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Scholarly Interest Report
         
Ronald J. Parry
Professor Emeritus
Professor Emeritus of Chemistry and Biochemistry and Cell Biology
 
e-mail:parry@rice.edu
 
  • B.A. (1964) Occidental College Chemistry (1964)
  • Ph.D. (1968) Brandeis University Organic Chemistry (1968)
 
Primary Department
   Department of Chemistry
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Department Affiliations
 
  • Department of BioSciences
  • Institute of Biosciences and Bioengineering
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    Websites
     Parry Research Group
     
    Research Areas
     Biosynthesis, Mechanistic Enzymology, Molecular Biology
     
    Research Statement
     Professor Parry's research interests are concerned with the biosynthesis of natural products and the mechanisms of enzymatic reactions. The current trend in these studies places an emphasis on the characterization of interesting biosynthetic reactions at the enzymatic level and on the application of molecular biology to the study of secondary metabolism. Recent publications have included investigations of the biosynthesis of the phytotoxin coronatine, the antibiotic aristeromycin, the antitumor agents sparsomycin and valanimycin.
     
    Research Statement
     Research in our laboratory is focused upon the biosynthesis of secondary metabolites, otherwise known as natural products. Many of these compounds exhibit a high degree of chemical complexity as well as important biological activity. Examples of such compounds include the important antibiotics erythromycin, penicillin, and vancomycin. The goals of our research are to discover novel biochemical reactions associated with specific biosynthetic pathways and to engineer biosynthetic gene clusters to produce new compounds with desirable biological activity.

    Several natural products are currently under intensive study in our laboratories. One of these compounds is the antitumor antibiotic valanimycin, an azoxy compound produced by Streptomyces viridifaciens. Valanimycin is a member of a growing class of natural products that contain N-N bonds. Although compounds with N-N bonds are widespread, little is known at present about the biochemistry involved in N-N bond formation. A major goal of this project is to discover the nature of the N-N bond forming chemistry. The entire cluster of genes required for valanimycin biosynthesis has now been cloned and sequenced, but the genes encoding the proteins responsible for N-N bond formation have not yet been identified.

    Two other ongoing projects are concerned with the biosynthesis of the phytotoxin coronatine and the biosynthesis of the antibiotics of the pyrrolomycin complex. Coronatine and the pyrrolomycins possess unusual structural features indicating that novel biochemistry is involved in their biosynthesis.
     
    Selected Publications
     Refereed articles
     

    R. J. Parry, S. Nishino, and J. Spain "Naturally-occurring Nitro Compounds." Nat. Prod. Rep., 28 (2011) : 152-167.

     
     

    D. R. Bignell, R. F. Seipke, J. C. Huguet-Tapia, A. H. Chambers, R. J. Parry, and R. Loria "Streptomyces scabies 87-22 contains a coronafacic acid-like biosynthetic gene cluster that contributes to plant-microbe interactions." Mol. Plant Microbe Interact, 23 (2010) : 161-175.

     
     

    Ram P. Garg and Ronald J. Parry "Regulation of valanimycin biosynthesis in Streptomyces Viridifaciens: characterization of VlmI as a Streptomyces antibiotic regulatory protein (SARP)." Microbiology, 156 (2010) : 472-483.

     
     

    Evan G. Johnson, Stuart B. Krasnoff, Dawn R. Bignell, Wen-Chuan Chung, Tao Tao, Ronald J. Parry, Rosemary Loria, and Donna M. Gibson "4-Nitrotryptophan is a Substrate for the Non-ribosomal Peptide Synthetase TxtB in the Thaxtomin A Biosynthetic Pathway ." Mol. Microbiol., 73 (2009) : 409-418.

     
     

    Ram P. Garg, Lawrence B. Alemany, Sean Moran, and Ronald J. Parry "Identification, Characterization, and Bioconversion of a New Intermediate in Valanimycin Biosynthesis ." J. Am. Chem. Soc., 131 (2009) : 9608-9609.

     
     

    R. P. Garg, X. L. Qian, L. B. Alemany, S. Moran, R. J. Parry "Investigations of Valanimycin Biosynthesis: Elucidation of the Role of Seryl-tRNA." Proc. Natl. Acad. Sci. U.S.A., 105 (2008) : 6543-6547.

     
     

    Xiujun Zhang, Lawrence B. Alemany, Hans-Peter Fiedler, Michael Goodfellow, and Ronald J. Parry "Biosynthetic Investigations of Lactonamycin and Lactonamycin Z: Cloning of the Biosynthetic Gene Clusters and Discovery of an Unusual Starter Unit." Antimicrob. Agents ChemotherIn Press

     
     

    Zhang, X., and Parry, R.J. "Cloning and characterization of the pyrrolomycin biosynthetic gene clusters from Actinosporangium vitaminophilum ATCC 31673 and Streptomyces sp. UC 11065." Antimicrob. Agents Chemother., 51 (2007) : 946-957.

     
     

    Heather F. Seidle, Robin D. Couch, and Ronald J. Parry "Characterization of a non-specific phosphopanthetheinyl transferase from Pseudomonas syringae pv syringae FF5." Arch. Biochem. Biophys, 446 (2006) : 167-174.

     
     

    Ram P. Garg, Jose M. Gonzalez, and Ronald J. Parry "Biochemical characterization of VlmL, a seryl tRNA synthetase encoded by the valanimycin biosynthetic gene cluster." J. Biol. Chem., 281 (2006) : 26785-26791.

     
     

    H. Seidle, V. Rangaswamy, R. Couch, C. L. Bender, and R. J. Parry "Characterization of Cfa1, a monofunctional acyl carrier protein involved in the biosynthesis of the phytotoxin coronatine." J. Bacteriol., 186 (2004) : 2499-2503.

     
     

    M. R. Buddha, T. Tao, R. J. Parry, and B. R. Crane "Regioselective nitration of tryptophan by a complex between bacterial nitric-oxide synthase and tryptophanyl-tRNA synthetase." J. Biol. Chem., 279 (2004) : 49567-49570.

     
     

    R. Couch, S. E. O'Connor, H. Seidle, C. T. Walsh, and R. J. Parry "Characterization of CmaA, an adenylation/thiolation didomain enzyme involved in the biosynthesis of coronatine." J. Bacteriol., 186 (2004) : 35-42.

     
     

    Couch, R., O'Connor, S.E., Seidle, H., Walsh, C.T., and Parry, R. "Characterization of CmaA, an adenylation/thiolation didomain enzyme involved in the biosynthesis of coronatine ." J. Bacteriol, 186 (2004) : 35-42.

     
     

    Seidle, H., Rangaswamy, V., Couch, R., Bender, C.L., and Parry, R.J. "Characterization of Cfa1, a monofunctional acyl carrier protein required for the biosynthesis of the phytotoxin coronatine ." J. Bacteriol., 186 (2004) : 24499-2503.

     
     

    Tao, T., Alemany, L.B., and Parry, R.J. "Valanimycin biosynthesis. Investigations of the mechanism of isobutylhydroxylamine incorporation ." Organic Lett., 5 (2003) : 1213-1215.

     
     

    Couch, R.D., Seidle, H., and Parry, R. "Construction of expression vectors to produce affinity tagged proteins in Pseudomonas." Biotechniques, 32 (2002) : 1230-1237.

     
     

    Garg, R.P., Ma, Y., Hoyt, J.C., and Parry, R. "Molecular characterization and analysis of the biosynthetic gene cluster for the azoxy antibiotic valanimycin." Molecular Microbiology, 46 (2002) : 505-517.

     
     

    Jiralerspong, S., Rangaswamy, V., Bender, C.L., and Parry, R.J. "Analysis of the enzymatic domains in the modular portion of the coronafacic acid polyketide Synthase.." Gene., 270 (2001) : 191-200.

     
     

    Ma, Y., Patel, J., and Parry, R.J. "A novel valanimycin-resistance detriment (vlmF) from Streptomyces viridifaciens MG456-hF10." Microbiology (UK), 146 (2000) : 345-352.

     
     Articles
     

    Schumacher, M.A., Bashor, C.J., Song, M.H., Otsu, K., Brennan, R.G., Ullmann, B., Zhu, S., and Parry, R. "The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase." Proceedings of the National Academy of Sciences, 99 (2002) : 78-83.

     
     Book chapters
     

    Parry, R.J. "Biosynthesis of sulfur-containing natural products." Comprehensive Natural Products Chemistry, 1 (1999)

     
     Other
     

    Skae, P., and Parry, R.J. "Determination of the stereochemistry of hydride transfer from NADPH to FAD catalyzed by VlmR, a flavin reductase from the valanimycin biosynthetic pathway.." Org. Lett., 3 (2001) : 1117-1119.

     
     

    Tao, T., and Parry, R.J. "Determination by enantioselective synthesis of the absolute configuration of CPE, a potential intermediate in coronatine biosynthesis.." Org. Letters., 3 (2001) : 3045-3047.

     
    Presentations
     Invited Talks
     

    Spearker.  "Biosynthesis of the Pyrrolomycins: Investigation and Manipulation." Office of Naval Research, Arlington VA. (May 24, 2007) With X. Zhang, W. Gong

     
     

    Presenter.  "Recent Investigations of Antibiotic Biosynthesis." Dept. of Biology, Trinity University, San Antonio, Texas. (November 13, 2006)

     
     

    Speaker.  "Recent Investigations of Antibiotic Biosynthesis." University of Montana, Missoula Montana. (April 25, 2005)

     
     

    Speaker.  "Investigations of the Production of High-energy Materials by Bionitration." Office of Naval Research - Green Chemistry Meeting, Arlington, VA. (11/22/04)

     
     

    Speaker.  "Recent Investigations of Antibiotic Biosynthesis." Dartmouth College, Hanover, N.H.. (July 21, 2004) With W. Li, Y. Ma, R. Garg, T. Tao, and P. Skae

     
     

    Speaker.  ""Chemical and Genetic Investigations of Natural Product Biosynthesis"." Texas A & M University, College Station, TX. (11/4/03)

     
     

    "Investigations of Valanimycin Biosynthesis." Dept. of Plant Pathology, Cornell University, Ithaca, NY. (June 15, 2002)

     
     Lectures
     

    "Recent Investigations of Valanimycin Biosynthesis." 7th Annual US-Japan Seminar on the Biosynthesis of Natural Products, La Jolla, California. (June 22-27, 2008)

     
     Other
     

    "Investigations of Coronatine Biosynthesis." Society for Industrial Microbiology Annual Meeting, San Diego, CA. (July 2000)

     
     

    "Genetic and Enzymological Investigations of Natural Product Biosynthesis." Merck Research Laboratories, Rahway NJ. (May 5, 1999)

     
     

    "Genetic and Enzymological Investigations of Natural Product Biosynthesis." The Gordon Conference on Natural Products Chemistry, Henniker, New Hampshire. (July 1998)

     
     Panelist
     

    "Investigations of Valanimycin Biosynthesis." DARPA panel, Dept. of Chemistry, Michigan State University. (September 19, 2002)

     
     Posters
     

    "Isolation and characterization of valanimycin hydrate, a new intermediate in valanimycin biosynthesis." 21st Enzyme Mechanisms Conference, Tucson, AZ. (January )

     
     

    Presenter.  "Mechanism of Valanimycin Biosynthesis in Streptomyces Viridifaciens." American Society of Microbiology, Toronto, Canada. (May 21, 2007) With R. Garg, X. Qian, L. Alemany, R. J. Parry

     
     Workshops
     

    "Biosynthesis of the Pyrrolomycins: Investigation and Manipulation." Arlington, Virginia. (June 7, 2010)

     
     

    "Biosynthesis of the Pyrrolomycins: Investigation and Manipulation." Denver, CO. (May 14, 2009)

     
     

    "Biosynthesis of the Pyrrolomycins: Investigation and Manipulation." Office of Naval Research, Arlington, Virginia. (July 23, 2008)

     
    Editorial Positions
     Associate Editor, Natural Products Research. (2010 - 2010)

     Associate Editor, Natural Products Research. (2011 - 2011)

     Associate Editor, Natural Products Research. Natural Products Research. (2009 - 2009)

     Associate Editor, Natural Product Research. (2004 - 2004)

     Associate Editor, Natural Product Research. (2003 - 2003)

     Associate Editor, Natural Product Research. (2006 - 2006)

     Associate Editor, Natural Products Letters. Harwood Academic Publishers. (2002 - 2002)

     Associate Editor, Natural Product Research. (2005 - 2005)

     Associate Editor, Natural Product Research. (2007 - 2007)

    Supervised Theses & Dissertations
     Michael Segura, Ph.D Directed Evolution and Structure-Function Studies of Oxidosqualene Cyclases. (2002) (Thesis Committee Member)

     Jay Deville, Ph. D. Research toward the total synthesis of lactonamycin and related polyketides. (2003) (Thesis Committee Member)

     David H. Maillett, Ph.D. Engineering Hemoglobins and Myoglobins for Efficient O2 Transport. (2003) (Thesis Committee Member)

     Beth E. Jackson, Ph.D. Yeast as a Host for Sesquiterpene Production. (2004) (Thesis Committee Member)

     Andrew Lee, Ph.D. Ligand-Binding Specificity of the RecA Nucleoprotein Filament: Homologous DNA, Metal Ions, and Nucleotides. (2005) (Thesis Committee Member)

     Renee LeClair, Ph.D. Elucidating the Mechanism of Triterpene Cyclization Using DNA Synthesis and Phylogenetic Approaches. (2005) (Thesis Committee Member)

     Michelle K. Calabretta, Ph.D. Biophysical Characterization of Gold Nanocrystal Protein Conjugates: Formation, Stoichiometry and Function. (2005) (Thesis Committee Member)

     Rui Li, M.A. Monitoring [2Fe2S]2+ Cluster Content of Human Glutaredoxin 2 (Grx2) Using Fluorescence Proteins. (2007) (Thesis Committee Member)

     Mariya Kolesnikova, Ph.D. Investigation of Triterpene Biosynthesis in Arabidopsis thaliana. (2008) (Thesis Committee Member)

     Caroline V McNeil, Ph.D. Metabolic engineering approaches to biosynthesize terpenoids in Saccharomyces cerevisiae. (2009) (Thesis Committee Member)

     Vital Srinivas, PhD Orthogonal Approaches for Studying Glycosaminoglycan Biopolymer. (2010) (Thesis Committee Member)

    Awards, Prizes, & Fellowships
     Member, American Society for Biochemistry and Molecular Biology

     Member, American Chemical Society

     Fellow, American Association for the Advancement of Science

     Member, Society for Industrial Microbiology

     Member, American Society for Microbiology

     Fellow, American Association for the Advancement of Science

     Member, American Chemical Society

     Member, American Society for Biochemistry and Molecular Biology

     Member, American Society for Microbiology