Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching

Robinson, Kirsten E.; Orans, Jillian; Kovach, Alexander R.; Link, Todd M.; Brennan, Richard G.

doi:10.1093/nar/gkt1171

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching

Journal Article · Wed Nov 27 00:00:00 EST 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt1171· OSTI ID:1625517

Robinson, Kirsten E. ^[1]; Orans, Jillian ^[2]; Kovach, Alexander R. ^[2]; Link, Todd M. ^[3]; Brennan, Richard G. ^[2]

Duke Univ., Durham, NC (United States). Dept. of Biochemistry; DOE/OSTI
Duke Univ., Durham, NC (United States). Dept. of Biochemistry
Univ. of Texas, Houston, TX (United States)

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A₁₅ and U₆ RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)₃A, (AU)₃A and (AC)₃A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)₃G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)_n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)₃G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)_n distal face-binding motif should be redefined as an (A-A-N)_n binding motif. TFQ data also demonstrated that the 5'-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.

View Accepted Manuscript (DOE)

Research Organization:: Duke University, Durham, NC (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1625517

Alternate ID(s):: OSTI ID: 1863982

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 4 Vol. 42; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii Nikulin, Alexey; Mikhailina, Alisa; Lekontseva, Natalia Taylor & Francis https://doi.org/10.6084/m9.figshare.3506333	text	January 2016
Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii Nikulin, Alexey; Mikhailina, Alisa; Lekontseva, Natalia Taylor & Francis https://doi.org/10.6084/m9.figshare.3506333.v1	text	January 2016
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein Dimastrogiovanni, Daniela; Fröhlich, Kathrin S.; Bandyra, Katarzyna J. eLife, Vol. 3 https://doi.org/10.7554/elife.05375	journal	December 2014

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