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| Status |
Public on Jul 02, 2024 |
| Title |
Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen |
| Organism |
Pseudomonas savastanoi pv. phaseolicola 1448A |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.
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| Overall design |
Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/39052478/
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| Contributor(s) |
HUA C, Huang J, Sun Y, Wang T, Deng X |
| Citation(s) |
39052478 |
| |
| Submission date |
Oct 20, 2022 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Xin DENG |
| E-mail(s) |
xindeng@cityu.edu.hk
|
| Phone |
852-34425693
|
| Organization name |
City University of Hong Kong
|
| Department |
Department of Biomedical Sciences
|
| Lab |
Dr Xin DENG's Lab
|
| Street address |
1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
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| Platforms (1) |
| GPL24018 |
Illumina HiSeq 2000 (Pseudomonas savastanoi pv. phaseolicola 1448A) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA892464 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE216157_DMS-seq-hfq-1.react.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE216157_DMS-seq-hfq-2.react.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE216157_DMS-seq-hfq-25_1.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE216157_DMS-seq-hfq-25_2.react.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE216157_RNA-seq.bed.gz |
98.6 Kb |
(ftp)(http) |
BED |
| GSE216157_Ribo-seq.bed.gz |
85.6 Kb |
(ftp)(http) |
BED |
| GSE216157_WT-KB_1.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE216157_WT-KB_2.react.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE216157_WT-MM_1.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE216157_WT-MM_2.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE216157_hrpL-MM_1.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE216157_hrpL-MM_2.react.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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