Graduate Program Information
My Contact Information

Professor of Biochemistry and Biophysics
Ph.D. Cornell University 1983

tRNA Biogenesis, Function and Quality Control

One major lab project focuses on understanding the biology of tRNA. tRNA plays a crucial role in translation, and numerous factors participate in its biogenesis, function, intracellular trafficking, and quality control. In the yeast Saccharomyces cerevisiae, cytoplasmic tRNAs have an average of 13 modifications, and there are a total of 25 chemically distinct modifications, many of which are highly conserved in different organisms, and of unknown function. We previously used a biochemical genomics approach to identify the genes encoding a number of different modification enzymes. We are currently focusing on the assignment of other activities to genes, and on two aspects of the biology of modifications: First, we are investigating the roles of modifications. We recently found evidence that lack of certain modifications can lead to rapid degradation of specific mature tRNAs, suggesting the existence of a quality control pathway that monitors the integrity of tRNA. We are currently working to define the components of this rapid tRNA decay pathway, the mechanism by which tRNAs are targeted for turnover, and the conditions under which this pathway is used. Second, we are defining the mechanisms by which modification enzymes recognize and act on their specific tRNA substrates. Since modifications have crucial roles in the cell, incorrect modification of a tRNA is likely to have catastrophic effects. We recently found that recognition of the tRNA^His anticodon is necessary and sufficient for Thg1 to add a guanine nucleotide to the 5' end of the tRNA, a reaction that is essential in wild type cells for proper translation. We are currently examining other modification enzymes to uncover the different mechanisms by which specificity is attained.

Functional Genomics

A second major lab project focuses on the design, construction and implementation of genomic methods to analyze protein structure and function (in collaboration with Elizabeth Grayhack). To facilitate parallel biochemical analysis of the proteome, we previously constructed two genomic libraries of strains in which nearly every yeast gene is expressed as a tagged fusion protein under regulated control. We are currently using these libraries to define new biochemical activities, and to help define cell circuitry by systematic analysis of genetic suppression caused by overexpression of genes. In addition, in collaboration with investigators at the Hauptman-Woodward Institute, we are developing methodology for high throughput expression and purification of protein complexes from yeast, for structural analysis by x-ray crystallography.

Visit my Lab Page

Recent Publications

Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM (2008) Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Genes Dev, 22:1369-80

Merritt EA, Holmes M, Buckner FS, Van Voorhis WC, Quartly E, Phizicky EM, Lauricella A, Luft J, DeTitta G, Neely H, Zucker F, Hol WG (2008) Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function. Acta Crystallogr Sect F Struct Biol Cryst Commun, 64:474-8

Kotelawala L, Grayhack EJ, Phizicky EM (2008) Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species. Rna, 14:158-69

Phizicky EM (2008) Waste not, want not: a case for tRNA repair. Nat Struct Mol Biol, 15:783-4

Jackman JE, Phizicky EM (2008) Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase. Biochemistry, 47:4817-25

Jackman JE, Grayhack EJ, Phizicky EM (2008) The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins. Methods Mol Biol, 488:383-93

Chernyakov I, Baker MA, Grayhack EJ, Phizicky EM (2008) Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications. Methods Enzymol, 449:221-37

Wilkinson ML, Crary SM, Jackman JE, Grayhack EJ, Phizicky EM (2007) The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. Rna, 13:404-13

Malkowski MG, Quartley E, Friedman AE, Babulski J, Kon Y, Wolfley J, Said M, Luft JR, Phizicky EM, DeTitta GT, Grayhack EJ (2007) Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing. Proc Natl Acad Sci U S A, 104:6678-83

Jackman JE, Kotelawala L, Grayhack EJ, Phizicky EM (2007) Identification and characterization of modification enzymes by biochemical analysis of the proteome. Methods Enzymol, 425:139-52

Phizicky EM, Grayhack EJ (2006) Proteome-scale analysis of biochemical activity. Crit Rev Biochem Mol Biol, 41:315-27

Jackman JE, Phizicky EM (2006) tRNAHis guanylyltransferase catalyzes a 3'-5' polymerization reaction that is distinct from G-1 addition. Proc Natl Acad Sci U S A, 103:8640-5

Jackman JE, Phizicky EM (2006) 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. Rna, 12:1007-14

Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, Phizicky EM (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell, 21:87-96

Graduate students in my laboratory work toward a Ph.D. degree in the following program[s]:

Ph.D. in Biochemistry
Ph.D. in Biophysics
Ph.D. in Genetics

Ph.D. candidates in my laboratory may also be affiliated with these programs:

Contact Information

E-Mail: Eric_Phizicky@urmc.rochester.edu

Eric Phizicky
Department of Biochemistry and Biophysics
University of Rochester School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, New York 14642

Office: Medical Center 3-7411
Telephone: (585) 275-7268; Fax: (585) 271-2683