Eric Phizicky

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. ncbi tRNA biology charges to the front
    Eric M Phizicky
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Genes Dev 24:1832-60. 2010
  2. ncbi Proteome-scale analysis of biochemical activity
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA
    Crit Rev Biochem Mol Biol 41:315-27. 2006
  3. ncbi Have tRNA, will travel
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester Medical School, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 102:11127-8. 2005
  4. ncbi Protein analysis on a proteomic scale
    Eric Phizicky
    University of Rochester School of Medicine, Department of Biochemistry and Biophysics, Box 712, 601 Elmwood Avenue, Rochester, New York 14642, USA
    Nature 422:208-15. 2003
  5. ncbi Do all modifications benefit all tRNAs?
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA
    FEBS Lett 584:265-71. 2010
  6. ncbi Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1
    Irina Chernyakov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Genes Dev 22:1369-80. 2008
  7. ncbi Rapid tRNA decay can result from lack of nonessential modifications
    Andrei Alexandrov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Mol Cell 21:87-96. 2006
  8. ncbi Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications
    Irina Chernyakov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, USA
    Methods Enzymol 449:221-37. 2008
  9. ncbi A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA
    Feng Xing
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, New York 14642, USA
    RNA 8:370-81. 2002
  10. ncbi Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C
    Weifeng Gu
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Mol Cell Biol 25:8191-201. 2005

Research Grants

  1. Biochemical Genomics Linking Genes and Activities
    Eric Phizicky; Fiscal Year: 2004
  2. tRNA Processing
    Eric Phizicky; Fiscal Year: 2007
  3. tRNA Processing
    Eric Phizicky; Fiscal Year: 2009
  4. tRNA Processing
    Eric M Phizicky; Fiscal Year: 2010
  5. TRNA SPLICING
    Eric Phizicky; Fiscal Year: 2002
  6. tRNA Processing
    Eric M Phizicky; Fiscal Year: 2011

Collaborators

  • Anita Hopper
  • Michael Snyder
  • Heng Zhu
  • Juan Alfonzo
  • HARMIT MALIK
  • Mark B Gerstein
  • M W Gray
  • Li A Kung
  • T R Hughes
  • Eric Z Yu
  • STANLEY H FIELDS
  • Jane E Jackman
  • Elizabeth J Grayhack
  • Irina Chernyakov
  • Andrei Alexandrov
  • Weifeng Gu
  • Feng Xing
  • Athulaprabha Murthi
  • Ethan A Merritt
  • Lakmal Kotelawala
  • Shawna L Hiley
  • Michelle A Steiger
  • Daniel M Gelperin
  • Neil P Shull
  • Robert A Cartlidge
  • Mark E Dumont
  • Hussam H Shaheen
  • Hsiao Yun Huang
  • Melanie A Preston
  • Tsung Po Lai
  • Helen Neely
  • Erin Quartly
  • George DeTitta
  • Joseph Luft
  • Joseph M Whipple
  • Wesley C Van Voorhis
  • Margaret Holmes
  • Melanie A Baker
  • Frank Zucker
  • Angela Lauricella
  • Wim G J Hol
  • Frederick S Buckner
  • Stacy Piccirillo
  • Michael A White
  • Axel Knebel
  • Haiyuan Yu
  • Lixia Jiang
  • Rebecca L Hurto
  • Yoshiko Kon
  • Mark Peggie
  • Nelson Lopez-Hoyo
  • Martha L Wilkinson
  • Philip Cohen
  • Kevin J Wise
  • Sherry L Spinelli
  • Douglas J LaCount
  • Marissa Vignali
  • Lori W Schoenfeld
  • Julie Babulski
  • Christina de Vries
  • Wim G Hol
  • Daniela De Rosa
  • Erin Quartley
  • Sarah F Mitchell
  • Rebecca K Montange
  • Amanda J Lohan
  • Mark R Martzen

Detail Information

Publications25

  1. ncbi tRNA biology charges to the front
    Eric M Phizicky
    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Genes Dev 24:1832-60. 2010
    ....
  2. ncbi Proteome-scale analysis of biochemical activity
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA
    Crit Rev Biochem Mol Biol 41:315-27. 2006
    ....
  3. ncbi Have tRNA, will travel
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester Medical School, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 102:11127-8. 2005
  4. ncbi Protein analysis on a proteomic scale
    Eric Phizicky
    University of Rochester School of Medicine, Department of Biochemistry and Biophysics, Box 712, 601 Elmwood Avenue, Rochester, New York 14642, USA
    Nature 422:208-15. 2003
    ....
  5. ncbi Do all modifications benefit all tRNAs?
    Eric M Phizicky
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA
    FEBS Lett 584:265-71. 2010
    ..The specificity of these enzymes is often enhanced by complex substrate recognition patterns and sub-cellular compartmentalization...
  6. ncbi Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1
    Irina Chernyakov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Genes Dev 22:1369-80. 2008
    ..The RTD pathway is the first to be implicated in the turnover of mature RNA species from the class of stable RNAs. These results and the results of others demonstrate that tRNA, like mRNA, is subject to multiple quality control steps...
  7. ncbi Rapid tRNA decay can result from lack of nonessential modifications
    Andrei Alexandrov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Mol Cell 21:87-96. 2006
    ..The degradation of an endogenous tRNA species at a rate typical of mRNA decay demonstrates a critical role of nonessential modifications for tRNA stability and cell survival...
  8. ncbi Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications
    Irina Chernyakov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, USA
    Methods Enzymol 449:221-37. 2008
    ..These approaches have been used successfully for several modification defects that result in tRNA turnover...
  9. ncbi A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA
    Feng Xing
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, New York 14642, USA
    RNA 8:370-81. 2002
    ..Yeast extract from a dus1-A strain is completely defective in modification of yeast pre-tRNAPhe, and RNA isolated from dus1-delta and dus2-delta strains is significantly depleted in dihydrouridine content...
  10. ncbi Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C
    Weifeng Gu
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Mol Cell Biol 25:8191-201. 2005
    ..We developed a new method to map m(5)C residues in RNA and localized the additional m(5)C to positions 48 and 50. This is the first documented example of the accumulation of additional modifications in a eukaryotic tRNA species...
  11. ncbi Identification and characterization of modification enzymes by biochemical analysis of the proteome
    Jane E Jackman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY, USA
    Methods Enzymol 425:139-52. 2007
    ....
  12. ncbi The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs
    Feng Xing
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    J Biol Chem 279:17850-60. 2004
    ..We show that each of the four Dus proteins has a distinct position specificity: Dus1p for U(16) and U(17), Dus2p for U(20), Dus3p for U(47), and Dus4p for U(20a) and U(20b)...
  13. ncbi A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae
    Neil P Shull
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine 601 Elmwood Avenue, Rochester, NY 14642, USA
    Nucleic Acids Res 33:650-60. 2005
    ..poa1-Delta mutants have no obvious growth defect at different temperatures in rich media, and analysis of yeast extracts suggests that approximately 90% of Appr1p processing activity originates from Poa1p...
  14. ncbi Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism
    Michelle A Steiger
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA
    RNA 11:99-106. 2005
    ..The high degree of conservation of these residues suggests that the entire Tpt1p family is involved in a similar two-step chemical reaction...
  15. ncbi Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9
    Jane E Jackman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    RNA 9:574-85. 2003
    ..Trm10p homologs are found widely in eukaryotes and many archaea, with multiple homologs in several metazoans, including at least three in humans...
  16. ncbi tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis
    Weifeng Gu
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Genes Dev 17:2889-901. 2003
    ..Surprisingly, despite its varied activities, Thg1p contains no recognizable catalytic or functional domains...
  17. ncbi Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
    Daniel M Gelperin
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    Genes Dev 19:2816-26. 2005
    ..Global analysis of glycosylated proteins identifies 109 new confirmed N-linked and 345 candidate glycoproteins, nearly doubling the known yeast glycome...
  18. ncbi Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae
    Athulaprabha Murthi
    Department of Molecular Genetics, Graduate Program in Molecular, Cellular, and Developmental Biology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
    Mol Biol Cell 21:639-49. 2010
    ..Finally, we implicate Tef1, the yeast orthologue of translation elongation factor eEF1A, in the tRNA reexport process and show that its subcellular distribution between the nucleus and cytoplasm is dependent upon Mtr10 and Msn5...
  19. ncbi tRNAHis guanylyltransferase adds G-1 to the 5' end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases
    Jane E Jackman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, New York 14642, USA
    RNA 12:1007-14. 2006
    ..Moreover, Thg1 and tRNA synthetases share two other features: They act in close proximity to one another at the top of the tRNA aminoacyl-acceptor stem, and the chemistry of their respective reactions is strikingly similar...
  20. ncbi The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins
    Jane E Jackman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York, USA
    Methods Mol Biol 488:383-93. 2008
    ..This technique is also broadly applicable to other classes of RNA-protein interactions, including RNA binding and RNA degradation, and can be used with any of the proteomic libraries that are available...
  21. ncbi tRNA transfers to the limelight
    Anita K Hopper
    Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
    Genes Dev 17:162-80. 2003
  22. ncbi Waste not, want not: a case for tRNA repair
    Eric M Phizicky
    Nat Struct Mol Biol 15:783-4. 2008
  23. ncbi Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function
    Ethan A Merritt
    Structural Genomics of Pathogenic Protozoa SGPP Consortium, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:474-8. 2008
    ..Together with the presence of an additional domain between strands beta6 and beta7 that is conserved in trypanosomatid genomes, this suggests that the function of these homologs has diverged from other members of the fold family...
  24. ncbi A facile method for high-throughput co-expression of protein pairs
    Andrei Alexandrov
    Structural Genomics of Pathogenic Protozoa (SGPP) Consortium and Center for Human Genetics and Molecular Pediatric Disease, University of Rochester Medical Center, Rochester, NY 14642, USA
    Mol Cell Proteomics 3:934-8. 2004
    ..This greatly facilitates co-expression for structural genomics projects that produce thousands of clones bearing identical origins and antibiotic markers...
  25. ncbi The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells
    Robert A Cartlidge
    MRC Protein Phosphorylation Unit, School of Life Sciences, MSI WTB complex, University of Dundee, Dundee, UK
    EMBO J 24:1696-705. 2005
    ..In contrast, expression of METTL1 or METTL1[S27A] partially rescued growth. These results demonstrate that METTL1 is inactivated by PKB and RSK in cells, and the potential implications of this finding are discussed...

Research Grants21

  1. Biochemical Genomics Linking Genes and Activities
    Eric Phizicky; Fiscal Year: 2004
    ..Application of these techniques to other organisms, including humans and pathogens, will greatly accelerate biochemical analysis and can be used to rapidly identify drug targets. ..
  2. tRNA Processing
    Eric Phizicky; Fiscal Year: 2007
    ..Many of these modifications are biochemically interesting and are located in important regions of the tRNA. Finally, the function of some tRNA modification enzymes will be studied in vivo. ..
  3. tRNA Processing
    Eric Phizicky; Fiscal Year: 2009
    ....
  4. tRNA Processing
    Eric M Phizicky; Fiscal Year: 2010
    ....
  5. TRNA SPLICING
    Eric Phizicky; Fiscal Year: 2002
    ..coli, by the construction and analysis of mutated phosphotransferase proteins, coupled with analysis of the growth defect and its likely cause in E. coli. ..
  6. tRNA Processing
    Eric M Phizicky; Fiscal Year: 2011
    ....