profile

Adrian R. Ferré-D'Amaré, Ph.D.

Senior Investigator

50 South Dr
Bethesda, MD 20814
United States

301-496-4096

Biography

Adrian R. Ferré-D'Amaré graduated from the Instituto Tecnológico y de Estudios Superiores de Monterrey in Mexico in 1990 with a B.S. in chemistry. He earned a Ph.D. in molecular biophysics from The Rockefeller University in 1995. He was a Jane Coffin Childs postdoctoral fellow at Yale University from 1995 to 1999. Dr. Ferré-D'Amaré was a Member of the Fred Hutchinson Cancer Research Center and an Affiliate Professor of Biochemistry at the University of Washington, Seattle, from 1999 to 2011. He was also an Investigator of the Howard Hughes Medical Institute (HHMI) from 2008 to 2011. He resigned from HHMI and joined the NHLBI in 2011 as a Senior Investigator and Chief of the Laboratory of RNA Biophysics and Cellular Physiology. Dr. Ferré-D'Amaré was a Rita Allen Foundation Scholar from 2001 to 2004, received the Eli Lilly and Company Research Award from the American Society for Microbiology in 2004 and was a Distinguished Young Scholar in Medical Research of the W.M. Keck Foundation from 2003 to 2008. Dr. Ferré-D'Amaré has authored or coauthored more than 100 papers. He is on the editorial board of the journal RNA and has served on many review panels for the National Institutes of Health, the National Science Foundation, as well as foreign and international scientific organizations.

Research

Research Interests
- Adrian R. Ferré-D'Amaré, Ph.D.

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.

Catalytic RNAs
- Adrian R. Ferré-D'Amaré, Ph.D.

RNAS

Catalytic RNAs (also called ribozymes) are responsible for essential physiologic functions in all organisms. An atomic-level understanding of their mechanism of action that is grounded in the principles of physics and chemistry is a prerequisite for the manipulation of ribozyme function in health and disease. By determining their crystal structures in multiple functional states, we have generated 'molecular movies' of the hairpin and glmS ribozymes in action. These studies revealed how ribozymes can preferentially stabilize the transition state of their reactions, and how the glmS ribozyme can employ a small molecule as a coenzyme. We have also analyzed several artificial ribozymes with biotechnological applications, including an RNA ligase ribozyme and flexizyme, an aminoacil-tRNA synthetase.

• Lau, M.W.L & Ferré-D'Amaré, A.R. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nature Chemical Biology 9, 805-810 (2013). [abstract]

• Ferré-D'Amaré, A.R. & Scott, W.G. The small self-cleaving ribozymes. Cold Spring Harbor Persp. Biol. (published online September 15, 2010). [abstract]

• Xiao, H., Murakami, H., Suga, H. & Ferré-D'Amaré, A.R. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

• Klein, D.J., & Ferré-D’Amaré, A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313, 1752-1756 (2006). [abstract]

• Rupert, P.B., Massey, A., Sigurdsson, S.Th. & Ferré-D'Amaré, A.R. Transition state stabilization by a catalytic RNA. Science 298, 1421-1424 (2002). [abstract]

Gene Regulatory RNAs
- Adrian R. Ferré-D'Amaré, Ph.D.

gene regulatory Non-coding RNAs play diverse roles in the control of the flow of genetic information, cellular homeostasis and adaptation, and virulence. Riboswitches are non-coding mRNA domains that directly bind to cognate ligands and modulate transcription, translation or splicing. Riboswitches have been discovered in archaea, bacteria and eukarya. We have studied bacterial riboswitches that respond to the intracellular concentration of a variety of metabolites such as vitamin B1, glucosamine-6-phosphate, and preQ1, that respond to starvation for specific amino acids, and that sense the concentration of molecules responsible for intracellular signaling (second messengers) such as c-di-AMP, c-di-GMP, and ZMP. Riboswitches control essential metabolic and signaling pathways in pathogenic bacteria, and represent attractive targets for the development of novel antibiotics. Moreover, our studies have led to the discovery of general principles for the function of non-coding RNAs, including mechanisms for RNA:RNA recognition and the use of quaternary and pseudo-quaternary structure for specificity, cooperativity and allostery.

• Jones, C.P. & Ferré-D'Amaré, A.R. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nature Struct. Mol. Biol. 22, 679-685 (2015). [abstract]

• Jones, C.P., & Ferré-D'Amaré, A.R. RNA quaternary structure and global symmetry. Trends Biochem. Sci. 40, 211-220 (2015). [abstract]

• Zhang, J. & Ferré-D'Amaré, A.R. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-366 (2013) [abstract]

• Zhang, J., Lau, M. & Ferré-D'Amaré, A.R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49, 9123-9131 (2010). [abstract]

• Klein, D.J., Edwards, T.E. & Ferré-D'Amaré, A.R. Cocrystal structure of a class-I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nature Struct. Mol. Biol. 16, 343-344 (2009). [abstract]

RNA-Protein Interactions
- Adrian R. Ferré-D'Amaré, Ph.D.

protein Many cellular proteins associate with RNAs either transiently or long-term to form ribonucleoprotein (RNP) complexes. Of particular interest have been (1) helicases, enzymes that remodel nucleic acid secondary structures; and (2) pseudouridine synthases, enzymes that catalyze the post-transcriptional modification of specific uridine residues to pseudouridines. Among many cellular helicases, DEAH helicases are noteworthy because of their activities range from remodeling of simple nucleic acid structures (such as duplexes and quadruplexes) to the reorganization of RNA within large RNPs. We have characterized, structurally and biophysica lly, DHX36, a helicase that exhibits stringent selectivity for G-quadruplex nucleic acids, finding that it employs binding energy alone for repetive unfolding, and requires ATP for substrate release. Recognition of G-quadruplexes by DHX36 regulates processes ranging from transcription to translation, and its deletion in mouse abrogates hematopiesis. Pseudouridine synthases are universally distributed, and their structural analysis revealed important new principles of RNA recognition by proteins including base flipping and recognition through enforced secondary structure. This led us to suggest that some of these enzymes, such as TruB, may primarily function as chaperones for RNA folding. The box H/ACA RNP is a multi-protein pseudouridine synthase that is conserved from archaea to humans, and it is required for a variety of biological processes: post-transcriptional RNA modification, ribosome biogenesis, and telomerase assembly and stability. In humans, mutations in either the RNA or protein subunits of this RNP result in dyskeratosis congenita, a disease that affects actively proliferating tissues (such as skin, intestinal lining and bone marrow –the latter linked to hematopoietic dysfunction). We have also successfully exploited RNP formation as strategy to improve the crystallizability of RNAs.

• Chen, M.C., Tippana, R., Demeshkina, N.A., Murat, P., Balasubramanian, S., Myong, S., & Ferré-D'Amaré, A.R. Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558,465-469 (2018). [abstract]

• Ferré-D'Amaré, A.R. Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs Methods 52: 159-167 (2010). [abstract]

• Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S. Mueller, E.G. & Ferré-D’Amaré, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24, 535-545 (2006). [abstract]

• Hamma, T., Reichow, S.L., Varani, G., & Ferré-D’Amaré, A.R. The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nature Struct. Mol. Biol. 12, 1101-1107 (2005). [abstract]

• Hoang, C. & Ferré-D'Amaré, A.R. Cocrystal structure of a tRNA Ψ55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107, 929-939 (2001). [abstract]

RNA Analogs of GFP
- Adrian R. Ferré-D'Amaré, Ph.D.

Analogs Tens of thousands of small and large non-coding RNAs have been identified in the human transcriptome, and new molecular tools are urgently needed to analyze their synthesis and turnover, transport and localization. While green fluorescent protein (GFP) and its many derivatives can be used to tag cellular RNAs, such an approach suffers from the large size of the tag (often many times larger than the RNA of interest), cryptic localization signals in the protein, slow maturation of the intrinsic chromophre of the protein, and high background fluorescence due to unbound protein. Fluorescent RNA analogs of GFP offer a fundamentally different and promising approach to the in vivo analysis of non-coding RNAs. Our crystallographic characterization of Spinach, an in vitro selected RNA that when bound to its exogenous chromophore is brighter than GFP and can be used to visualize RNAs in live cells, revealed an unprecedented structure built around a G-quadruplex. We are employing structure-guided engineering approaches to optimize Spinach as well as other fluorescent RNAs that are analogs of, among others, yellow and red fluorescent proteins (YFP and RFP).

• Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., & Ferré-D'Amaré, A.R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature Struct. Mol. Biol. 21, 658-663 (2014). [abstract]

• Warner, K.D., Sjekloca, L., Song, W., Filonov, G.S., Jaffrey, S.R., & Ferré-D'Amaré, A.R. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nature Chem. Biol. 13, 1195-1201 (2017).[abstract]

• Trachman, R.J. III, Demeshkina, N.A., Lau, M.W.L., Panchapakesan, S.S.S., Jeng, S.C.Y., Unrau, P.J., & Ferré-D'Amaré, A.R. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nature Chem. Biol. 13, 807-813 (2017). [abstract]

• Trachman, R.J. III, Truong, L., & Ferré-D'Amaré, A.R. Structural principles of fluorescent RNA aptamers. Trends Pharacol. Sci. 38, 928-939 (2017). [abstract]

RNA in Signal Transduction
- Adrian R. Ferré-D'Amaré, Ph.D.

Transduction Riboswitches sense the intracellular concentration of small molecules and respond by altering transcription, translation or splicing of specific groups of genes. Of particular interest are bacterial riboswitches that respond to the concentration of intracellular signals (second messengers) such as c-di-AMP, c-di-GMP, and ZMP. These second messengers are broadly employed by bacteria to respond to extracellular insults, to control changes in lifestyle (e.g., from motile or planktonic to sessile) and to address imbalances in intermediate metabolism. The second messenger c-di-GMP (cyclic diguanylate) is critical for biofilm formation. Biofilms are typically refractory to antibiotics and other bactericidal and bacteriostatic interventions, and because they colonize most medical devices, are a major cause of human morbidity and mortality in clinical settings. C-di-GMP riboswitches control a diverse set of genes in many pathogenic bacteria. Our study of these riboswitches is important for understanding the signaling pathways that lead to bacterial adaptation, virulence, and the mammalian immune response, and may lead to riboswitch-targeted strategies to overcome bacterial infections.

• Jones, C.P. & Ferré-D'Amaré, A.R. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nature Struct. Mol. Biol. 22, 679-685 (2015). [abstract]

• Baird, N.J., Inglese, J., & Ferré-D'Amaré, A.R. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nature Comm. 6, 8898 (2015). [abstract]

• Jones, C.P., & Ferré-D'Amaré, A.R. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. EMBO J. 33, 2692-2703 (2014). [abstract]

• Wood, S., Ferré-D'Amaré, A.R. & Rueda, D. Allosteric tertiary interactions pre-organize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem. Biol. 7, 920-927 (2012). [abstract]

• Kulshina, N., Baird, N.J., & Ferré-D'Amaré, A.R. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nature Struct. Mol. Biol. 16, 1212-1217 (2009). [abstract]

Small Molecule Recognition by RNA
- Adrian R. Ferré-D'Amaré, Ph.D.

molecule The ability of RNAs to interact specifically with small molecules underlies their function as ribozymes and riboswitches. We employ X-ray crystallography to determine the stereochemical principles of RNA-small molecule interactions, and a variety of biochemical and biophysical methods (such as calorimetry, various spectroscopies, light and X-ray scattering and hydrodynamics) to characterize their kinetics and thermodynamics. The majority of antibiotics in clinical use target the RNA component of the ribosome. Thus, RNA is a validated target for clinical intervention with small-molecule therapeutics. We employ a combination of synthetic chemistry, in vitro and in vivo screening and structural biology to discover new ligands to RNAs and to develop them into high-affinity, high specificity binders. These efforts to modulate RNA function with small molecules aim to lay the foundation for the discovery of antibiotic classes that function through previously untapped biological pathways.

• Baird, N.J., Inglese, J., & Ferré-D'Amaré, A.R. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nature Comm. 6, 8898 (2015). [abstract]

• Warner, K.D., & Ferré-D'Amaré, A.R. Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches. Meth. Enzymol. 549C, 221-233 (2014). [abstract]

• Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C. & Ferré-D'Amaré, A.R. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595 (2014). [abstract]

• Deigan, K.E. & Ferré-D'Amaré, A.R. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc. Chem. Res. 44, 1329-1338 (2011). [abstract]

• Edwards, T.E., & Ferré-D’Amaré, A.R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14, 1459-1468 (2006). [abstract]

RNA Folding and Dynamics
- Adrian R. Ferré-D'Amaré, Ph.D.

folding Biological functions of RNA such as small molecule recognition and catalysis require that RNAs fold into complex three-dimensional structures that are specified by their sequences. Moreover, different moieties of these folded structures sample a variety of conformations at diverse timescales. Crystallographic studies elucidate the folded conformations of RNAs, and can indirectly provide information on dynamics. For instance, comparison of structures of the domains of the hairpin ribozyme free and docked demonstrated that this RNA undergoes dramatic rearrangements upon assembly. Yet, its active site is remarkably rigid once assembled. Structural, biochemical and in vitro evolution studies of flexizyme suggest that this artificial ribozyme takes advantage of flexibility to achieve higher substrate specificity through induced fit. Examination of riboswitches bound to diverse ligands indicates that the conformation and stability of these gene-regulatory RNAs are modulated by the small molecules. Direct examination of folding and flexibility by small-angle X-ray scattering confirms this.

• Baird, N.J., & Ferré-D'Amaré, A.R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19, 167-176 (2013). [abstract]

• Baird, N.J. & Ferré-D'Amaré, A.R. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA 16, 598-609 (2010). [abstract]

• Xiao, H., Murakami, H., Suga, H. & Ferré-D'Amaré, A.R. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

• Klein, D.J., Been, M.D. & Ferré-D'Amaré, A.R. Essential role of an active-site guanine in glmS ribozyme catalysis. J. Am. Chem. Soc. 129, 14858-14859 (2007). [abstract]

• Rupert, P.B. & Ferré-D’Amaré, A.R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786 (2001). [abstract]

Molecular Evolution
- Adrian R. Ferré-D'Amaré, Ph.D.

evolution The process of evolution can readily be studied in vitro with RNA because this nucleic acid can function both as a repository of genetic information and as a catalyst. We have developed methodology that combines in vitro selection of RNA with next-generation DNA sequencing technology that allows the rapid analysis of the fitness landscape of RNAs. This approach can be extended to the study of clinically important biological systems in which diversity is generated, for instance the immune system and virus-host genetic interactions. Our structural and biochemical studies also have resulted in the comparison of mechanistic strategies employed by naturally an artificially evolved RNAs, and of the delineation of the evolutionary history of RNA-modifying enzymes.

• Lau, M.W.L & Ferré-D'Amaré, A.R. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nature Chemical Biology 9, 805-810 (2013). [abstract]

• Pitt, J.N. & Ferré-D'Amaré, A.R. Rapid construction of empirical RNA fitness landscapes. Science 330, 376-379 (2010). [abstract]

• Pitt, J.N. & Ferré-D'Amaré, A.R. Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J. Am. Chem. Soc. 131, 3532-3540 (2009). [abstract]

• Xiao, H., Murakami, E., Suga, H. & Ferré-D'Amaré, A.R. Structural basis for specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

• Xiao, H., Edwards, T.E. & Ferré-D'Amaré, A.R. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem. Biol. 15, 1125-1137 (2008). [abstract]

Methods
- Adrian R. Ferré-D'Amaré, Ph.D.

Methods New methods drive progress in the experimental sciences. In addition to the development of techniques for the synthesis and characterization of biological molecules, we have a long-standing interest in methods to enable the preparation of highly-ordered crystals of nucleic acids, proteins, and their complexes. These are key to their structure determination by X-ray crystallography. Important advances include domain elucidation by mass spectrometry, construct engineering to improve crystallizability, and pre-crystallization analysis of monodispersity. Another area of biomedical research where we have contributed new methods is in the analysis of in vitro selection experiments.

• Lau, M.W. & Ferré-D'Amaré, A.R. In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods (2016). [abstract]

• Baird, N.J., Inglese, J., & Ferré-D'Amaré, A.R. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nature Comm. 6, 8898 (2015). [abstract]

• Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C. & Ferré-D'Amaré, A.R. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595 (2014). [abstract]

• Zhang, J., & Ferré-D'Amaré, A.R. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22, 1363-1371 (2014). [abstract]

• Pitt, J.N., Rajapakse, I., & Ferré-D'Amaré, A.R. SEWAL: an open-source platform for next-generation sequence analysis and visualization. Nucleic Acids Res. 38, 7908-7915 (2010). [abstract]

Publications