Dataset Information

RNA-dependent solubility of Escherichia coli proteome: Structural hub, disorder, and chaperone network

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Bitnara Han

LAB HEAD: Kwang Pyo Kim

PROVIDER: PXD040618 | Pride | 2024-05-24

REPOSITORIES: Pride

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			Action	DRS
	WC_Proteinfolding_FASP_TMT_F10_R1_20170917.raw	Raw
	WC_Proteinfolding_FASP_TMT_F10_R2_20170919.raw	Raw
	WC_Proteinfolding_FASP_TMT_F11_R1_20170917.raw	Raw
	WC_Proteinfolding_FASP_TMT_F11_R2_20170919.raw	Raw
	WC_Proteinfolding_FASP_TMT_F12_R1_20170917.raw	Raw

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Publications

RNA-dependent proteome solubility maintenance in <i>Escherichia coli</i> lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network.

Park Chan C Han Bitnara B Choi Yura Y Jin Yoontae Y Kim Kwang Pyo KP Choi Seong Il SI Seong Baik L BL

RNA biology 20240101 1

Protein aggregation, a consequence of misfolding and impaired proteostasis, can lead to cellular malfunctions such as various proteinopathies. The mechanisms protecting proteins from aggregation in complex cellular environments have long been investigated, often from a protein-centric viewpoint. However, our study provides insights into a crucial, yet overlooked actor: RNA. We found that depleting RNAs from <i>Escherichia coli</i> lysates induces global protein aggregation. Our quantitative mass ...[more]

PMID: 38361426

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