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:
-
- 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}
}
Web of Science
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