Riboswitches are regulatory RNAs that recognize specific small molecules, usually key metabolites, and "switch" downstream gene expression on or off at either the transcriptional or translational level. The discovery of these short cis-acting RNA elements has drastically changed our understanding of genetic regulatory mechanisms. Riboswitches are especially prevalent in Gram-positive bacteria, exemplified by Bacillus subtilis as a model organism, but are also found to control essential genes in important pathogens such as Bacillus anthracis, Staphylococcus, Enterococcus, Streptococcus, Listeria, Clostridium, and Mycobacterium. This and other characteristics have attracted increasing attention to riboswitch-mediated regulation. The three distinct classes of S-adenosyl methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolution solutions to achieve specific SAM recognition. We recently determined the crystal structures of SAM riboswitches from two classes, the E. faecalis SMK box and the B. subtilis S box. These structures shed light into the how SAM is specifically recognized, but did not provide enough evidence to support the large SAM-dependent conformational changes observed in the previous genetic and biochemical studies. To fully understand their structure-functional relationship and conformational dynamics, we propose to: (1) Understand the ligand recognition mechanism in the SMK box riboswitch. (2) Characterize the ligand-free SMK conformation and search for eukaryotic riboswitches. (3) Carry out chemical probing experiments to reveal ligand-induced conformational dynamics in the SMK RNA

Public Health Relevance

The described structure-function studies of SAM riboswitches include practical applications to rationally design specific riboswitch inhibitors that may contain antibiotic activities and to develop a fluorescent RNA tagging system for the research community to track the location, concentration, and movement of RNA in living cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086766-03
Application #
8204462
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2010-01-01
Project End
2014-11-30
Budget Start
2011-12-01
Budget End
2012-11-30
Support Year
3
Fiscal Year
2012
Total Cost
$306,233
Indirect Cost
$108,233
Name
Cornell University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Hayes, Robert P; Xiao, Yibei; Ding, Fran et al. (2016) Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature 530:499-503
Price, Ian R; Gaballa, Ahmed; Ding, Fang et al. (2015) Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 57:1110-23
Grigg, Jason C; Ke, Ailong (2015) Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches. Methods Enzymol 558:213-32
Price, Ian R; Grigg, Jason C; Ke, Ailong (2014) Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta 1839:931-938
Huo, Yanwu; Nam, Ki Hyun; Ding, Fang et al. (2014) Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nat Struct Mol Biol 21:771-7
Liu, Jun-Jie; Bratkowski, Matthew A; Liu, Xueqi et al. (2014) Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nat Struct Mol Biol 21:95-102
Grigg, Jason C; Ke, Ailong (2013) Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 21:2025-32
Grigg, Jason C; Chen, Yujie; Grundy, Frank J et al. (2013) T box RNA decodes both the information content and geometry of tRNA to affect gene expression. Proc Natl Acad Sci U S A 110:7240-5
Grigg, Jason C; Ke, Ailong (2013) One platform, five brands: how nature cuts the cost on riboswitches. J Mol Biol 425:1593-5
Grigg, Jason C; Ke, Ailong (2013) Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch. RNA Biol 10:1761-4

Showing the most recent 10 out of 21 publications