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Title: Structural basis for guanidine sensing by the ykkC family of riboswitches

Abstract

Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. In this work, we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem–loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation–π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification—a previously unappreciated aspect of bacterial physiology.

Authors:
 [1];  [1];  [1]
  1. Cornell Univ., Ithaca, NY (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1430300
Grant/Contract Number:  
AC02-06CH11357; R41 GM103403; S10 RR029205
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
RNA
Additional Journal Information:
Journal Volume: 23; Journal Issue: 4; Journal ID: ISSN 1355-8382
Publisher:
Cambridge University Press
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; Dickeya dadantii; RNA structure; gene regulation; guanidine; orphan riboswitch

Citation Formats

Battaglia, Robert A., Price, Ian R., and Ke, Ailong. Structural basis for guanidine sensing by the ykkC family of riboswitches. United States: N. p., 2017. Web. doi:10.1261/rna.060186.116.
Battaglia, Robert A., Price, Ian R., & Ke, Ailong. Structural basis for guanidine sensing by the ykkC family of riboswitches. United States. https://doi.org/10.1261/rna.060186.116
Battaglia, Robert A., Price, Ian R., and Ke, Ailong. 2017. "Structural basis for guanidine sensing by the ykkC family of riboswitches". United States. https://doi.org/10.1261/rna.060186.116. https://www.osti.gov/servlets/purl/1430300.
@article{osti_1430300,
title = {Structural basis for guanidine sensing by the ykkC family of riboswitches},
author = {Battaglia, Robert A. and Price, Ian R. and Ke, Ailong},
abstractNote = {Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. In this work, we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem–loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation–π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification—a previously unappreciated aspect of bacterial physiology.},
doi = {10.1261/rna.060186.116},
url = {https://www.osti.gov/biblio/1430300}, journal = {RNA},
issn = {1355-8382},
number = 4,
volume = 23,
place = {United States},
year = {Tue Jan 17 00:00:00 EST 2017},
month = {Tue Jan 17 00:00:00 EST 2017}
}

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Cited by: 35 works
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Works referenced in this record:

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