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Philip Farabaugh


Biological Sciences
Biological Sciences Bldg, Room BS 478 (BIOL Main Office)
Postdoc, Cornell University (1981)
Ph D, Harvard University (1978)
BA, University of California San Diego (1972)
Research Interests

Our laboratory has been concerned with odd events that occur during protein synthesis. We originally discovered programmed +1 translational frameshifting in the Ty family of retrotransposons about 30 years ago and spent many years thoroughly exploring its mechanism. At the end of that work, we discovered we had been studying how the Ty elements manipulated the translation system to drastically increase the frequency of translational errors by forcing decoding by an "incorrect" tRNA—one that makes fewer than three base pairs with the mRNA. We became intrigued with the associated issue of "misreading", where incorrect tRNAs are occasionally accepted into the ribosome resulting in an incorrect protein being produced. Our work has identified a general mechanism responsible for these errors in which non-Watson/Crick base pairs mimic the structure of the standard A•U and G•C pairs, forcing errors that cause specific misreading errors at high frequency. We continue to explore the mechanism(s) underlying these errors and the ways the cell ensures that their frequency doesn't get out of hand.

Teaching Interests

As a molecular geneticist, I have taught a range of courses from the introductory level (BIOL 100 Concepts of Biology, BIOL 302 Molecular and General Genetics), advanced (BIOL 414/614 Eukaryotic Molecular Genetics, BIOL 426/626 Approaches to Molecular Biology) and graduate seminars (BIOL 770 - Graduate Seminar in Molecular Biology).

Contracts, Fellowships, Grants, and Sponsored Research

Farabaugh, Philip J. (Co-Principal) Stansfield, Ian (Co-Principal) Synthetic gene circuits to measure and mitigate translational stress during heterologous protein expression Grant (Funded) Sponsored by National Science Foundation (Jul 30, 2016 – Jul 30, 2020)

Farabaugh, Philip J. Role of phosphorylation of ribosomal proteins in translational accuracy Sponsored Research (Funded) Sponsored by UMBC-SRAIS (Jul 1, 2013 – Jun 30, 2014)

Farabaugh, Philip J. 2013 Teacher Quality in Biology Program at UMBC Grant (Funded) Sponsored by Maryland Higher Education Commission, Improving Teacher Quality (Nov 27, 2012 – Mar 31, 2014)

Farabaugh, Philip J. The UMBC GAANN Doctoral Program in the Biological Scienc Grant (Funded) Sponsored by U.S. Department of Education (Aug 16, 2012 – Aug 15, 2015)

Farabaugh, Philip J. ARRA: Molecular genetics of translational accuracy ARRA - Recovery Act (Funded) Sponsored by National Institute of General Medical Sciences, NIH (Jul 20, 2009 – Jun 30, 2012)

Farabaugh, Philip J. Molecular genetics of translational accuracy Grant (Funded) Sponsored by National Institute of General Medical Sciences, NIH (May 15, 2007 – Apr 30, 2009)

Farabaugh, Philip J. Molecular Basis of Translational Recoding in Yeast Grant (Funded) Sponsored by National Institute of General Medical Sciences, NIH (Aug 1, 1989 – Mar 31, 2007)

Farabaugh, Philip J. Molecular Basis of Translational Recording in Yeast Grant (Funded) Sponsored by National Institute of General Medical Sciences, NIH (Aug 1, 1989 – Mar 31, 2007)

Intellectual Contributions

vol. Online before print Oxford Yeast

Nucleic Acids Research

4 vol. 44 1871-81 London, England, United Kingdom Nucleic acids research

vol. 6 22 Mobile DNA

8 vol. 21 1454-68 RNA (New York, N.Y.)

8 vol. 39 355-362 Cambridge, MA Trends in Biochemical Sciences

1 vol. 20 9-15 Cold Spring Harbor, NY RNA

15 vol. 33 2918-2929 Washington, DC Molecular and Cellular Biology

vol. 16 1797-1808 Cold Spring Harbor, NY RNA

vol. 185 1193-1205 Genetics

vol. 15 1100-1109 Cold Spring Harbor, NY RNA

vol. 15 889-897 Cold Spring Harbor, NY RNA

The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. 1 vol. 13 87-96 RNA (New York, N.Y.)

Evolution of +1 programmed frameshifting signals and frameshift-regulating tRNAs in the order Saccharomycetales. 4 vol. 63 545-61 Journal of molecular evolution

Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes vol. 26 438-447 Mol Cell Biol

vol. 3 331-338 Eukaryotic Cell

vol. 9 760-768 RNA

Shifty ciliates: frequent programmed translational frameshifting in Euplotids vol. 111 763-766 Cell

vol. 27 178-183 Trends Biochem Sci

Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. vol. 66 249-58 Cold Spring Harbor symposia on quantitative biology

vol. 64 131-170 Prog Nucl Acid Res Mol Biol

vol. 4 1005-1015 Mol Cell

How translational accuracy influences reading frame maintenance, vol. 18 1427-1434 EMBO J

vol. 1 471-482 Mol Cell

vol. 30 507-528 Annu Rev Genetics

vol. 60 103-134 Microbiol Rev

vol. 14 8107-8116 Mol Cell Biol

vol. 74 93-103 Cell

vol. 62 339-352 Cell


(Author & Presenter) (Author) (Author) (Author) (Author) 27th tRNA Conference Poster The pattern of misreading error frequencies in vivo supports a molecular mimicry model for tRNA misreading International Union of Biochemistry and Molecular Biology Strasbourg, France

(Author) (Author) (Author & Presenter) Translational Control Poster Control of translational missense errors in Saccharomyces cerevisiae by phosphorylation of Ser176 of ribosomal protein uS5 by both Ctk1 and Tor/Pkc1 pathways Cold Spring Harbor Laboratory Cold Spring Harbor, NY