Raymond Trievel, Ph.D.

Associate Professor, Biological Chemistry

4301C MSRB3, Box 5606

(734) 647-0889

Appointments

Biological Chemistry, Medical School

Areas of Interest

The Trievel laboratory uses a combination of biochemical and biophysical approaches to study the structures, mechanisms, and substrate specificities of a variety of enzymes, with a particularly focus on chromatin modifying enzymes. Techniques used in the lab include crystallography, enzyme kinetics, calorimetry, and other biophysical and biochemical approaches. Current projects include:

1) Structural and functional studies of chromatin modifying enzymes: Our laboratory utilizes biochemical and structural approaches to investigate the mechanisms of enzymes that catalyze chromatin modifications with a particular emphasis on lysine methyltransferase and demethylases. We are also developing new assays and reagents that will facilitate high-throughput characterization of these enzymes. Our collective efforts are yielding insight into the molecular mechanisms underlying the establishment and maintenance of chromatin modification states and will furnish avenues for developing novel therapeutics that target lysine methyltransferases and demethylases to treat cancer and other chromatin modification-linked diseases.

2) Mechanisms of S-Adenosylmethionine (AdoMet)-dependent methyltransferases: AdoMet-dependent methyltransferases methylate a wide array of biological substrates, including proteins, DNA, RNA, carbohydrates, and small molecules. A survey of high-resolution crystal structures has revealed that unconventional carbon-oxygen (CH---O) hydrogen bonds coordinate the AdoMet methyl group in all classes of methyltransferases. Biochemical, crystallographic, computational, and NMR dynamic analyses of the lysine methyltransferase SET7/9 demonstrate that CH---O hydrogen bonds are important for AdoMet binding and catalysis, and appear to promote methyl transfer by restricting methyl motion and stabilizing the transition state. Together, these results yield insights into AdoMet recognition and catalysis in AdoMet-dependent methyltransferases and illustrate that methyl CH---O hydrogen bonding represents a convergent evolutionary feature of these enzymes that mediates a universal mechanism for methyl transfer.

3) Structure-function studies and high-throughput screening (HTS) for inhibitors of homocitrate synthase (HCS), a target for antifungal drug design: HCS catalyzes the first and committed step in lysine biosynthesis in fungi by condensing 2-oxoglutarate and acetyl-CoA to yield homocitrate. This enzyme is essential to lysine homoeostasis and is a target for the discovery of new antifungal drugs to treat aspergillosis. We have determined the first crystal structure of HCS, yielding insights into its catalytic mechanism and feedback inhibition by L-lysine. In addition, we have completed a pilot HTS for inhibitors of HCS and identified several compounds with IC50 values in the low micromolar range. These results provide a foundation for a large scale HTS and for evaluation of the efficacy of the inhibitors in blocking the growth of Aspergillus fumigatus, the fungal pathogen that is primarily responsible for aspergillosis.

Laboratory Members:

Paul A Del Rizzo, Postdoctoral Fellow

Graduate Program Affiliations

Biological Chemistry Graduate Program
Biophysics Graduate Program
Cellular Biotechnology Training Program
Cellular & Molecular Biology Program
Chemical Biology Doctoral Program
Chemical Biology Interface Training Program

Lab Alumni

Stacie Bulfer (Biological Chemistry Graduate Student, 2005-2010) – Postdoctoral Fellow, University of California San Francisco (Michelle Arkin)
Jean-Francois Couture (Postdoctoral Fellow, 2004-2007) – Associate Professor of Biochemistry, Microbiology and Immunology, University of Ottawa
Paul Del Rizzo (Postdoctoral Fellow, 2008-2013) – Research Scientist, Cayman Chemical
Glenn Hauk (Biochemistry Undergraduate Student, 2004) – Postdoctoral Fellow, Johns Hopkins University (James Berger)
Scott Horowitz (Biophysics Graduate Student, 2009-2013) – Postdoctoral Fellow, University of Michigan (James Bardwell)
Swathi Krishnan (Biological Chemistry Graduate Student, 2009-2012) – Postdoctoral Fellow, New York University (Danny Reinberg)
Jennifer Nimtz (Biochemistry Undergraduate Student, 2011-2012) – MD Student, Michigan State University
Patricia Amparo Ortiz-Tello (Biochemistry Undergraduate Student, 2005-2007) – MD/PhD Student, Stanford University

Honors & Awards

2010 Margaret C. Etter Early Career Award, American Crystallographic Association
2010 University of Michigan Basic Science Research Award
2004 NIH Fellowship Award for Research Excellence
2003 Keystone Symposium Scholarship
2000-2003 Intramural Research Training Fellowship, National Institutes of Health
1996-2000 Howard Hughes Medical Institute Predoctoral Fellowship

Published Articles or Reviews

Bulfer SL, Scott EM, Pillus L, Trievel RC. (2010) Structural basis for L-lysine feedback inhibition of homocitrate synthase. J Biol Chem. 2010 Jan 19 [Epub ahead of print]. PMID: 20089861

Bulfer S.L., Scott E.M., Couture J.-F., Pillus L., and Trievel R.C. (2009) Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis. J Biol Chem. 284, 35769-35780. PMID: 19776021

Takahashi Y.H., Lee J.S., Swanson S.K., Saraf A., Florens L., Washburn M.P., Trievel R.C., and Shilatifard A. (2009) Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1. Mol Cell Biol. 29, 3478-3486. PMID: 19398585

Raunser S., Magnani R., Huang Z., Houtz R.L., Trievel R.C., Penczek P.A., and Walz T. (2009) Rubisco in complex with Rubisco large subunit methyltransferase. Proc Natl Acad Sci USA. 106, 3160-3165. PMID: 19208805

Couture J.-F., Dirk L.M., Brunzelle J.S., Houtz R.L., and Trievel R.C. (2009) Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci USA. 105, 20659-64. PMID: 19088188

Couture J.-F., Collazo E., Ortiz-Tello P.A., Brunzelle J.S., and Trievel R.C. (2007) Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol. 14, 689-695. PMID: 17589523

Couture J.-F., Collazo E., and Trievel R.C. (2006) Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol. 13, 140-146. PMID: 16829960

Couture J.-F., Hauk G., Thompson M.J., Blackburn G.M., and Trievel R.C. (2006) Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases. J Biol Chem. 281, 19280-19287. PMID: 16682405

Couture J.-F., Collazo E., Hauk G., and Trievel R.C. (2006) Structural basis for the methylation site specificity of SET7/9. Nat Struct Mol Biol. 13, 140-146. PMID: 16415881

Couture J.-F., Collazo E., Brunzelle J., and Trievel R.C. (2005) Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev. 19, 1455-1465. PMID: 15933070

Collazo E., Couture J.-F., Bulfer S., and Trievel R.C. (2005) A coupled fluorescent assay for histone methyltransferases. Anal. Biochem. 342, 86-92. PMID: 15958184

Select Research Articles Horowitz S, Adhikari U, Dirk LM, Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, and Trievel RC. (2014) Manipulating Unconventional CH-Based Hydrogen Bonding in a Methyltransferase via Noncanonical Amino Acid Mutagenesis. ACS Chem Biol. 9, 1692-7.

Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, and Trievel RC. (2013) Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc. 135, 15536-48.

Krishnan S and Trievel RC. (2013) Structural and functional analysis of JMJD2D reveals molecular basis for site-specific demethylation among JMJD2 demethylases. Structure. 21, 98-108.

Krishnan S, Collazo E, Ortiz-Tello PA, and Trievel RC. (2012) Purification and assay protocols for obtaining highly active Jumonji C demethylases, Anal Biochem. 420, 48-53.

Horowitz S, Yesselman JD, Al-Hashimi HM, and Trievel RC. (2011) Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. J. Biol. Chem. 286, 18658-63.

Bulfer SL, McQuade TJ, Larsen MJ, and Trievel RC. (2011) Application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. Anal Biochem. 410, 133-40.

Del Rizzo PA, Couture J-F, Dirk LM, Strunk BS, Roiko MS, Brunzelle JS, Houtz RL, and Trievel RC. (2010) SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation. J. Biol. Chem. 285, 31849-58.

Bulfer SL, Scott EM, Pillus L, and Trievel RC. (2010) Structural basis for L-lysine feedback inhibition of homocitrate synthase. J Biol Chem. 285, 10446-53.

Bulfer SL, Scott EM, Couture JF, Pillus L, Trievel RC. (2009) Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis. J Biol Chem. 284, 35769-80.

Couture J-F, Dirk LM, Brunzelle JS, Houtz RL, and Trievel RC. (2008) Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci USA. 105, 20659-64.

Couture J-F, Collazo E, Ortiz-Tello PA, Brunzelle JS, and Trievel RC. (2007) Specificity and Mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol. 14, 689-95.

Couture J-F, Collazo E, and Trievel RC. (2006) Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol. 13, 698-703.

Couture J-F, Hauk G, Thompson MJ, Blackburn GM, and Trievel RC. (2006) Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases, J Biol Chem. 281, 19280-7.

Couture J-F, Collazo E, Hauk G, and Trievel RC. (2006) Structural basis for the methylation site specificity of SET7/9. Nat Struct Mol Biol. 13, 140-6.

Couture J-F, Collazo E, Brunzelle JS, and Trievel RC. (2005) Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev. 19, 1455-65.

Collazo E, Couture J-F, Bulfer S, and Trievel RC. (2005) A coupled fluorescent assay for histone methyltransferases. Anal Biochem. 342, 86-92.

Invited Reviews Del Rizzo PA and Trievel RC. (2014) Molecular basis for substrate recognition by lysine methyltransferases and demethylases. Biochim Biophys Acta. Advanced online publication.

Fick RJ and Trievel RC. (2013) An overview of chromatin modifications. Biopolymers. 99, 95-7.

Horowitz S and Trievel RC. (2012) Carbon-oxygen hydrogen bonding in biological structure and function. J Biol Chem. 287, 41576-82.

Del Rizzo PA and Trievel RC. (2011) Substrate and product specificities of SET domain methyltransferases. Epigenetics. 6, 1059-67.

Krishnan S, Horowitz S, and Trievel RC. (2011) Structure and function of histone H3 lysine 9 methyltransferases and demethylases. Chembiochem. 12, 254-63.