|
| Status |
Public on Apr 01, 2024 |
| Title |
Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation II |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. Together, these functions ensure bacterial survival and recovery from N-starvation. Mammalian polyphosphate associates with P-bodies but not stress granules suggesting that polyphosphate’s interaction with select RNA binding proteins contributed to the evolution of functionally and compositionally distinct condensates in higher organisms.
|
| |
|
| Overall design |
Determination of RNA bound by Hfq during nitrogen starvation via RIP-seq of RNA bound to Hfq-mCherry from wild-type and delta-ppk E. coli strains starved for nitrogen
|
| |
|
| Contributor(s) |
Guan J, Hurto RL, Rai A, Azaldegui C, Ortiz-Rodriguez L, Biteen JS, Freddolino PL, Jakob U |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 21, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Lydia Freddolino |
| E-mail(s) |
lydsf@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Biological Chemistry
|
| Lab |
Freddolino Lab
|
| Street address |
1150 W. Medical Center Dr., MSRB 3 room 3315
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-0600 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL33080 |
NextSeq 2000 (Escherichia coli str. K-12 substr. MG1655) |
|
| Samples (56)
|
|
| This SubSeries is part of SuperSeries: |
| GSE241322 |
Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation |
|
| Relations |
| BioProject |
PRJNA1007675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241319_input_abundances_vs_dppk_t0.csv.gz |
338.4 Kb |
(ftp)(http) |
CSV |
| GSE241319_input_abundances_vs_dppk_t06.csv.gz |
334.4 Kb |
(ftp)(http) |
CSV |
| GSE241319_input_abundances_vs_dppk_t12.csv.gz |
332.8 Kb |
(ftp)(http) |
CSV |
| GSE241319_input_abundances_vs_dppk_t24.csv.gz |
334.2 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pullVinp_minus_dppk_pullVinp_t0.csv.gz |
343.7 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pullVinp_minus_dppk_pullVinp_t06.csv.gz |
309.6 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pullVinp_minus_dppk_pullVinp_t12.csv.gz |
316.9 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pullVinp_minus_dppk_pullVinp_t24.csv.gz |
335.5 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pulldown_vs_input_t0.csv.gz |
346.8 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pulldown_vs_input_t06.csv.gz |
349.9 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pulldown_vs_input_t12.csv.gz |
348.8 Kb |
(ftp)(http) |
CSV |
| GSE241319_wt_pulldown_vs_input_t24.csv.gz |
352.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...