Research Interests

Ribonucleic acids (RNA) are remarkable molecules. In addition to serving their classical role as carriers of genetic information, they are also cellular machines that perform enzymatic and regulatory functions previously only ascribed to proteins. Furthermore, since RNA molecules are simultaneously capable of carrying genetic information and functioning as catalysts, they can be subjected to evolutionary selection pressures and may have formed the basis for ancestral life. Finally, RNA’s central role in life suggests that its potential therapeutic value is barely tapped but already clinically validated: approximately 80 percent of antibiotics in use today target a single type of RNA-containing enzyme, the ribosome, and most do so by targeting its non-coding RNA component.

Dr. Ferré-D’Amaré studies RNA molecules in their many guises. His laboratory develops and exploits fundamental biophysical approaches to understanding the function of ribozymes (catalytic RNAs) and the interactions between RNA and proteins at the level of atomic structure. Dr. Ferré-D’Amaré is also interested in the role of RNA molecules in gene regulation and signal transduction (e.g., riboswitches, non-coding mRNA domains that directly bind to specific small molecules or macromolecules and control transcription, translation, or splicing). He and his colleagues focus on the way RNA molecules fold into three-dimensional structures and how they are modified post-transcriptionally, and use this information rationally to design new molecular tools. Finally, he uses the dual function of RNA molecules as information carriers and catalytic agents to artificially evolve them, study their properties, and engineer them.

Among his varied research interests, Dr. Ferré-D’Amaré has several programs with strong translational implications. The first is a discovery initiative for small molecule antibiotic leads that bind to riboswitches. Riboswitches have been largely ignored as targets for drug discovery, yet their central role is clear in clinically important phenomena such as bacterial biofilm formation. Biofilms are assemblages of bacteria that adhere to biological and non-biological substrates and resist existing treatment. Their formation is regulated by cyclic-di-GMP-sensing riboswitches. Dr. Ferré-D’Amaré's laboratory has identified many compounds that bind specifically to bacterial riboswitches. He is currently developing these leads into more potent molecules, in collaboration with colleagues at Cambridge University, NCATS and NCI. Unlike mammalian cells, bacteria and yeast have rigid cell walls that form a protective exoskeleton. Dr. Ferré-D’Amaré’s second translational research focus is on the role of a catalytic RNA—glmS—in controlling the synthesis of the bacterial cell wall. GlmS operates not only as a catalytic RNA but also as a riboswitch and controls cell wall biosynthesis. By determining its crystal structures in multiple functional states, Dr. Ferré-D’Amaré's laboratory has generated "molecular movies" of the glmS ribozyme in action. These studies have revealed how the glmS ribozyme can employ a small molecule as a coenzyme. The glmS ribozyme is being studied as a potentially valuable target for novel antibiotics, and also an experimental platform with which to understand how RNA targets can evolve antibiotic resistance. Finally, Dr. Ferré-D’Amaré's interest in non-coding RNA biology has led him to structural and molecular engineering studies of fluorescent RNAs. Much like green fluorescent protein (GFP) and its variants transformed the study of proteins, fluorescent RNAs have the potential to revolutionize the in vivo study of the tens of thousands of non-coding RNAs that have been discovered in the human transcriptome. Dr. Ferré-D’Amaré and colleagues elucidated the structural basis for fluorescence of several RNA-chromophore complexes, and are leveraging this knowledge to generate optimized tools to study the synthesis, maturation, targeting, localization and turnover of RNAs that play essential roles in metabolism, development and disease progression.

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Catalytic RNAs

Ribozymes are non-coding RNAs that can precisely position reactants and accelerate chemical reactions by preferentially stabilizing their transition states.  Some fundamental biological processes (such as translation, splicing and tRNA maturation) are universally catalyzed by ribozymes. Several ribozymes are also known to play key roles in the replications and virulence of important human pathogens.

Gene-regulatory RNAs

Our group has made numerous breakthroughs in the study of riboswitches, which are non-coding mRNA domains that regulate gene expression in response to the intracellular concentration of their cognate ligands. Depending on the riboswitch, ligands range from simple ions and metabolites to second messengers to other RNA molecules. Many riboswitches control virulence of bacteria, and therefore are attractive targets for novel antibacterials.

New tools for RNA cell biology

Tens of thousands of non-coding RNAs have been discovered in the human transcriptome, and new tools for studying them in live cells are urgently needed.  Fluorescent RNAs offer the prospect of revolutionizing the study of RNA in the same way that green fluorescent protein (GFP) and its homologs transformed the study of proteins.  Through structure-guided engineering and optimization of fluorescent RNAs, we develop new tools for the analysis of expression, turnover, trafficking and localization of non-coding RNAs.