PXD040618

PXD040618 is an original dataset announced via ProteomeXchange.

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

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.

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]

submitter keyword: RNA, Chaperone, Aggregation, Protein folding, Proteomics, LC-MS/MS

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD040618

PRIDE project URI

• PRIDE
  1. PXD040618
     1. Label: PRIDE project
     2. Name: RNA-dependent solubility of Escherichia coli proteome: Structural hub, disorder, and chaperone network