Scanning iron response regulator binding sites using RNA-seq and Dap-seq in the Brucella genome
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ABSTRACT:
PROVIDER: PRJNA888101 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21838803_1.fastq.gz | Fastqsanger.gz | |||
| SRR21838803_2.fastq.gz | Fastqsanger.gz | |||
| SRR21838804_1.fastq.gz | Fastqsanger.gz | |||
| SRR21838804_2.fastq.gz | Fastqsanger.gz | |||
| SRR21838805_1.fastq.gz | Fastqsanger.gz |
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Project description:Brucella spp. are gram-negative, facultative intracellular pathogens that cause brucellosis in humans and animals. Iron is an essential element required for all organisms. Iron response regulator (Irr) is a crucial transcriptional regulator and can affect the growth and iron uptake of Brucella. The growth rate of Brucella melitensis M5-90 irr mutant was significantly lower than that of B. melitensis M5-90 under normal or iron-sufficient conditions, however, the growth rate of the B. melitensis M5-90 irr mutant was significantly higher than that of B. melitensis M5-90 under iron-limited conditions. In addition, irr mutation significantly reduced iron uptake under iron-limited conditions. Currently, bhuA (a heme transporter), bhuQ (heme utilization oxygenase Q), and RirA (iron-responsive regulator) have been identified as iron metabolism genes and are regulated by the Irr protein. These results suggest that the Irr protein has multiple target genes in the Brucella genome that are involved in iron metabolism. Therefore, a combination of RNA-seq and Dap-seq was used to investigate the other iron metabolism genes that are also regulated by the Irr protein in Brucella. A total of seven genes were identified as target genes for Irr in this study and the expression levels of these seven genes were similar in both the RNA-seq and qRT-PCR results. Furthermore, the DNA bases C and G and amino acids asparagine, arginine, histidine, and serine were predicted as predominant docking sites for DNA and Irr using the HDOCK server. The electrophoretic mobility shift assay confirmed that six out of the seven genes, namely rirA (BME_RS13665), membrane protein (BME_RS01725), hypothetical protein (BME_RS09560), Iron transporter (BME_RS14525), cation-transporting P-type ATPase (BME_RS10660), and 2Fe-2S binding protein (BME_RS13655), interact with the Irr protein. In summary, our results identified six genes regulated by the Irr protein that may participate in iron metabolism. In addition, from the RNA-seq results, the mutation of irr resulted in the down/upregulation of many genes that are associated with the bacterial secretion system, lipopolysaccharides, and flagellar assembly, and these three components are the main virulence factors for Brucella. Collectively, these results provide valuable insights for the exploration of Brucella iron metabolism and its effects on virulence.
2023-06-21 | GSE215027 | GEO
Project description:Iron is an essential element required for all organisms. Iron response regulator (Irr) is a crucial transcriptional regulator and can affect the growth and iron uptake of Brucella. The growth rate of Brucella melitensis M5-90 irr mutant was significantly lower than that of B. melitensis M5-90 under normal or iron-sufficient conditions, however, the growth rate of the B. melitensis M5-90 irr mutant was significantly higher than that of B. melitensis M5-90 under iron-limited conditions. In addition, irr mutation significantly reduced iron uptake under iron-limited conditions. Previous studies suggested that the Irr protein has multiple target genes in the Brucella genome that are involved in iron metabolism. Therefore, in the present study, a Dap-seq approach was used to investigate the other iron metabolism genes that are also regulated by the Irr protein in Brucella. A total of seven genes were identified as target genes for Irr in this study and the expression levels of these seven genes was identified using qRT-PCR. The electrophoretic mobility shift assay confirmed that six out of the seven genes, namely rirA (BME_RS13665), membrane protein (BME_RS01725), hypothetical protein (BME_RS09560), ftrA (BME_RS14525), cation-transporting P-type ATPase (zntA) (BME_RS10660), and 2Fe-2S binding protein (BME_RS13655), interact with the Irr protein. Furthermore, the iron utilization and growth assay experiments confirmed that rirA was involve in iron metabolism and growth of Brucella. In summary, our results identified six genes regulated by the Irr protein that may participate in iron metabolism, and the rirA was identified as a regulon of Irr and it also plays a role in iron metabolism of Brucella. Collectively, these results provide valuable insights for the exploration of Brucella iron metabolism.
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Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.
2016-05-25 | GSE60142 | GEO
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens.
2012-12-01 | GSE34503 | GEO
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens.
2012-12-01 | GSE34501 | GEO
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens.
2012-12-01 | GSE34498 | GEO
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens.
2012-12-01 | GSE34495 | GEO
Project description:Brucella melitensis and Brucella canis differ by ~75 genes yet B. melitensis is highly virulent for humans while B. canis is considered rarely pathogenic. No identified bacterial factors or mechanisms account for this difference in virulence. To identify functional differences of these two bacteria, gene transcription was examined during infection of murine macrophages and compared to bacteria grown in broth. Our analysis identified transcriptional differences in macrophage infection between B. melitensis and B. canis genes involved in iron transport. Increased transcription of the TonB, enterobactin, and ferric anguibactin transport systems were observed in B. canis but not B. melitensis during infection of macrophages. Therefore, iron appears as an important requirement during the first 24h of infection by B. canis but not for B. melitensis and provides strategies for controlling these pathogens. Comparison of total bacterial RNA from Brucella canis infected murine macrophages to broth grown bacteria
2012-12-01 | E-GEOD-34503 | biostudies-arrayexpress