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Title: Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1];  [2];  [1];  [3];  [1];  [1];  [1];  [3];  [2];  [1]
  1. Univ. of Rochester School of Medicine and Dentistry, Rochester, NY (United States)
  2. Univ. of Michigan, Ann Arbor, MI (United States)
  3. Univ. of California, Irvine, CA (United States)
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PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, in this paper we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1–P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ~0.6 s-1) and undocking (kundock ~1.1 s-1). Finally, discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.

Research Organization:
Univ. of Rochester School of Medicine and Dentistry, Rochester, NY (United States)
Sponsoring Organization:
USDOE; National Inst. of Health (NIH) (United States)
Grant/Contract Number:
GM063162; RR026501; GM062357; GM076485; GM103393; RR001209
OSTI ID:
1349644
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, Issue 27; ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 48 works
Citation information provided by
Web of Science

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Cited By (15)

Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples journal January 2020
Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch journal September 2019
Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch journal May 2016
Structural Studies of the 3′,3′-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation journal November 2018
A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control journal October 2019
Sulfur-substitution-induced base flipping in the DNA duplex journal January 2019
Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics journal October 2018
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview journal January 2018
A mechanism for ligand gated strand displacement in ZTP riboswitch transcription regulation preprint February 2019
Observation of preQ 1 -II riboswitch dynamics using single-molecule FRET journal October 2018
Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples journal September 2020
Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix journal November 2018
Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription journal June 2018
Nanomechanics and co-transcriptional folding of Spinach and Mango journal September 2019
Molecular dynamics simulation on the allosteric analysis of the c‐di‐GMP class I riboswitch induced by ligand binding journal July 2018

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
preQ1 riboswitch
gene regulation
crystal structure
single-molecule FRET
molecular dynamics