Structure of the Escherichia coli ProQ RNA-binding protein
- Grecia M. Gonzalez1,
- Steven W. Hardwick1,
- Sarah L. Maslen2,
- J. Mark Skehel2,
- Erik Holmqvist3,
- Jörg Vogel4,5,
- Alex Bateman6,
- Ben F. Luisi1 and
- R. William Broadhurst1
- 1Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- 2MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- 3Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, 75124 Uppsala, Sweden
- 4RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, D-97080 Wurzburg, Germany
- 5Helmholtz Institute for RNA-based Infection Research (HIRI), University of Würzburg, D-97080 Wurzburg, Germany
- 6European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Corresponding authors: bfl20{at}cam.ac.uk, rwb1002{at}cam.ac.uk
Abstract
The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.
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Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.060343.116.
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Freely available online through the RNA Open Access option.
- Received December 10, 2016.
- Accepted February 3, 2017.
This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.