DOCSLIB.ORG

David E. Cane Publications 1. EJ Corey and David E. Cane

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

David E. Cane Publications 1. E. J. Corey and David E. Cane, "The Synthesis of Olefins from β-Hydroxyphosphonamides. Stereochemistry and Extension to the Formation of Conjugated Dienes," J. Org. Chem., 34, 3053 (1969). 2. E. J. Corey and David E. Cane, "The Metalation-Alkylation of Ynamines," J. Org.Chem., 35, 3405 (1970). 3. E. J. Corey and David E. Cane, "A New Method for the Controlled Hydroxymethylation of Ketones," J. Org. Chem., 36, 3070 (1971). 4. E. J. Corey, David E. Cane, and Lawrence Libit, "The Synthesis of Racemic α-trans- and β-trans-Bergamotene," J. Am. Chem. Soc., 93, 7013, (1971). 5. D. Arigoni, David E. Cane, Beat Mueller and Christopher Tamm, "The Mode of Incorporation of Farnesyl Pyrophosphate into Verrucarol," Helv. Chim. Acta, 56, 2946 (1973). 6. David E. Cane and Ronald H. Levin, "Application of Carbon-13 Magnetic Resonance to Isoprenoid Biosynthesis. I. Ovalicin," J. Am. Chem. Soc., 97, 1982 (1975). 7. David E. Cane and Ronald H. Levin, "Application of Carbon-13 Magnetic Resonance to Isoprenoid Biosynthesis. II. Ovalicin and the Use of Double-Labeled Mevalonate," J. Am. Chem. Soc., 98, 1183 (1976). 8. David E. Cane and Robert B. Nachbar, "Biosynthesis of Fomannosin from [1,2-13C]-Acetate," Tetrahedron Lett. 2097-2100 (1976). 9. David E. Cane and G. G. S. King, "The Biosynthesis of Ovalicin: Isolation of β-trans-Bergamotene," Tetrahedron Lett.., 4737 (1976). 10. David E. Cane and Stephen L. Buchwald, "Application of Deuterium Magnetic Resonance to Biosynthetic Studies I; Biosynthesis of Ovalicin," J. Am. Chem. Soc., 99, 6132 (1977). 11. David E. Cane and Radha Iyengar, "The Absolute Configuration of Cyclonerodiol," Tetrahedron Lett., 3511 (1977). 12. David E. Cane, Robert B. Nachbar, Jon Clardy, and Janet Finer, "The Absolute Configuration of Fomannosin," Tetrahedron Lett., 4277 (1977). 13. David E. Cane and Ming-Shi Shiao, "Biosynthesis of Cyclonerodiol," J. Am. Chem. Soc., 100, 3203 (1978). 14. David E. Cane and Pushpalatha N. Murthy, "Application of Deuterium Magnetic Resonance to Biosynthetic Studies II. Rosenonolactone Biosynthesis and the Stereochemistry of a Biological SN2' Reaction," J. Am. Chem. Soc., 99, 8327 (1977). 15. David E. Cane and Robert B. Nachbar, "Stereochemical Studies of Isoprenoid Biosynthesis. Biosynthesis of Fomannosin from [1,2-13C]-Acetate," J. Am. Chem. Soc., 100, 3208 (1978). 16. David E. Cane and R. Iyengar, "Conversion of Farnesyl and Nerolidyl Pyrophosphate to Cyclonerodiol by a Cell-Free System from Gibberella Fujikuroi," J. Am. Chem. Soc.,100, 3256 (1978). 17. David E. Cane, Radha Iyengar, and Ming-Shi Shiao, "Cyclonerodiol Biosynthesis and the Stereochemistry of the Conversion of Farnesyl to Nerolidyl Pyrophosphate," J. Am. Chem. Soc., 100, 7122 (1978) 18. C. Richard Hutchinson, Amos H. Heckendorf, J. L. Straughn, P. E. Dadonna and David E. Cane, "The Biosynthesis of Camptothecin. III. Definition of Strictosamide as the Penultimate Biosynthetic Precursor Assisted by 13C and 2H NMR Spectroscopy," J. Am. Chem. Soc., 101, 3358 (1979). 19. David E. Cane, Thomas Rossi, and J. Paul Pachlatko, "The Biosynthesis of Pentalenolactone," Tetrahedron Lett., 3639-3642 (1979). 20. David E. Cane and Radha Iyengar, "Carbon-Carbon Bond Cleavage During Lithium Aluminum Hydride Reduction of a Terminal Propargyl Alcohol," Tetrahedron Lett., 2871 (1979). 21. David E. Cane and Thomas Rossi, "The Isolation and Structural Elucidation of Pentalenolactone E," Tetrahedron Lett., 2973 (1979). 22. David E. Cane and Radha Iyengar, "The Enzymatic Conversion of Farnesyl to Nerolidyl Pyrophosphate: Role of the Pyrophosphate Moiety," J. Am. Chem. Soc., 101, 3385-3388[1, 2] (1979). 23. David E. Cane and Robert B. Nachbar, "Biosynthesis of Fomannosin. 2H NMR Evidence Against Postulated Hydride Shifts," Tetrahedron Lett., 21, 432 (l980). 24. David E. Cane, "The Stereochemistry of Allylic Pyrophosphate Metabolism," Tetrahedron Report, Tetrahedron, 36, 1109 (1980). 25. David E. Cane, Radha Iyengar and Ming-Shi Shiao, "Cyclonerodiol Biosynthesis and the Enzymatic Conversion of Farnesyl to Nerolidyl Pyrophosphate," J. Am. Chem. Soc., 103, 914 (1981). 26. David E. Cane, Thomas Rossi, Ann Marie Tillman, and J. Paul Pachlatko, "Stereochemical Studies of 13 2 Isoprenoid Biosynthesis. Biosynthesis of Pentalenolactone from [UL- C6]-Glucose and [6- H2]-Glucose," J. Am. Chem. Soc., 103, 1838 (1981). 27. David E. Cane, "The Biosynthesis of Sesquiterpenes," in "Biosynthesis of Isoprenoid Compounds," Vol 1, J. W. Porter, S. L. Spurgeon, ed., J. W. Wiley & Sons, New York, 1981, pp 283-374 28. David E. Cane, Heinz Hasler, Joan Materna, Nera Cagnoli-Bellavita, Paolo Ceccherelli, Gian Federico Madruzza, and Judith Polonsky, "2H NMR Determination of the Stereochemistry of an Allylic Displacement Reaction in the Biosynthesis of Virescenol B," J. Chem. Soc. Chem. Commun., 280 (1981). 29. David E. Cane, Stephen Swanson, and Pushpalatha P.N. Murthy, "Trichodiene Biosynthesis and the Enzymatic Cyclization of Farnesyl Pyrophosphate," J. Am. Chem. Soc., 103, 2136 (1981). 30. C. Richard Hutchinson, Itsuo Kurobane, David E. Cane, Heinz Hasler, and A. G. McInnes, "Biosynthesis of 2 Macrolide Antibiotics IV. Stereochemistry of Hydrogen Labeling of Brefeldin A by [2- H3]-Acetate," J. Am. Chem. Soc., 103, 2477 (1981). 31. David E. Cane, Heinz Hasler, and Tzyy-Chyau Liang, "Macrolide Biosynthesis. Origin of the Oxygen Atoms in the Erythromycins," J. Am. Chem. Soc., 103, 5960 (1981). 32. David E. Cane, Tzyy-Chyau Liang, and Heinz Hasler, "Polyether Biosynthesis. Origin of the Oxygen Atoms of Monensin A," J. Am. Chem. Soc., 103, 5962 (1981). 13 33. Steven J. Gould and David E. Cane, "The Biosynthesis of Streptonigrin from [UL- C6]-D-Glucose. Origin of the Quinoline Quinone," J. Am. Chem. Soc., 104, 343 (1982). 34. David E. Cane, Akio Saito, Rodney Croteau,John Shaskus, and Mark Felton, "The Enzymatic Cyclization of Geranyl Pyrophosphate to Bornyl Pyrophosphate. Role of the Pyrophosphate Moiety," J.Am. Chem. Soc., 104, 5831 (1982). 35. David E. Cane, Tzyy-Chyau Liang, and Heinz Hasler, "Polyether Biosynthesis II. Origin of the Oxygen Atoms of Monensin A," J. Am. Chem. Soc., 104, 7274 (1982). 2 36. Ann Marie Tillman and David E. Cane, "Pentalenolactone F, A New Metabolite Isolated from Streptomyces. Isolation and Structure Elucidation," J. Antibiot., 36, 170-172 (1983). 37. David E. Cane, Walter D. Celmer, and John W. Westley, "A Unified Stereochemical Model of Polyether Structure and Biogenesis," J. Am. Chem. Soc., 105, 3594-3600 (1983). 38. David E. Cane and Ann Marie Tillman, "Pentalenene Biosynthesis and the Enzymatic Cyclization of Farnesyl Pyrophosphate," J. Am. Chem. Soc., 105, 122-124 (1983). 39. David E. Cane, "Enzyme-Level Studies of the Biosynthesis of Natural Products," in "Enzyme Chemistry, Impact and Applications" C. J. Suckling, ed., Chapman and Hall, London, 1984, pp. 196-231. 40. David E. Cane, Heinz Hasler, Paul B. Taylor, and Tzyy-Chyau Liang, "Macrolide Biosynthesis. II. Origin of the Carbon Skeleton and Oxygen Atoms of the Erythromycins," Tetrahedron, 39, 3449 (1983). 41. David E. Cane, Tzyy-Chyau Liang, Louis Kaplan, Mary K. Nallin, Marvin D. Schulman, Otto D. Hensens, Alan W. Douglas, and George Albers-Schonberg, "The Biosynthetic Origin of the Carbon Skeleton and Oxygen Atoms of the Avermectins", J. Am. Chem. Soc., 105, 4110 (1983). 42. David E. Cane, "Cell-Free Studies of Monoterpene and Sesquiterpene Biosynthesis," Biochem. Soc. Trans., 11, 510-516 (1983). 43. R. Croteau, John Shaskus, David E. Cane, Akio Saito, and Conway Chang, "The Enzymatic Cyclization of [1- 18O]Geranyl Pyrophosphate to l-endo-Fenchol," J. Am. Chem. Soc., 106, 1142 (1984). 44. David E. Cane and Chi-Ching Yang, "The Biosynthetic Origin of the Carbon Skeleton and Oxygen Atoms of Nargenicin A1," J. Am. Chem. Soc., 106, 784 (1984). 45. Rodney Croteau and David E. Cane, "Monoterpene and Sesquiterpene Cyclases," in "Methods in Enzymology. Steroids and Isoprenoids," Vol. 110, J. H. Law and H. C. Rilling, eds., Academic Press, New York, 1985; pp 383-405. 46. David E. Cane, Yvonne G. Whittle, and Tzyy-Chyau Liang, "The Biosynthesis of Quadrone and Terrecyclic Acid," Tetrahedron Lett., 25, 1119 (1984). 47. David E. Cane and Pulikkottil J. Thomas, "The Synthesis of (dl)-Pentalenolactones E and F," J. Am. Chem. Soc., 106, 5295 (1984). 48. David E. Cane, Christopher Abell, and Ann Marie Tillman, "Pentalenene Biosynthesis and the Enzymatic Cyclization of Farnesyl Pyrophosphate. Proof that the Cyclization is Catalyzed by a Single Enzyme," Bioorganic Chemistry, 12, 312 (1984). 49. David E. Cane and Chi-Ching Yang, "Nargenicin Biosynthesis. Late Stage Oxidations and Absolute Configuration," J. Antibiot., 38, 423-426 (1985). 50. David E. Cane, Hyun-Joon Ha, Christopher Pargellis, Felix Waldmeier, Stephen Swanson, and Pushpalatha P. N. Murthy, "Trichodiene Biosynthesis and the Stereochemistry of the Enzymatic Cyclization of Farnesyl Pyrophosphate," Bioorganic Chemistry, 13, 246 (1985). 51. David E. Cane, "Isoprenoid Biosynthesis. Stereochemistry of the Cyclization of Allylic Pyrophosphates," Acc. Chem. Res., 18, 220 (1985). 52. Rodney B. Croteau, John J. Shaskus, Britta Renstrom, N. Mark Felton, David E. Cane, Akio Saito, and Conway Chang, "Mechanism of the Pyrophosphate Migration in the Enzymatic Cyclization of Geranyl and Linalyl Pyrophosphate to (+)- and (-)-Bornyl Pyrophosphate," Biochemistry, 24, 7077 (1985). 3 53. David E. Cane, "Stereochemical Studies of Natural Products Biosynthesis," Ann. N. Y. Acad. Sci., 471, 130-137 (1986). 54. David E. Cane,
Recommended publications
  • Origins of Isoprenoid Diversity: a Study of Structure-Function Relationships in Sesquiterpene Synthases" (2003)

    Origins of Isoprenoid Diversity: a Study of Structure-Function Relationships in Sesquiterpene Synthases" (2003)

    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2003 ORIGINS OF ISOPRENOID DIVERSITY: A STUDY OF STRUCTURE- FUNCTION RELATIONSHIPS IN SESQUITERPENE SYNTHASES Bryan T. Greenhagen University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Greenhagen, Bryan T., "ORIGINS OF ISOPRENOID DIVERSITY: A STUDY OF STRUCTURE-FUNCTION RELATIONSHIPS IN SESQUITERPENE SYNTHASES" (2003). University of Kentucky Doctoral Dissertations. 440. https://uknowledge.uky.edu/gradschool_diss/440 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Bryan T. Greenhagen The Graduate School University of Kentucky 2003 1 ORIGINS OF ISOPRENOID DIVERSITY: A STUDY OF STRUCTURE-FUNCTION RELATIONSHIPS IN SESQUITERPENE SYNTHASES. ________________________________________ ABSTRACT OF DISSERTATION ________________________________________ A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Agriculture at the University of Kentucky by Bryan T. Greenhagen Lexington, KY Director: Dr. Joseph Chappell, Professor Lexington, KY Copyright © Bryan T. Greenhagen 2003 2 ABSTRACT OF DISSERTATION ORIGINS OF ISOPRENOID DIVERSITY: A STUDY OF STRUCTURE-FUNCTION RELATIONSHIPS IN SESQUITERPENE SYNTHASES. Plant sesquiterpene synthases catalyze the conversion of the linear substrate farnesyl diphosphate, FPP, into a remarkable array of secondary metabolites. These secondary metabolites in turn mediate a number of important interactions between plants and their environment, such as plant-plant, plant-insect and plant-pathogen interactions.
  • Generated by SRI International Pathway Tools Version 25.0, Authors S

    Generated by SRI International Pathway Tools Version 25.0, Authors S

    Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000725805Cyc: Streptomyces xanthophaeus Cellular Overview Connections between pathways are omitted for legibility.
  • 1 AMINO ACIDS Commonly, 21 L-Amino Acids Encoded by DNA Represent the Building Blocks of Animal, Plant, and Microbial Proteins

    1 AMINO ACIDS Commonly, 21 L-Amino Acids Encoded by DNA Represent the Building Blocks of Animal, Plant, and Microbial Proteins

    1 AMINO ACIDS Commonly, 21 L-amino acids encoded by DNA represent the building blocks of animal, plant, and microbial proteins. The basic amino acids encountered in proteins are called proteinogenic amino acids 1.1). Biosynthesis of some of these amino acids proceeds by ribosomal processes only in microorganisms and plants and the ability to synthesize them is lacking in animals, including human beings. These amino acids have to be obtained in the diet (or produced by hydrolysis of body proteins) since they are required for normal good health and are referred to as essential amino acids. The essential amino acids are arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The rest of encoded amino acids are referred to as non-essential amino acids (alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine). Arginine and histidine are classified as essential, sometimes as semi-essential amino acids, as their amount synthesized in the body is not sufficient for normal growth of children. Although it is itself non-essential, cysteine (classified as conditionally essential amino acid) can partly replace methionine, which is an essential amino acid. Similarly, tyrosine can partly replace phenylalanine. 1.1 The glutamic acid group 1.1.1 Glutamic acid and glutamine Free ammonium ions are toxic to living cells and are rapidly incorporated into organic compounds. One of such transformations is the reaction of ammonia with 2-oxoglutaric acid from the citric acid cycle to produce L-glutamic acid. This reaction is known as reductive amination. Glutamic acid is accordingly the amino acid generated first as both constituent of proteins and a biosynthetic precursor.
  • Molecular and Functional Analysis of Nicotinate Catabolism in Eubacterium Barkeri

    Molecular and Functional Analysis of Nicotinate Catabolism in Eubacterium Barkeri

    Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri Ashraf Alhapel, Daniel J. Darley, Nadine Wagener, Elke Eckel, Nora Elsner, and Antonio J. Pierik* Laboratorium fu¨r Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universita¨t, D-35032 Marburg, Germany Edited by Perry A. Frey, University of Wisconsin, Madison, WI, and approved June 29, 2006 (received for review March 1, 2006) The anaerobic soil bacterium Eubacterium barkeri catabolizes nic- complex (see Fig. 1). Based on the identified intermediates, otinate to pyruvate and propionate via a unique fermentation. A several anticipated enzymes were purified and characterized: full molecular characterization of nicotinate fermentation in this nicotinate dehydrogenase (12), 6-hydroxynicotinate reductase organism was accomplished by the following results: (i) A 23.2-kb (7), 2-methyleneglutarate mutase, and 3-methylitaconate DNA segment with a gene cluster encoding all nine enzymes was isomerase (13, 14). These findings outlined the nicotinate fer- cloned and sequenced, (ii) two chiral intermediates were discov- mentation pathway and placed the identified intermediates in an ered, and (iii) three enzymes were found, completing the hitherto enzymatic framework. unknown part of the pathway. Nicotinate dehydrogenase, a (non- The nicotinate dehydrogenase contains [2Fe-2S] clusters (15), selenocysteine) selenium-containing four-subunit enzyme, is en- FAD and molybdopterin cytosine dinucleotide (16), and has an coded by ndhF (FAD subunit), ndhS (2 x [2Fe-2S] subunit), and by unusual subunit composition [50, 37, 33, and 23 kDa (17)]. It has the ndhL͞ndhM genes. In contrast to all enzymes of the xanthine labile (nonselenocysteine) selenium (18) also identified in pu- dehydrogenase family, the latter two encode a two-subunit mo- rine dehydrogenase from Clostridium purinolyticum and xanthine lybdopterin protein.
  • Loss of Quaternary Structure Is Associated with Rapid Sequence Divergence in the OSBS Family

    Loss of Quaternary Structure Is Associated with Rapid Sequence Divergence in the OSBS Family

    Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family Denis Odokonyeroa, Ayano Sakaib, Yury Patskovskyc, Vladimir N. Malashkevichc, Alexander A. Fedorovc, Jeffrey B. Bonannoc, Elena V. Fedorovc, Rafael Toroc, Rakhi Agarwald, Chenxi Wanga, Nicole D. S. Ozerovaa, Wen Shan Yewe, J. Michael Sauderf, Subramanyam Swaminathand, Stephen K. Burleyg,h,i,j,k, Steven C. Almoc,l, and Margaret E. Glasnera,1 aDepartment of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128; bInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Departments of cBiochemistry and lPhysiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461; dBiosciences Department, Brookhaven National Laboratory, Upton, NY 11973; eDepartment of Biochemistry, National University of Singapore, Singapore 117597; fLilly Biotechnology Center, San Diego, CA 92121; gBioMaPS Institute for Quantitative Biology, hResearch Collaboratory for Structural Bioinformatics Protein Data Bank, iCenter for Integrative Proteomics Research, jRutgers Cancer Institute of New Jersey, and kDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8076 Edited by Douglas L. Theobald, Brandeis University, Waltham, MA, and accepted by the Editorial Board May 2, 2014 (received for review October 3, 2013) The rate of protein evolution is determined by a combination of OSBS family is much faster than other families in the enolase su- selective pressure on protein function and biophysical constraints perfamily. For example, the average pairwise amino acid sequence on protein folding and structure. Determining the relative con- identity of OSBSs from 66 species is 26%, and the most divergent tributions of these properties is an unsolved problem in molecular family members share <15% identity.
  • Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme

    Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme

    Metabolites 2014, 4, 612-628; doi:10.3390/metabo403000x OPEN ACCESS metabolites ISSN 2218-1989 www.mdpi.com/journal/metabolites/ Article Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme Jürgen E. W. Polle 1,2,*, Peter Neofotis 1,2, Andy Huang 1, William Chang 1, Kiran Sury 1 and Eliza M. Wiech 1 1 Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA; E-Mails: [email protected] (P.N.); [email protected] (A.H.); [email protected] (W.C.); [email protected] (K.S.); [email protected] (E.M.W.) 2 The Graduate Center of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-718-951-5000; Fax: +1-718-951-4659. Received: 13 June 2014; in revised form: 25 July 2014 / Accepted: 28 July 2014 / Published: 4 August 2014 Abstract: The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11].
  • Functional and Physiological Discovery in the Mannonate Dehydratase Subgroup of the Enolase Superfamily

    Functional and Physiological Discovery in the Mannonate Dehydratase Subgroup of the Enolase Superfamily

    FUNCTIONAL AND PHYSIOLOGICAL DISCOVERY IN THE MANNONATE DEHYDRATASE SUBGROUP OF THE ENOLASE SUPERFAMILY BY DANIEL JOSEPH WICHELECKI DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor John Gerlt, Chair Professor John Cronan Professor Scott Silverman Professor Wilfred van der Donk ABSTRACT In the current post-genomic world, the exponential amassing of protein sequences is overwhelming the scientific community’s ability to experimentally assign each protein’s function. The use of automated, homology-based annotations has allowed a reprieve from this efflux of data, but has led to widespread misannotation and nonannotation in protein sequence databases. This dissertation details the functional and physiological characterization of the mannonate dehydratase subgroup (ManD) of the enolase superfamily (ENS). The outcome affirms the dangers of homology-based annotations while discovering novel metabolic pathways. Furthermore, the experimental verification of these pathways ( in vitro and in vivo ) has provided a platform to test the general strategies for improved functional and metabolic characterization being developed by the Enzyme Function Initiative (EFI). Prior to this study, one member of the ManD subgroup had been characterized and was shown to dehydrate D-mannonate to 2-keto-3-deoxy-D-gluconate. Forty-two additional members of the ManD, selected from across the sequence space of the subgroup, were screened for activity and kinetic constants were determined. The members of the once isofunctional subgroup were found to differ in both catalytic efficiency and substrate specificity: 1) high 3 4 -1 -1 efficiency (k cat /K M = 10 to 10 M s ) dehydration of D-mannonate, 2) low efficiency (k cat /K M = 10 1 to 10 2 M-1s-1) dehydration of D-mannonate and/or D-gluconate, and 3) no-activity with either D-mannonate or D-gluconate (or any other acid sugar tested).
  • Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    Metabolites 2015, 5, 636-658; doi:10.3390/metabo5040636 OPEN ACCESS metabolites ISSN 2218-1989 www.mdpi.com/journal/metabolites/ Review Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production Martin C. Lai 1 and Ethan I. Lan 2,* 1 Undergraduate Honors Program of Nano Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; E-Mail: [email protected] 2 Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +886-3-571-2121 (ext. 59719); Fax: +886-3-575-1898. Academic Editor: Peter Meikle Received: 2 July 2015 / Accepted: 22 October 2015 / Published: 27 October 2015 Abstract: Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the diversity of bioproducts synthesized by engineered cyanobacteria, the metabolic pathways used, and the current engineering strategies used for increasing their titers. Keywords: metabolic engineering; cyanobacteria 1. Introduction Increasing concerns over energy and environmental problems prompted the need to develop renewable chemicals and fuels. Advances in genetic manipulation and genomics understanding enabled rapid advancement of microbial cell factory development. Once the enzymatic and genetic information for metabolic pathways producing important commodity biochemicals are solved, these genetic parts are then transferred to other organisms capable of utilizing diverse bioresources for growth.
  • The Enolase Superfamily: a General Strategy for Enzyme-Catalyzed Abstraction of the R-Protons of Carboxylic Acids†

    The Enolase Superfamily: a General Strategy for Enzyme-Catalyzed Abstraction of the R-Protons of Carboxylic Acids†

    + + Biochemistry 1996, 35, 16489-16501 16489 The Enolase Superfamily: A General Strategy for Enzyme-Catalyzed Abstraction of the R-Protons of Carboxylic Acids† ,‡ §,| ⊥,# Patricia C. Babbitt,* Miriam S. Hasson, Joseph E. Wedekind, David R. J. Palmer,r William C. Barrett,r ⊥ ⊥ § ‡ , George H. Reed, Ivan Rayment, Dagmar Ringe, George L. Kenyon, and John A. Gerlt* r Department of Pharmaceutical Chemistry, UniVersity of California, San Francisco, California 94143-0446, Departments of Biochemistry and Chemistry and Rosenstiel Center for Basic Biomedical Research, Brandeis UniVersity, Waltham, Massachusetts 02154-9110, The Institute for Enzyme Research and Department of Biochemistry, UniVersity of Wisconsin, Madison, Wisconsin 53706, and Department of Biochemistry, UniVersity of Illinois, Urbana, Illinois 61801 ReceiVed July 5, 1996X ABSTRACT: We have discovered a superfamily of enzymes related by their ability to catalyze the abstraction of the R-proton of a carboxylic acid to form an enolic intermediate. Although each reaction catalyzed by these enzymes is initiated by this common step, their overall reactions (including racemization, â-elimination of water, â-elimination of ammonia, and cycloisomerization) as well as the stereochemical consequences (syn Vs anti) of the â-elimination reactions are diverse. Analysis of sequence and structural similarities among these proteins suggests that all of their chemical reactions are mediated by a common active site architecture modified through evolution to allow the enolic intermediates to partition to different products in their respective active sites Via different overall mechanisms. All of these enzymes retain the ability to catalyze the thermodynamically difficult step of proton abstraction. These homologous proteins, designated the “enolase superfamily”, include enolase as well as more metabolically specialized enzymes: mandelate racemase, galactonate dehydratase, glucarate dehydratase, muconate-lactonizing enzymes, N-acylamino acid racemase, â-methylaspartate ammonia-lyase, and o-succinylbenzoate synthase.
  • Enzymatic Reaction Mechanism of Cis-Aconitate Decarboxylase Based

    Enzymatic Reaction Mechanism of Cis-Aconitate Decarboxylase Based

    www.nature.com/scientificreports OPEN Enzymatic reaction mechanism of cis‑aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis Hye Lin Chun1, So Yeon Lee1, Sung Hoon Lee1, Chang Sup Lee2 & Hyun Ho Park1* Itaconate, which is formed by decarboxylation of cis‑aconitate—an intermediate metabolite in the tricarboxylic acid cycle—has been used as a building block in polymer synthesis and is an important chemical in several biomedical and industrial applications. Itaconate is an immunometabolite with antibacterial, antiviral, immunoregulatory, and tumor‑promoting activities. Recent focus has been on the role of itaconate in the feld of immunology, with immune-responsive gene 1 (IRG1) being identifed as the cis‑aconitate decarboxylase responsible for itaconate production. We solved the structure of IRG1 from Bacillus subtilis (bsIRG1) and showed that IRG1 adopts either a closed or an open conformation; bsIRG1 was in the open form. A1 and A2 loops around the active site are fexible and can control the formation of the open and closed forms of IRG1. An in silico docking simulation showed that only the open form of IRG1 can accommodate the substrate. The most energetically favorable position of cis-aconitate in the active site of bsIRG1 involved the localization of C2 and C5 of cis-aconitate into the H102 region and H151 region of bsIRG1, respectively. Based on the structural study of bsIRG1, compared with IDS epimerase, and in silico docking simulation, we proposed two tentative enzymatic reaction mechanisms of
  • Diene Synthase for the Production of Novel Products

    Diene Synthase for the Production of Novel Products

    Engineering Selina-4(15),7(11)-diene synthase for the Production of Novel Products Emily Turri Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Astbury Centre for Structural Molecular Biology September 2020 The candidate confirms that the work submitted is her own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Emily Turri to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. © 2020 The University of Leeds and Emily Turri 2 Acknowledgements Throughout my PhD I have been extremely lucky to receive support and encouragement from family, friends, colleagues and the university. Without these people and their support, this thesis would not be possible. First, I would like to thank my supervisors Alan Berry and Adam Nelson for their encouragement, guidance and patience over these four years. I would also like to thank Glyn Hemsworth and Nasir Khan for their continued advice and support. I am very grateful to Glyn Hemsworth, Sheena Radford, David Brockwell and John Blacker for letting me use their equipment while offering me direction to give me the best results. In addition, I would like to thank James Ault, Rachel George, Mary Bayana, Mark Howard and Ricardo Labes for their technical assistance and biochemical analysis. My PhD experience would have been nothing without the present and past members of the Hemrry’s and Radford’s with specific thanks to Jess, Alex, Jess and Dan.
  • Phytohormones and Volatile Organic Compounds, Like Geosmin, in the Ectomycorrhiza of Tricholoma Vaccinum and Norway Spruce (Picea Abies)

    Phytohormones and Volatile Organic Compounds, Like Geosmin, in the Ectomycorrhiza of Tricholoma Vaccinum and Norway Spruce (Picea Abies)

    Mycorrhiza (2021) 31:173–188 https://doi.org/10.1007/s00572-020-01005-2 ORIGINAL ARTICLE Phytohormones and volatile organic compounds, like geosmin, in the ectomycorrhiza of Tricholoma vaccinum and Norway spruce (Picea abies) Oluwatosin Abdulsalam1 · Katharina Wagner1 · Sophia Wirth1 · Maritta Kunert2 · Anja David2 · Mario Kallenbach2 · Wilhelm Boland2 · Erika Kothe1 · Katrin Krause1 Received: 21 June 2020 / Accepted: 11 November 2020 / Published online: 18 November 2020 © The Author(s) 2020 Abstract The ectomycorrhizospheric habitat contains a diverse pool of organisms, including the host plant, mycorrhizal fungi, and other rhizospheric microorganisms. Diferent signaling molecules may infuence the ectomycorrhizal symbiosis. Here, we investigated the potential of the basidiomycete Tricholoma vaccinum to produce communication molecules for the interac- tion with its coniferous host, Norway spruce (Picea abies). We focused on the production of volatile organic compounds and phytohormones in axenic T. vaccinum cultures, identifed the potential biosynthesis genes, and investigated their expression by RNA-Seq analyses. T. vaccinum released volatiles not usually associated with fungi, like limonene and β-barbatene, and geosmin. Using stable isotope labeling, the biosynthesis of geosmin was elucidated. The geosmin biosynthesis gene ges1 of T. vaccinum was identifed, and up-regulation was scored during mycorrhiza, while a diferent regulation was seen with mycorrhizosphere bacteria. The fungus also released the volatile phytohormone ethylene and excreted salicylic and abscisic acid as well as jasmonates into the medium. The tree excreted the auxin, indole-3-acetic acid, and its biosynthesis intermediate, indole-3-acetamide, as well as salicylic acid with its root exudates. These compounds could be shown for the frst time in exudates as well as in soil of a natural ectomycorrhizospheric habitat.