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| Status |
Public on Aug 12, 2023 |
| Title |
The LysR‐type transcription factor LsrB regulates beta‐lactam resistance in Agrobacterium tumefaciens |
| Platform organism |
Agrobacterium fabrum |
| Sample organisms |
Agrobacterium fabrum str. C58; Agrobacterium fabrum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant. Sequencing was done on the Illumina NovaSeq 6000 platform. Wild-type samples that derived from the same experiment were published previously (Kraus et al., 2020) (GEO accession: GSE150941). In the vtlR/lsrB mutant around 800 protein coding genes and around 80 sRNA coding genes were downregulated or upregulated at least three-fold (p value ≤ 0.05). Overall, the results demonstrate the huge regulatory effect of LsrB on the transcriptome of A. tumefaciens. Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20.
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| Overall design |
Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type, a vtlR/lsrB deletion mutant (∆atu2186).
Re-analysed Samples:
GSM4561620 SAMN14984052 SRX8370442
GSM4561621 SAMN14984051 SRX8370443
GSM4561622 SAMN14984050 SRX8370444
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| Web link |
https://onlinelibrary.wiley.com/doi/10.1111/mmi.15191
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| Contributor(s) |
Schmidt JJ, Remme DC, Eisfeld J, Brandenburg VB, Bille H, Narberhaus F |
| Citation(s) |
37985428 |
| Submission date |
Aug 07, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Franz Narberhaus |
| E-mail(s) |
franz.narberhaus@rub.de
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| Organization name |
Ruhr University Bochum
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| Department |
Microbial Biology
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| Street address |
Universitätstraße 150
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| City |
Bochum |
| State/province |
NRW |
| ZIP/Postal code |
44780 |
| Country |
Germany |
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| Platforms (1) |
| GPL33656 |
Illumina NovaSeq 6000 (Agrobacterium fabrum) |
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| Samples (3) |
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| Relations |
| Reanalysis of |
GSM4561620 |
| Reanalysis of |
GSM4561621 |
| Reanalysis of |
GSM4561622 |
| BioProject |
PRJNA1003054 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE240243_Delta_lsrB_vs_WT_24.csv.csv.gz |
308.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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