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Molecular cell
01 16, 2020;77 (2): 411-425.e7.

RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles.

Sahar Melamed, Philip P Adams, Aixia Zhang, Hongen Zhang, Gisela Storz
Author Information
  1. Sahar Melamed: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA. Electronic address: sahar.melamed@nih.gov.
  2. Philip P Adams: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.
  3. Aixia Zhang: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.
  4. Hongen Zhang: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.
  5. Gisela Storz: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA. Electronic address: storzg@mail.nih.gov.
PMID: 31761494 DOI: 10.1016/j.molcel.2019.10.022

Abstract

Base pairing RNAs modulate gene expression in all studied organisms. In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is mediated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To examine the global contribution of the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq to identify RNA pairs bound to this protein. The RNA-RNA interactome for ProQ contains hundreds of pairs. Intriguingly, a significant fraction of the ProQ-bound RNA pairs are also found associated with Hfq, indicating overlapping, complementary, or competing roles for the two proteins. Characterization of one novel RNA pair bound by both chaperones revealed that while Hfq is required for RNA sponge-mediated downregulation of the sRNA, ProQ can inhibit this regulation. Overall, our results uncover increased complexity in RNA regulatory networks involving RNA chaperone proteins, RNases, sRNAs, and mRNAs.

Keywords

RNA chaperone RNA sponge RNase II RNase III RybB ribose small RNAs

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Grants

  1. ZIA HD001608-27/Intramural NIH HHS

MeSH Term

Base Pairing
DNA, Bacterial
Escherichia coli
Escherichia coli Proteins
Gene Expression Regulation, Bacterial
Host Factor 1 Protein
Molecular Chaperones
Protein Domains
RNA, Bacterial
RNA, Messenger
RNA, Small Untranslated
RNA-Binding Proteins

Chemicals

DNA, Bacterial
Escherichia coli Proteins
Hfq protein, E coli
Host Factor 1 Protein
Molecular Chaperones
ProQ protein, E coli
RNA, Bacterial
RNA, Messenger
RNA, Small Untranslated
RNA-Binding Proteins
Journal Article Research Support, N.I.H., Intramural
Article has an altmetric score of 41

Word Cloud

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