David E Graham

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. pmc Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast
    Guillermina Rosas-Sandoval
    Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 99:16707-12. 2002
  2. doi request reprint Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase
    David E Graham
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    Biochem J 424:467-78. 2009
  3. pmc Methanogens with pseudomurein use diaminopimelate aminotransferase in lysine biosynthesis
    David E Graham
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 0165, USA
    FEBS Lett 582:1369-74. 2008
  4. pmc Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis
    Randy M Drevland
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Biol Chem 283:28888-96. 2008
  5. pmc Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae
    Teresa N Giles
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    J Bacteriol 189:7376-83. 2007
  6. pmc Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae
    Conor B Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    J Bacteriol 190:7431-40. 2008
  7. pmc Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme
    Teresa N Giles
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
    J Biol Chem 283:25829-38. 2008
  8. pmc Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains
    Teresa N Giles
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    BMC Evol Biol 9:166. 2009
  9. pmc Enzymatic analysis of uridine diphosphate N-acetyl-D-glucosamine
    Seema C Namboori
    Institute for Cellular and Molecular Biology and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Anal Biochem 381:94-100. 2008
  10. pmc Acetamido sugar biosynthesis in the Euryarchaea
    Seema C Namboori
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    J Bacteriol 190:2987-96. 2008

Research Grants

  1. Archaeal gene recruitment by the Chlamydiales
    David Graham; Fiscal Year: 2008

Collaborators

  • Teresa N Giles
  • Abdul Waheed
  • Meng Zhao
  • George Georgiou
  • Li Zhou
  • E V Koonin
  • Hong Li
  • Seema C Namboori
  • Randy M Drevland
  • Karl O Stetter
  • Dieter Soll
  • Guillermina Rosas-Sandoval
  • Conor B Smith
  • James G Elkins
  • Sunna Helgadóttir
  • Martin Keller
  • Mircea Podar
  • Nicole D Kezmarsky
  • Elizabeth Waters
  • Nikos Kyrpides
  • Brian P Hedlund
  • Paul Richardson
  • Alla Lapidus
  • Eugene Goltsman
  • Yunhua Jia
  • Phil Hugenholtz
  • Celine Brochier-Armanet
  • Gerhard Wanner
  • Victor Kunin
  • Lennart Randau
  • Kerrie Barry
  • Yuri Wolf
  • Iain Anderson
  • David R J Palmer
  • Kira S Makarova
  • Huimin Xu
  • Robert H White
  • Xiaoying Lin
  • Mary Barnstead
  • Eric Mathur
  • Michiel Noordewier
  • Toby Richardson
  • Ivan Ahel
  • Randall Bolanos
  • Melvin Simon
  • Jingwei Ni
  • Keith Kretz
  • Karen Y Beeson
  • Jay M Short
  • Mark D Adams
  • Lisa Bibbs
  • Granger G Sutton
  • Michael J Hohn
  • Jesse Rinehart
  • Alexandre Ambrogelly
  • L Rogelio Cruz-Vera
  • David Wei
  • Gabriel Guarneros

Detail Information

Publications21

  1. pmc Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast
    Guillermina Rosas-Sandoval
    Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 99:16707-12. 2002
    ..Deletions in Saccharomyces cerevisiae of the pth2 (YBL057c) or pth (YHR189w) orthologs were viable, as was the double deletion strain, implying that the canonical Pth and Pth2 enzymes are not essential for yeast viability...
  2. doi request reprint Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase
    David E Graham
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    Biochem J 424:467-78. 2009
    ..These differences in coenzyme M biosynthesis afford the opportunity to develop methanogen inhibitors that discriminate between the classes of methanogenic archaea...
  3. pmc Methanogens with pseudomurein use diaminopimelate aminotransferase in lysine biosynthesis
    David E Graham
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 0165, USA
    FEBS Lett 582:1369-74. 2008
    ..In contrast marine methanogens from the Methanococcales, which lack pseudomurein, appear to use a different diaminopimelate pathway for lysine biosynthesis...
  4. pmc Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis
    Randy M Drevland
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Biol Chem 283:28888-96. 2008
    ..The variation in substrate specificity among these enzymes correlated with the amino acid sequences of a flexible loop in the small subunits...
  5. pmc Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae
    Teresa N Giles
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    J Bacteriol 189:7376-83. 2007
    ..These genes are the first evidence that obligately intracellular chlamydiae may encounter acidic conditions. Alternatively, this system could reduce the host cell arginine concentration and produce inhibitors of nitric oxide synthase...
  6. pmc Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae
    Conor B Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    J Bacteriol 190:7431-40. 2008
    ..The chlamydial AaxC transporter was resistant to cadaverine, L-lysine and L-ornithine, which inhibit the E. coli AdiC antiporter...
  7. pmc Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme
    Teresa N Giles
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
    J Biol Chem 283:25829-38. 2008
    ..ArgDC activity has evolved through convergent evolution at least five times, demonstrating the utility of this enzyme and the plasticity of amino acid decarboxylases...
  8. pmc Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains
    Teresa N Giles
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    BMC Evol Biol 9:166. 2009
    ..Molecular evolution techniques were applied to determine the relaxation of selection and the scope of aax gene inactivation in the Chlamydiales...
  9. pmc Enzymatic analysis of uridine diphosphate N-acetyl-D-glucosamine
    Seema C Namboori
    Institute for Cellular and Molecular Biology and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Anal Biochem 381:94-100. 2008
    ..This procedure can be adapted for the high-throughput analysis of changes in cellular UDP-GlcNAc concentrations in time series experiments or inhibitor screens...
  10. pmc Acetamido sugar biosynthesis in the Euryarchaea
    Seema C Namboori
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    J Bacteriol 190:2987-96. 2008
    ..These UDP-acetamido sugars are predicted to be precursors for flagellin and S-layer protein modifications and for the biosynthesis of methanogenic coenzyme B...
  11. pmc Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii
    Randy M Drevland
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    J Bacteriol 189:4391-400. 2007
    ....
  12. pmc Transcriptional regulation of the Escherichia coli gene rraB, encoding a protein inhibitor of RNase E
    Li Zhou
    Section of Microbiology and Molecular Genetics, University of Texas at Austin, Austin, Texas 78712, USA
    J Bacteriol 191:6665-74. 2009
    ....
  13. pmc Biosynthesis of phosphoserine in the Methanococcales
    Sunna Helgadóttir
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    J Bacteriol 189:575-82. 2007
    ..All methanogenic archaea apparently share this pathway, providing sufficient phosphoserine for the tRNA-dependent cysteine biosynthetic pathway...
  14. ncbi request reprint Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F(420) biosynthesis
    David E Graham
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0308, USA
    Arch Microbiol 180:455-64. 2003
    ..Therefore a radical reaction mechanism is proposed for the biosynthesis of FO...
  15. ncbi request reprint Identification and characterization of a L-tyrosine decarboxylase in Methanocaldococcus jannaschii
    Nicole D Kezmarsky
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0308, USA
    Biochim Biophys Acta 1722:175-82. 2005
    ..Homologs of this gene are widely distributed among euryarchaea but are not specifically related to known bacterial or plant tyrosine decarboxylases...
  16. ncbi request reprint Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes
    David E Graham
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0308, USA
    J Biol Chem 277:13421-9. 2002
    ..A diverse group of microbes and plants have homologs of ComA that could have been recruited for sulfolactate or sulfolipid biosyntheses...
  17. pmc The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism
    Elizabeth Waters
    Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 100:12984-8. 2003
    ..equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome...
  18. pmc A korarchaeal genome reveals insights into the evolution of the Archaea
    James G Elkins
    Lehrstuhl fur Mikrobiologie und Archaeenzentrum, Universitat Regensburg, D 93053 Regensburg, Germany
    Proc Natl Acad Sci U S A 105:8102-7. 2008
    ..In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form...
  19. pmc Glutathione synthetase homologs encode alpha-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses
    Hong Li
    Department of Biochemistry 0308, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Proc Natl Acad Sci U S A 100:9785-90. 2003
    ..The analogous pathways for glutathione, F420, folate, and murein peptide biosyntheses illustrate convergent evolution of nonribosomal peptide biosynthesis through the recruitment of single-step amino acid ligases...
  20. ncbi request reprint A divergent archaeal member of the alkaline phosphatase binuclear metalloenzyme superfamily has phosphoglycerate mutase activity
    David E Graham
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0308, USA
    FEBS Lett 517:190-4. 2002
    ..We show that the genes at M. jannaschii loci MJ0010 and MJ1612 encode thermostable enzymes with phosphoglycerate mutase activity. Phylogenetic analyses suggest that this gene family arose before the divergence of the archaeal lineage...
  21. ncbi request reprint Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis
    David E Graham
    Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 0308, USA
    J Biol Chem 277:23500-7. 2002
    ..Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria...

Research Grants1

  1. Archaeal gene recruitment by the Chlamydiales
    David Graham; Fiscal Year: 2008
    ..Results from these experiments will support future microbiological studies of the role of this system in chlamydial infection and survival in the host cell. [unreadable] [unreadable] [unreadable]..