Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq

PLoS One. 2012;7(11):e50892. doi: 10.1371/journal.pone.0050892. Epub 2012 Nov 30.

Abstract

In Escherichia coli the RNA chaperone Hfq is involved in riboregulation by assisting base-pairing between small regulatory RNAs (sRNAs) and mRNA targets. Several structural and biochemical studies revealed RNA binding sites on either surface of the donut shaped Hfq-hexamer. Whereas sRNAs are believed to contact preferentially the YKH motifs present on the proximal site, poly(A)(15) and ADP were shown to bind to tripartite binding motifs (ARE) circularly positioned on the distal site. Hfq has been reported to bind and to hydrolyze ATP. Here, we present the crystal structure of a C-terminally truncated variant of E. coli Hfq (Hfq(65)) in complex with ATP, showing that it binds to the distal R-sites. In addition, we revisited the reported ATPase activity of full length Hfq purified to homogeneity. At variance with previous reports, no ATPase activity was observed for Hfq. In addition, FRET assays neither indicated an impact of ATP on annealing of two model oligoribonucleotides nor did the presence of ATP induce strand displacement. Moreover, ATP did not lead to destabilization of binary and ternary Hfq-RNA complexes, unless a vast stoichiometric excess of ATP was used. Taken together, these studies strongly suggest that ATP is dispensable for and does not interfere with Hfq-mediated RNA transactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / metabolism*
  • Binding Sites
  • Crystallography, X-Ray
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Host Factor 1 Protein / chemistry*
  • Host Factor 1 Protein / metabolism*
  • Hydrolysis
  • Ligands
  • Models, Molecular
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / metabolism*
  • Nucleic Acid Renaturation
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA, Bacterial / metabolism*

Substances

  • Escherichia coli Proteins
  • Hfq protein, E coli
  • Host Factor 1 Protein
  • Ligands
  • Molecular Chaperones
  • Protein Subunits
  • RNA, Bacterial
  • Adenosine Triphosphate
  • Adenosine Triphosphatases

Grants and funding

The work was supported by grants F1722 (KDC) and F1720 (UB), in the framework of the Special Research Program (SFB17) on “Modulators of RNA fate and function” by the Austrian Science Fund. HH was supported by the doctoral program ‘RNA-Biology’ (W-1207). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.