URMC / Labs / Phizicky Lab / Publications Publications Phizicky EMHopper AK The Life and Times of a tRNA.; RNA (New York, N.Y.). 2023 Apr 13. Tasak MPhizicky EM Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay path way in evolutionarily distant yeast species.; PLoS genetics; Vol 18(7), pp. e1010215. 2022 Jul 28. Funk HMDiVita DJSizemore HEWehrle KMiller CLWFraley MEMullins AKGuy ARPhizicky EMGuy MP Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7.; ACS omega; Vol 7(16). 2022 Apr 26. Han LMarcus EPhizicky EM A semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes.; Methods in enzymology; Vol 658. 2021. De Zoysa TPhizicky EM Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences.; PLoS genetics; Vol 16(8). 2020 Aug 25. Payea MJHauke ACDe Zoysa TPhizicky EM Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast.; RNA (New York, N.Y.). 2019 Oct 16. Ramos JHan LLi YHagelskamp FKellner SMAlkuraya FSPhizicky EMFu D Formation of tRNA wobble inosine in humans is disrupted by a millennia-old mutation causing intellectual disability.; Molecular and cellular biology. 2019 Jul 01. Shaheen RTasak MMaddirevula SAbdel-Salam GMHSayed ISMAlazami AMAl-Sheddi TAlobeid EPhizicky EMAlkuraya FS PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly.; Human genetics. 2019 Feb 18. Han LPhizicky EM A rationale for tRNA modification circuits in the anticodon loop.; RNA (New York, N.Y.). 2018 Jul 19. Zimmerman SMKon YHauke ACRuiz BYFields SPhizicky EM Conditional accumulation of toxic tRNAs to cause amino acid misincorporation.; Nucleic acids research. 2018 Jul 11. Han LGuy MPKon YPhizicky EM Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway.; PLoS genetics; Vol 14(3). 2018 Mar 29. Payea MJSloma MFKon YYoung DLGuy MPZhang XDe Zoysa TFields SMathews DHPhizicky EM Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.; RNA (New York, N.Y.). 2017 Dec 19. Patra BKon YYadav GSevold AWFrumkin JPVallabhajosyula RRHintze AØstman BSchossau JBhan AMarzolf BTamashiro JKKaur ABaliga NSGrayhack EJAdami CGalas DJRaval APhizicky EMRay A A genome wide dosage suppressor network reveals genomic robustness.; Nucleic acids research; Vol 45(1). 2017 Jan 09. Hrabeta-Robinson EMarcus ECozen AEPhizicky EMLowe TM High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq).; Methods in molecular biology (Clifton, N.J.); Vol 1562. 2017. Han LMarcus ED'Silva SPhizicky EM S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates.; RNA (New York, N.Y.). 2016 Dec 21. Shaheen RHan LFaqeih EEwida NAlobeid EPhizicky EMAlkuraya FS A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition.; Human genetics. 2016 Apr 7. Guy MPShaw MWeiner CLHobson LStark ZRose KKalscheuer VMGecz JPhizicky EM Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1.; Human mutation; Vol 36(12). 2015 Dec. Cozen AEQuartley EHolmes ADHrabeta-Robinson EPhizicky EMLowe TM ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.; Nature methods; Vol 12(9). 2015 Sep. Phizicky EMHopper AK tRNA processing, modification, and subcellular dynamics: past, present, and future.; RNA (New York, N.Y.); Vol 21(4). 2015 Apr. Han LKon YPhizicky EM Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast.; RNA (New York, N.Y.); Vol 21(2). 2015 Feb. Payea MJGuy MPPhizicky EM Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway.; Methods in enzymology; Vol 560. 2015. Shaheen RAbdel-Salam GMGuy MPAlomar RAbdel-Hamid MSAfifi HHIsmail SIEmam BAPhizicky EMAlkuraya FS Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism.; Genome biology; Vol 16. 2015. Guy MPPhizicky EM Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes.; RNA (New York, N.Y.); Vol 21(1). 2015 Jan. Zhang XWalker RCPhizicky EMMathews DH Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.; Journal of chemical theory and computation; Vol 10(8). 2014 Aug 12. Guy MPYoung DLPayea MJZhang XKon YDean KMGrayhack EJMathews DHFields SPhizicky EM Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.; Genes & development; Vol 28(15). 2014 Aug 1. Pop CRouskin SIngolia NTHan LPhizicky EMWeissman JSKoller D Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.; Molecular systems biology; Vol 10. 2014. Guy MPPhizicky EM Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification.; RNA biology; Vol 11(12). 2014. Preston MAD'Silva SKon YPhizicky EM tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae.; RNA (New York, N.Y.); Vol 19(2). 2013 Feb. Guy MPPodyma BMPreston MAShaheen HHKrivos KLLimbach PAHopper AKPhizicky EM Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop.; RNA (New York, N.Y.); Vol 18(10). 2012 Oct. Dewe JMWhipple JMChernyakov IJaramillo LNPhizicky EM The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications.; RNA (New York, N.Y.); Vol 18(10). 2012 Oct. Grant TDSnell EHLuft JRQuartley ECorretore SWolfley JRSnell MEHadd APerona JJPhizicky EMGrayhack EJ Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase.; Nucleic acids research; Vol 40(8). 2012 Apr. Whipple JMLane EAChernyakov ID'Silva SPhizicky EM The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA.; Genes & development; Vol 25(11). 2011 Jun 01. D'Silva SHaider SJPhizicky EM A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop.; RNA (New York, N.Y.); Vol 17(6). 2011 Jun. Phizicky EMHopper AK tRNA biology charges to the front.; Genes & development; Vol 24(17). 2010 Sep 1. Preston MAPhizicky EM The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase.; RNA (New York, N.Y.); Vol 16(5). 2010 May. Murthi AShaheen HHHuang HYPreston MALai TPPhizicky EMHopper AK Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae.; Molecular biology of the cell; Vol 21(4). 2010 Feb 15. Phizicky EMAlfonzo JD Do all modifications benefit all tRNAs?; FEBS letters; Vol 584(2). 2010 Jan 21. Quartley EAlexandrov AMikucki MBuckner FSHol WGDeTitta GTPhizicky EMGrayhack EJ Heterologous expression of L. major proteins in S. cerevisiae: a test of solubility, purity, and gene recoding.; Journal of structural and functional genomics; Vol 10(3). 2009 Sep. Phizicky EM Waste not, want not: a case for tRNA repair.; Nature structural & molecular biology; Vol 15(8). 2008 Aug. Merritt EAHolmes MBuckner FSVan Voorhis WCQuartly EPhizicky EMLauricella ALuft JDeTitta GNeely HZucker FHol WG Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function.; Acta crystallographica. Section F, Structural biology and crystallization communications; Vol 64(Pt 6). 2008 Jun 1. Chernyakov IWhipple JMKotelawala LGrayhack EJPhizicky EM Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.; Genes & development; Vol 22(10). 2008 May 15. Jackman JEPhizicky EM Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase.; Biochemistry; Vol 47(16). 2008 Apr 22. Kotelawala LGrayhack EJPhizicky EM 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 (New York, N.Y.); Vol 14(1). 2008 Jan. Jackman JEGrayhack EJPhizicky EM The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins.; Methods in molecular biology (Clifton, N.J.); Vol 488. 2008. Chernyakov IBaker MAGrayhack EJPhizicky EM Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications.; Methods in enzymology; Vol 449. 2008. Malkowski MGQuartley EFriedman AEBabulski JKon YWolfley JSaid MLuft JRPhizicky EMDeTitta GTGrayhack EJ Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing.; Proceedings of the National Academy of Sciences of the United States of America; Vol 104(16). 2007 Apr 17. Wilkinson MLCrary SMJackman JEGrayhack EJPhizicky EM The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4.; RNA (New York, N.Y.); Vol 13(3). 2007 Mar. Jackman JEKotelawala LGrayhack EJPhizicky EM Identification and characterization of modification enzymes by biochemical analysis of the proteome.; Methods in enzymology; Vol 425. 2007. Phizicky EMGrayhack EJ Proteome-scale analysis of biochemical activity.; Critical reviews in biochemistry and molecular biology; Vol 41(5). 2006 Sep. Jackman JEPhizicky EM tRNAHis guanylyltransferase catalyzes a 3'-5' polymerization reaction that is distinct from G-1 addition.; Proceedings of the National Academy of Sciences of the United States of America; Vol 103(23). 2006 Jun 6.