indicated that the genes involved in oxidative phosphorylation, ribosome, nitrogen metabolism, tyrosine metabolism and two-component system were significantly affected.
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Project description:The macrophage-Brucella interaction is critical for the establishment of a chronic Brucella infection. Smooth virulent B. suis strain 1330 (S1330) prevents macrophage cell death. However, rough attenuated B. suis strain VTRS1 induces strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774. A1 cells infected with S1330 or VTRS1.
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Project description:This SuperSeries is composed of the following subset Series: GSE35612: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (acute phase) GSE35613: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (chronic 1 phase) GSE35614: Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (chronic 2 phase) Refer to individual Series
2012-02-08 | E-GEOD-35615 | biostudies-arrayexpress
Project description:Brucellosis is one of the most common zoonotic epidemics with a serious threat to public health and livestock development in many countries across the world. Vaccination is a key control strategy toward preventing brucellosis in high-prevalence regions. Recently, a rough-type Brucella melitensis mutant strain (RM57) induced from a B. melitensis strain M1981 showed protective effects in guinea pigs indicating that it is a good vaccine candidate. In this study, stress response assays were performed to reveal the mechanisms underlying virulence attenuation of RM57. In addition, a genome-wide transcriptome profile of RM57 was analyzed relative to the parent strain M1981 in order to reveal genetic factors controlling the phenotypes. Our results indicated a similar sensitivity to various stress conditions in RM57 owing to a lack of significant differences from its parent strain. Transcriptome analysis showed that a total of 1,205 genes were differentially expressed between RM57 and M1981 with gene ontology terms revealing that these genes are involved in energy production and conversion, translation, ribosomal structure, and biogenesis. Pathway enrichment analysis revealed that genes involved in oxidative phosphorylation, ribosome, nitrogen metabolism, tyrosine metabolism, and two-component system were significantly affected. As a result of these differences at the molecular level, the function of type IV secretion system in RM57 was found to be affected leading to reduced virulence of the RM57 mutant strain in both macrophage and mice infection models.
| S-EPMC6966878 | biostudies-literature
Project description:The macrophage-Brucella interaction is critical for the establishment of a chronic Brucella infection. Smooth virulent B. suis strain 1330 (S1330) prevents macrophage cell death. However, rough attenuated B. suis strain VTRS1 induces strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774. A1 cells infected with S1330 or VTRS1. Murine J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 or VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 0, 1, 2, 4, 8, 24, and 48 h post infection. The RNA samples were stored at -80 ºC until an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) was used to assess the concentrations and quality of RNA samples. Total RNA (20 µg) per sample was used for hybridization with Affymetrix mouse GeneChip 430 2.0 array. Preparation of cDNA, hybridization, quality controls and scanning of the GeneChip 430 2.0 arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) .
2011-06-24 | E-GEOD-21117 | biostudies-arrayexpress
Project description:Purpose:To uncover the related mechanisms underlie virulence attenuation of Brucella canis MucR mutant strain. Methods:Three Brucella canis RM6/66 strains and three Brucella canis ΔmucR strains were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer. An Illumina platform was used to perform the transcriptome sequencing. Results: The results revealed that expressions of 694 genes were significantly different between RM6/66 and ΔmucR. Data analysis showed that in the COG term, the different expressed genes involved in translation, ribosomal structure and biogenesis, signal transduction mechanisms, energy production and conversion, intracellular trafficking, secretion, and vesicular transport, and extracellular structures were significantly affected. Pathway enrichment analysis indicated that the genes involved in ribosome, oxidative phosphorylation, aminoacyl-tRNA biosynthesis and protein export were significantly enriched.
2021-01-24 | GSE155748 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.
2012-02-08 | GSE35612 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.
2012-02-08 | GSE35614 | GEO
Project description:The study demonstrated the gene expression through microarray analysis of total mRNA in rams experimentally infected with a rough (R) virulent strain of Brucella ovis in reproductive organs (epididymus, testicles, ampolae, vesicular glands, bulbourethral glands) and a pool of lymph nodes (inguinal and scrotal) at three different times: acute phase (60 days post challenge [dpc]), chronic phase 1 (120dpc), and chronic phase 2 (240dpc) of infection. To further define the gene expression changes associated with infected rams, the profiles of a control group (0 dpc) of rams was compared using the Affymetrix Bovine Genome Array. Of the 23,000 genes that were analyzed on the array, B. ovis infection in rams’ tissues revealed 139, 930 and 744 Differentially Expressed Genes (DEGs) in the acute, chronic 1, and chronic phase 2 of infection, respectively. Among the three phases of infection, 44 DEGs (30 known and 14 unknown genes) were expressed in common. The biological functions of immune cell trafficking, immunological disease, infectious disease, inflammatory disease, inflammatory response and cellular movement were significant at the three phases of infection. The results support the first microarray analysis of ram tissues infected with an R strain of B. ovis.
2012-02-08 | GSE35613 | GEO
Project description:To explore the role of Brucella BI-1 in Brucella suis S2, we constructed the Brucella BI-1 deletion mutant strain and its complementary strain. We then determined the effect of Brucella BI-1 deletion on the physiological characteristics of Brucella suis S2 and revealed them via integrated transcriptomic and proteomic analyses. Brucella BI-1 deletion altered the membrane properties of Brucella suis S2 and decreased its resistance to acidic pH, H2O2, polymyxin B, and lincomycin. Additionally, deleting Brucella BI-1 led to defective growth, cell division, and viability in Brucella suis S2. In conclusion, our results revealed that Brucella BI-1 is a bacterial cytoprotective protein involved in membrane homeostasis, cell division, and stress resistance in Brucella suis S2.
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