PXD040618 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | RNA-dependent solubility of Escherichia coli proteome: Structural hub, disorder, and chaperone network |
Description | Protein aggregation is a complex phenomenon involving aberrant folding and proteostasis that leads to various proteopathies. Despite extensive efforts, the maintenance of protein solubility against aggregation remains ill-defined, especially in complex cellular environments. In this study, we show that the depletion of RNAs from Escherichia coli lysates results in global protein aggregation. Using quantitative mass spectroscopic analysis, we identified significant proteins (>900) from the whole E. coli proteome whose solubility maintenance is dependent on RNA. Proteome-wide characterization revealed that RNA dependence was highly enriched among acidic proteins, intrinsically disordered proteins, and structural hub proteins. Notably, the solubility of representative molecular chaperones [Trigger factor (TF), DnaJ, and GroES] is largely dependent on RNA, suggesting a hitherto unknown hierarchical relationship between RNA-based chaperone (chaperna) and protein-based molecular chaperones. Our findings provide new insights into proteome solubility maintenance and misfolding-associated proteopathy in vivo, where proteins, from birth to death, stably or transiently associate with RNAs. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:42:26.414.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Bitnara Han |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-03-06 05:18:22 | ID requested | |
1 | 2024-05-24 01:18:47 | announced | |
⏵ 2 | 2024-10-22 06:42:27 | announced | 2024-10-22: Updated project metadata. |
Publication List
10.1080/15476286.2024.2315383; |
Park C, Han B, Choi Y, Jin Y, Kim KP, Choi SI, Seong BL, lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network. RNA Biol, 21(1):1-18(2024) [pubmed] |
Keyword List
submitter keyword: RNA, Chaperone, Aggregation, Protein folding, Proteomics, LC-MS/MS |
Contact List
Kwang Pyo Kim |
contact affiliation | Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea. & Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea. |
contact email | kimkp@khu.ac.kr |
lab head | |
Bitnara Han |
contact affiliation | Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea. |
contact email | skfk1003@naver.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD040618
- Label: PRIDE project
- Name: RNA-dependent solubility of Escherichia coli proteome: Structural hub, disorder, and chaperone network