MARTHA J. FEDOR
Position: Professor
Citizenship: USA
Address:
Phone: (858) 784-2770
Email: mfedor@scripps.edu
FAX: (858) 784-2779
Department of Chemical Physiology,
Department of Cell and Molecular Biology and
The Skaggs Institute for Chemical Biology
The Scripps Research Institute, MB35
10550 North Torrey Pines Road
La Jolla, CA 92037
Education:
Institution
Degree
University of Michigan
Ann Arbor, Michigan
B.S.
1976
Zoology
University of California
Berkeley, California
Ph.D.
1982
Molecular Biology
Honors:
Year Conferred
Field
Leukemia Society of America Postdoctoral Fellow
Bank of America Giannini Foundation Postdoctoral Fellow
Phi Beta Kappa
Major Research Interests: Nucleic acids folding and function
Professional Positions:
2011 to present:
Professor - Department of Chemical Physiology
The Scripps Research Institute
2007 to 2011:
Associate Professor - Department of Chemical Physiology
The Scripps Research Institute
1997 to present
Associate Professor - Department of Molecular Biology and
The Skaggs Institute for Chemical Biology
The Scripps Research Institute
1991 to 1997
Assistant Professor - Department of Biochemistry and Molecular Biology
University of Massachusetts Medical Center
Area of Research: RNA Folding and Catalysis
1988 to 1990
Postdoctoral Fellow - Department of Chemistry and Biochemistry
University of Colorado at Boulder
Principal Investigator: Dr. Olke C. Uhlenbeck
Area of Research: Hammerhead Ribozyme Kinetic Mechanism
1982 to 1988
Postdoctoral Fellow - Department of Structural/Cell Biology
Stanford University School of Medicine
Principal Investigator: Dr. Roger D. Kornberg
Area of Research: Chromatin Structure of the GAL1-10 Transcription Unit
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1977 to 1982
Graduate Student - Department of Molecular Biology
University of California, Berkeley
Principal Investigator: Dr. Ellen Daniell
Area of Research: Adenovirus Chromatin Structure and Gene Regulation
Professional Activities:
Facilitator for Biochemistry, Molecular Genetics, Genetics, and Evolution Discussion Group at the
Center for Scientific Review’s Biomolecular Open House at the National Institutes of Health,
Bethesda, Maryland, December 18, 2007.
Ad hoc Review Panels
American Cancer Society Nucleic Acids and Proteins Scientific Review Committee, 1992.
American Cancer Society Institutional Research Grants Committee, Univ. Mass., February 1994.
Joint Infrastructure Fund, The Wellcome Trust, November 1999.
The Petroleum Research Fund, 2000.
The Wellcome Trust, 2000.
National Science Foundation, September 2001.
The Wellcome Trust. 2004.
Member, Quinquennial Review Committee of the Cancer Research UK Nucleic Acid Structure
Research Group at the University of Dundee, May 25th, 2004.
National Cooperative Drug Discovery Group for HIV Special Review Committee, NIH-NIAID, 1993.
NIH, GM A-2 Study Section, January 1994.
NIGMS MBRS Cellular and Molecular Biology Review Panel, October 2-3, 1996.
NIH, Molecular Biology Study Section, February 11-12, 1999.
NIH, Biochemistry Study Section, June 17-18, 1999.
NIGMS ZRG PBC BCS Special Emphasis Panel, March 5-6, 2002.
NIH, Biochemistry Study Section, October 17-18, 2002.
NIGMS ZRG PBC BCS Special Emphasis Panel, December 2-3, 2002.
NIH, EUREKA Peer Review Panel, February-April, 2009.
National Science Foundation, March 2009.
NIH, Basic Sciences Distinguished Editorial Panel, July 20-21, 2009.
Member, CSR College of Reviewers, January 2010 to present.
NIH, EUREKA Peer Review Panel, February-April, 2010.
NSABB Journal Editors' Roundtable on Current Review Practices for Dual-Use Research, NIH,
January 13, 2011.
Chair, NIH Program Project review panel, March 2011.
Quality and Renewal Panel, Uppsala University, March-May, 2011.
Natural Sciences Expert Panel for the Midterm Evaluation of Linnaeus Grants, February 2012,
Sweden.
Study Section Service
Member, NIH, Biochemistry Study Section, July 2003 through June 2004.
Member, NIH MSFA Study Section, July 2004 through February 2007.
Chair, NIH MSFE Study Section, February, 2007 through June, 2008.
Session Chair at Meetings
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Ribozymes Session Chair, American Society of Biochemistry and Molecular Biology / Biophysical
Society Meeting, Houston, Texas, February 9-13, 1992.
Session Coordinator, RNA Folding, RNA 2000, Madison, Wisconsin, May 30-June 4, 2000.
Session Chair, Catalytic Nucleic Acids, Nucleic Acids Gordon Research Conference, Salve Regina
University, Newport, Rhode Island, June 1-6, 2003.
Session Chair, Nucleic Acid Enzymology, Enzymes, Coenzymes & Metabolic Pathways Gordon
Research Conference, University of New England, July 13-18, 2008.
Session Coordinator, Catalytic RNA, RNA 2009, Madison, Wisconsin, May 26-31, 2010.
Meeting Organization
Co-organizer, RNA Based Life Meeting, Indiana University, November 16-18, 2001.
Co-organizer, RNA 2004, Ninth Annual Meeting of the RNA Society, Madison, Wisconsin, June 1-6,
2004.
Vice-Chair, Nucleic Acids Gordon Research Conference, Salve Regina University, Newport, Rhode
Island, June 6-11, 2004.
Co-chair, Nucleic Acids Gordon Research Conference, Salve Regina University, Newport, Rhode
Island, June 5-10, 2005.
Co-organizer, Chemical Biology of RNA Symposia, ASBMB Annual Meeting, April 2010.
Professional Society Service
Chair, RNA Society Nominations Committee, 1999.
Member, Board of Directors of the RNA Society, 2001-2002.
Chair, RNA Society Nominations Committee, 2005.
Co-Chair, RNA Society Junior Scientists Committee, 2009 to 2012.
Member, RNA Society Nominations Committee, 2011.
Professional Society Memberships
American Association for the Advancement of Science
American Chemical Society
American Society for Biochemistry and Molecular Biology
RNA Society
Editorial Boards
Member, Editorial Board of RNA, January 1, 2005 to present.
Member, Editorial Board of the Journal of Biological Chemistry, July 1, 2003 through March 15, 2006.
Associate Editor, Journal of Biological Chemistry, March 15, 2006 to December 31, 2010.
Editor in Chief, Journal of Biological Chemistry, January 1, 2011 to present.
Teaching (1997-2012):
Lecturer, Molecular Biology, 2000, 2002, 2004, 2005, 2006, 2007, 2008, 2009
Lecturer, Chemistry and Structure, 1998, 2000, 2002, 2003, 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012
Co-director, Moderator, Molecular Biology, 2010, 2011, 2012
Publications:
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Fedor, M. J. and Daniell, E. (1980) Acetylation of Histone-like Proteins of Adenovirus Type 5.
J. Virol., 35, 637-643.
Daniell, E., Groff, D.E., and Fedor, M. J. (1981) Structure of Adenovirus Chromatin at Different
Stages of Infection. Mol. Cell. Biol., 1, 1094-1105.
Fedor, M.J. (1982) Structure and Function of Adenovirus Chromatin. Ph.D. Dissertation.
University of California, Berkeley.
Daniell, E., Burg, J. L., and Fedor, M. J. (1982) DNA and Histone Synthesis in Butyrate-Inhibited
BSC-1 Cells infected with SV40. Virology, 116, 196-206.
Daniell, E. and Fedor, M. J. (1982) Transcription of Adenovirus Cores In Vitro: Major RNA
Products Differ from those made from a DNA Template. Proc. Natl. Acad. Sci., 79, 1834-1838.
Fedor, M. J. and Daniell, E. (1983) Ionic and Nonionic Interactions in Adenoviral Nucleoprotein
Complexes. J. Virol., 47, 370-375.
Fedor, M. J. and Daniell, E. (1983) DNase I Cleavage of Adenoviral Nucleoprotein. Nucleic Acids
Res., 11, 4417-4434.
Fedor, M. J., Lue, N. F., and Kornberg, R. D. (1988) Statistical Positioning of Nucleosomes by
Specific Protein-Binding to an Upstream Activating Sequence in Yeast. J. Mol. Biol., 204, 109-127.
Fedor, M. J. and Kornberg, R. D. (1989) Upstream Activating Sequence-Dependent Alteration of
Chromatin Structure and Transcription Activation of the Yeast GAL1-GAL10 Genes. Mol. Cell.
Biol., 9, 1721-1732.
Uhlenbeck O. C., Dahm, S. C., Ruffner, D. E., and Fedor, M. J. (1989) Structure and Mechanism of
the Hammerhead Self-cleaving Domain. Nucleic Acids Symp. Ser., 21, 95-96.
Fedor, M. J. and Uhlenbeck, O. C. (1990) Substrate Sequence Effects on "Hammerhead" RNA
Catalytic Efficiency. Proc. Natl. Acad. Sci., 87, 1668-1672.
Fedor, M. J. (1992) Chromatin Structure and Gene Expression. Current Opinion in Cell Biology, 4,
436-443.
Fedor, M. J. and Uhlenbeck, O. C. (1992) Kinetics of Intermolecular Cleavage by Hammerhead
Ribozymes. Biochemistry, 31, 12042-12054.
Fedor, M. J. (1994) A Slippery Grip. News and Views. Nature Structural Biology, 1, 267-269.
Hegg, L. A. and Fedor, M. J. (1995) Kinetics and Thermodynamics of Intermolecular Catalysis by
Hairpin Ribozymes. Biochemistry, 34, 15813-15828.
Fedor, M. J. (1997) Capturing a Speeding Locomotive. Book Review. Cell, 88, 589-592.
Donahue, C. P. and Fedor, M. J. (1997) Kinetics of Hairpin Ribozyme Cleavage in Yeast. RNA, 3,
961-973.
Nesbitt, S., Hegg, L. A. and Fedor, M. J. (1997) An Unusual pH-independent and Metal-IonIndependent Mechanism for Hairpin Ribozyme Catalysis. Chemistry & Biology, 4, 619-630.
Fedor, M. J. (1998) Ribozymes. Current Biology, 8, R441-R443.
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Nesbitt, S. M., Erlacher, H. A. and Fedor, M. J. (1999) The Internal Equilibrium of the Hairpin
Ribozyme: Temperature, Ion and pH Effects. J. Mol. Biol., 286, 1009-1024.
Fedor, M. J. (1999) Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation.
Biochemistry, 38, 11040-11050.
Fedor, M. J., Donahue, C. P. and Nesbitt, S. M. (2000) Hairpin Ribozyme Activity In Vitro and In
Vivo. In Ribozymes. Technology and Applications, pp. 205-226 (R.K. Gaur and G. Krupp, Eds.)
Eaton Publishing, Natick, MA.
Donahue, C. P., Yadava, R. S., Nesbitt, S. M. and Fedor M. J. (2000) The Kinetic Mechanism of the
Hairpin Ribozyme in Vivo: Influence of RNA Helix Stability on Intracellular Cleavage Kinetics. J.
Mol. Biol., 295, 693-707.
Fedor, M. J. (2000) Structure and Function of the Hairpin Ribozyme. Review. J. Mol. Biol., 297,
269-291.
Yadava, R. S., Choi, A. J., Lebruska, L. L. and Fedor, M. J. (2001) Hairpin Ribozymes with Fourway Helical Junctions Mediate Intracellular RNA Ligation. J. Mol. Biol. 309, 893-902.
Lebruska, L. L., Kuzmine, I. I., and Fedor M. J. (2002) Rescue of an Abasic Hairpin Ribozyme by
Cationic Nucleobases: Evidence for a Novel Mechanism of RNA Catalysis. Chemistry & Biology,
9, 465-473.
Fedor, M. J. (2002) The Role of Metal Ions in RNA Catalysis. Current Opinion in Structural
Biology, 12, 289-295.
Fedor, M. J. (2002) RNA Biochemistry From A to Z. Book review. Cell, 109, 20-22.
Fedor, M.J. (2002) The Catalytic Mechanism of the Hairpin Ribozyme. Biochemical Society
Transactions, 30(6), 1109-1115.
Fedor, M.J. and Westhof, E. (2002) Ribozymes: The First 20 Years. Meeting Report. Molecular
Cell, 10, 703-704.
Fedor, M.J. (2004) Determination of Kinetic Parameters for Hammerhead and Hairpin Ribozymes.
In Catalytic Nucleic Acid Enzymes, Methods in Molecular Biology, 252, 19-32, The Humana Press,
New Jersey.
Yadava, R.S., Mahen, E.M., and Fedor, M.J. (2004) Kinetic Analysis of Ribozyme-Substrate
Complex Formation in Yeast. RNA, 10(5), 863–879.
Kuzmin, Y.I., Da Costa, C.P., and Fedor, M.J. (2004) Role of an Active Site Guanine in Hairpin
Ribozyme Catalysis Probed by Exogenous Nucleobase Rescue, J. Mol. Biol., 340(2), 233-251.
Fedor, M.J. and Williamson, J.R. (2005) The catalytic diversity of RNAs. Solicited review. Nat.
Rev. Mol. Cell Biol. 6, 399-412.
Kuzmin, Y.I., Da Costa, C.P., Cottrell, J.W. and Fedor, M.J. (2005) Role of an Active Site Adenine
in Hairpin Ribozyme Catalysis. J. Mol. Biol. 349, 989–1010.
Mahen, E.M., Harger, J.H., Calderon, E.M., and Fedor, M.J. (2005) Kinetics and Thermodynamics
make Different Contributions to RNA Folding In Vitro and In Yeast. Mol. Cell. 19, 27-37.
Da Costa, C.P., Fedor, M.J. and Scott, L. (2007) 8-Azaguanine Reporter of Purine Ionization States
in Structured RNAs. J. Am. Chem. Soc., 129, 3426-3432.
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Cottrell, J.W., Kuzmin, Y.I. and Fedor M.J. (2007) Functional Analysis of Hairpin Ribozyme Active
Site Architecture. J. Biol. Chem., 282, 13498-13507.
Fedor, M.J. (2008) Alternative Splicing Minireview Series: Combinatorial Control Facilitates
Splicing Regulation of Gene Expression and Enhances Genome Diversity. J. Biol. Chem., 283, 12091210.
Fedor, M.J. (2009) Comparative Enzymology and Structural Biology of RNA Self-Cleavage. Annu.
Rev. Biophys. 38, 271-299.
Liu, L., Cottrell, J.W., Scott, L.G. and Fedor M.J. (2009) Direct Measurement of the Ionization State
of an Essential Guanine in the Hairpin Ribozyme. Nat. Chem. Biol., 5, 351-357.
Watson, P.Y. and Fedor, M.J. (2009) Determination of Intracellular RNA Folding Rates using Selfcleaving RNAs. Methods Enzymol. 468, 259-286.
Mahen, E.M., Watson, P.Y., Cottrell, J.W. and Fedor, M.J. (2009) mRNA Secondary Structures Fold
Sequentially but Exchange Rapidly In Vivo. PLoS Biol. 8(2), e1000307. PMID: 20161716
Watson, P.Y. and Fedor, M.J. (2011) The glmS Riboswitch Integrates Signals from Activating and
Inhibitory Metabolites In Vivo, Nat. Struct. Molec. Biol. 18(3), 359-363.
Cottrell, J.W., Scott, L.G., and Fedor, M.J. (2011) The pH Dependence of Hairpin Ribozyme
Catalysis Reflects Ionization of an Active Site Adenine. J. Biol. Chem. 286, 17658-17664.
Viladoms, J., Scott, L.G. and Fedor, M.J. (2011) An Active-site Guanine Participates in glmS
Ribozyme Catalysis in its Protonated State. J. Am. Chem. Soc., 133, 18388-18396.
Watson, P.Y., Fedor, M.J. (2012) The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis.
Nature Chem. Biol., 8(12), 963-965.
Viladoms, J. and Fedor, M.J. (2012) The glmS ribozyme cofactor is a general acid-base catalyst. J.
Am. Chem. Soc., 134(46), 19043-19049.
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