skip to main content

DOE PAGESDOE PAGES

Title: Structural analysis of a class III preQ 1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

PreQ 1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ 1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HL out-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ 1-III riboswitch aptamer forms a HL out-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 preQ 1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ 1 binds tightly (K D,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 preQ 1 enhances P4 reorientation toward P1–P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (k dock ~0.6 s -1) and undocking (k undock ~1.1 s -1). Finally, discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics tomore » modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.« less
Authors:
 [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)
Publication Date:
Grant/Contract Number:
GM063162; RR026501; GM062357; GM076485; GM103393; RR001209
Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 112; Journal Issue: 27; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Research Org:
Univ. of Rochester School of Medicine and Dentistry, Rochester, NY (United States)
Sponsoring Org:
USDOE; National Inst. of Health (NIH) (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; preQ1 riboswitch; gene regulation; crystal structure; single-molecule FRET; molecular dynamics
OSTI Identifier:
1349644