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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Project description:Methyloversatilis universalis FAM5 utilizes single carbon compounds such as methanol or methylated amines as a sole source of carbon and energy. Expression profiling reveals distinct sets of genes altered during growth on methanol vs methylamine. Growth on methanol results in activation of mdh2 and a number of known accessory proteins. As expected, all genes for N-methylglutamate pathway were induced during growth on methylated amine. Among other functions, responding to a switch from methanol to methylated amines, are a heme-containing amine dehydrogenase (QHNDH), a PQQ-dependent methanol dehydrogenase homologue, a distant homologue of formaldehyde activating enzyme (fae3), molybdenum containing formate dehydrogenase, a set of transporters homologues to urea/ammonium transporters and amino-acid permeases. Genes encoding the PQQ-dependent methanol dehydrogenase and associated cytochrome, the enzymes from the assimilatory H4F-dependent pathway, and the tungsten-containing aldehyde oxidoreductase were down-regulated during growth on methylamine. Genes essential for carbon assimilation (serine cycle) and H4MTP-pathway for formaldehyde oxidation show similar level of expression on both C1-carbon sources. Phenotypic analysis of mutants lacking functional QHNDH had no growth defect on C1-compounds. M. universalis FAM5 strain with the methylene-tetrahydrofolate dehydrogenase lesion, a key enzyme of the H4-folate pathway, were not able to use any C1-compound, methanol or methylated amines. Methyloversatilis universalis FAM5 possesses three homologs of the formaldehyde activating enzymes. The relative expression of two of the formaldehyde activating enzyme (fae1) and fae2 did not change after the shift from methanol to methylamine growth. The relative expression of the third homologs, fae3, was significantly upregulated by methylamine. Single and double fae 2 and fae 3 mutants display similar to wild type growth M-BM- on methanol or methylamine. Strains lacking fae1 lost the ability to grow on both C1-compounds. However upon incubation on methylated amines the fae1-mutant produce revertants (fae1R ). The revertant strains displayed an impaired growth on methylamine but were not able to use methanol. Double mutations in fae1RM-BM- / fae3 or fae1R/fae2 and triple mutant fae1R/fae2/fae3 showed similar to fae1R phenotype. The metabolic pathways for utilization methanol and methylamine in Methyloversatilis universalis FAM5 are reconstructed. Methyloversatilis universalis FAM5 grown on methanol and methylamine with two biologial replicates for each condition. RNA-Seq was used for transcriptomics.

Dataset Information

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

Dataset's files

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.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

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

Dataset's files

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

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.