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| Status |
Public on Nov 16, 2023 |
| Title |
Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus |
| Organism |
Caulobacter vibrioides |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus, and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the conserved, Hfq-bound sRNA RusT is transcriptionally controlled by the conserved NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis we determine 16 candidate target transcripts, more than half of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limiting.
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| Overall design |
Examination of NtrX-HA whole genome binding/occupancy (ChIP-Seq) in Caulobacter crescentus.
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| Contributor(s) |
Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH, Fröhlich K |
| Citation(s) |
38511926 |
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| Submission date |
Nov 15, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Patrick H. Viollier |
| E-mail(s) |
[email protected]
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| Organization name |
University of Geneva, Faculty of Medicine / CMU
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| Department |
Dept. Microbiology and Molecular Medicine
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| Street address |
Rue Michel Servet 1
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| City |
Geneva 4 |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL24555 |
Illumina NextSeq 500 (Caulobacter vibrioides) |
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| Samples (2) |
| GSM7903192 |
ChIP-Seq_NtrX-HA_Caulobacter_crescentus_CB15_ntrX::ntrX-HA |
| GSM7903193 |
Total-Input_NtrX-HA_Caulobacter_crescentus_CB15_ntrX::ntrX-HA |
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| Relations |
| BioProject |
PRJNA1040925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE247928_NtrX-HA_ChIP-seq_profiles_RPM_normalized_Full_trace_50bp_resolution_.xlsx |
4.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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