A widely used means of genetic regulation in bacteria is a non-protein coding RNA element called a riboswitch. These are cis-acting elements found in the leader sequence of mRNAs and regulate gene expression by directly binding small molecule metabolites to a highly structured receptor domain. This receptor directs folding of a secondary structural switch in a downstream regulatory domain that in turn interfaces with the expression machinery (either RNA polymerase or the ribosome). In a broad spectrum of bacteria, particularly Firmicutes and Fusobacteria, central metabolic pathways including purine, amino acid, and cofactor biosynthesis and transport are regulated by riboswitches. Furthermore, genes essential for survival or virulence are under riboswitch control in a number of medically important pathogens including Listeria monocytogenes, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis making them of great interest as novel targets for designing antimicrobial therapeutics. In addition, riboswitches are increasingly serving as powerful model systems for developing the tools and methodologies for the design of small molecules that target other RNAs of medical interest. Towards the long-term goal of developing a molecular understanding of how RNA interacts with small molecules and the mechanisms it uses to regulate gene expression, we are using S-adenosylmethionine (SAM)-binding riboswitches as a model system. This proposal details a set of interconnected specific aims that addresses fundamental questions related to these research goals: (1) what is the range of structural diversity across SAM-responsive riboswitches, (2) what is the nature of the unbound structure of SAM-I superfamily riboswitches, (3) which structural features of the aptamer and expression domains play functional roles in regulation, and (4) do binding thermodynamics or kinetics dictate the regulatory response? To address these questions, a combination of approaches including X-ray crystallography, small-angle X-ray scattering (SAXS), and various biochemical and molecular biological approaches will be utilized in a set of experiments specifically designed to study the structure/function linkage. A deeper knowledge of how RNA specifically interacts with small molecules will help pave the way for a new generation of therapeutics that target non-protein coding RNAs that are pervasive in both bacteria and eukaryotes.

Public Health Relevance

Riboswitches are a form of RNA-based gene regulation widely utilized in bacteria, including a number of medically important pathogenic bacteria such as L. monocytogenes, S. aureus, M. tuberculosis, P. aeruginosa and Streptococcus species. The proposed research seeks to develop an atomic-level understanding of how these RNAs regulate gene expression in bacteria through their ability to directly bind small molecules. These studies serve to further our understanding as to how to exploit RNAs as targets of therapeutics via structure-based drug design or manipulate bacterial physiology to address health issues related to the composition of human microbiome.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM083953-08
Application #
8841744
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Lewis, Catherine D
Project Start
2008-05-01
Project End
2016-04-30
Budget Start
2015-05-01
Budget End
2016-04-30
Support Year
8
Fiscal Year
2015
Total Cost
$300,325
Indirect Cost
$94,505
Name
University of Colorado at Boulder
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
007431505
City
Boulder
State
CO
Country
United States
Zip Code
80303
Ozdilek, Bagdeser A; Thompson, Valery F; Ahmed, Nasiha S et al. (2017) Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding. Nucleic Acids Res 45:7984-7996
Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej et al. (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 23:655-672
Batey, Robert T; Kieft, Jeffrey S (2016) Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol 1320:219-32
Wostenberg, Christopher; Ceres, Pablo; Polaski, Jacob T et al. (2015) A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol 427:3473-3490
Trausch, Jeremiah J; Marcano-Velázquez, Joan G; Matyjasik, Michal M et al. (2015) Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch. Chem Biol 22:829-37
Trausch, Jeremiah J; Xu, Zhenjiang; Edwards, Andrea L et al. (2014) Structural basis for diversity in the SAM clan of riboswitches. Proc Natl Acad Sci U S A 111:6624-9
Batey, Robert T (2014) Advances in methods for native expression and purification of RNA for structural studies. Curr Opin Struct Biol 26:1-8
Ceres, Pablo; Trausch, Jeremiah J; Batey, Robert T (2013) Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res 41:10449-61
Ceres, Pablo; Garst, Andrew D; Marcano-Velázquez, Joan G et al. (2013) Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth Biol 2:463-72
Garst, Andrew D; Edwards, Andrea L; Batey, Robert T (2011) Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol 3:

Showing the most recent 10 out of 20 publications