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Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli

Klein, Thomas ; Funke, Franziska ; Rossbach, Oliver ; Lehmann, Gerhard ; Vockenhuber, Michael ; Medenbach, Jan ; Suess, Beatrix ; Meister, Gunter ; Babinger, Patrick (2023)
Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli.
In: International Journal of Molecular Sciences, 2023, 24 (14)
doi: 10.26083/tuprints-00024407
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Item Type: Article
Type of entry: Secondary publication
Title: Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli
Language: English
Date: 11 August 2023
Place of Publication: Darmstadt
Year of primary publication: 2023
Publisher: MDPI
Journal or Publication Title: International Journal of Molecular Sciences
Volume of the journal: 24
Issue Number: 14
Collation: 23 Seiten
DOI: 10.26083/tuprints-00024407
Corresponding Links:
Origin: Secondary publication DeepGreen
Abstract:

An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur.

Uncontrolled Keywords: metabolic enzymes, REM hypothesis, RNA-binding protein, prokaryotes, SELEX, unconventional RNA binding, MS2 phage, quinone oxidoreductase
Status: Publisher's Version
URN: urn:nbn:de:tuda-tuprints-244075
Additional Information:

This article belongs to the Special Issue Small Prokaryotic Proteins Interacting with Nucleic Acids 2.0

Classification DDC: 500 Science and mathematics > 540 Chemistry
500 Science and mathematics > 570 Life sciences, biology
Divisions: Interdisziplinäre Forschungsprojekte > Centre for Synthetic Biology
Date Deposited: 11 Aug 2023 12:09
Last Modified: 19 Oct 2023 13:58
SWORD Depositor: Deep Green
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/24407
PPN: 512472661
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