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| Status |
Public on Aug 11, 2021 |
| Title |
RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis. |
| Organism |
Bordetella pertussis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Bordetella pertussis has been shown to encode regulatory RNAs, yet the post-transcriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. RNA-Seq analysis showed differential expression of ~25% of the B. pertussis transcriptome in each mutant with only 28% overlap between data sets. Both endonucleases exhibited substantial impact on genes involved in amino acid uptake e.g. ABC transporters, and in virulence e.g. the type III secretion system, and the autotransporters vag8, tcfA and brkA. Interestingly, mutations in RNase III and RNase E drove the stability of many transcripts, including those involved in virulence, in opposite directions; a result that was validated by qPCR and immunoblot for tcfA and brkA. Of note, whereas similar mutations to RNase E in E. coli have subtle effects on transcript stability, a striking >20-fold reduction in four gene transcripts, including tcfA and vag8, was observed in B. pertussis. We further compared our data set to the regulon controlled by the RNA chaperone Hfq to identify B. pertussis loci influenced by regulatory RNAs. This analysis identified ~120 genes and 19 operons potentially regulated at the post-transcriptional level. Thus, our findings revealed how changes in RNase III- and RNase E-mediated RNA turnover influence pathways associated with virulence and cellular homeostasis. Moreover, we highlighted loci potentially influenced by regulatory RNAs, providing insights into the post-transcriptional regulatory networks involved in fine tuning B. pertussis gene expression.
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| Overall design |
A total of 15 samples, representing three genotypes (wild type and two mutants), with five replicates each.
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| Contributor(s) |
Ifill G, Blimkie T, Lee AH, Mackie GA, Chen Q, Stibitz S, Hancock RE, Fernandez RC |
| Citation(s) |
34406853 |
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| Submission date |
Jan 05, 2021 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Travis Blimkie |
| E-mail(s) |
travis.m.blimkie@gmail.com
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| Organization name |
University of British Columbia
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| Department |
MICB
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| Lab |
REW Hancock Lab
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| Street address |
2259 Lower Mall Research Station
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| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
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| Platforms (1) |
| GPL29570 |
Illumina HiSeq 2500 (Bordetella pertussis) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA689835 |
| SRA |
SRP300530 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164312_RAW.tar |
220.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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