Ya-Ming Hou

Ya-Ming Hou

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Ya-Ming Hou

Publications by authors named "Ya-Ming Hou"

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How to Untie a Protein Knot.

Structure 2019 Aug;27(8):1190-1191

Department of Biochemistry and Molecular Biology, Thomas Jefferson University Philadelphia, PA 19107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.07.008DOI Listing
August 2019

TrmD: A Methyl Transferase for tRNA Methylation With mG37.

Enzymes 2017;41:89-115. Epub 2017 Apr 12.

Center of New Technologies, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1016/bs.enz.2017.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054489PMC
June 2019

tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance.

Cell Syst 2019 Apr 10;8(4):302-314.e8. Epub 2019 Apr 10.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712193007
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http://dx.doi.org/10.1016/j.cels.2019.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483872PMC
April 2019

Loss-of-function mutations in Lysyl-tRNA synthetase cause various leukoencephalopathy phenotypes.

Neurol Genet 2019 Apr 18;5(2):e565. Epub 2019 Apr 18.

Department of Neurology (C.S., J.S., C.Z., J. Lu, J.X., S. Luo, J. Lin), Huashan Hospital, Fudan University, Shanghai, China; Baylor Genetic Laboratories (Y.J., Z.N., M.L.L., M.W., R.E.P., H.M., Y.Y.), Houston, TX; Department of Radiology (Y.L.), Huashan Hospital, Fudan University; Department of Pathology (Y.W., M.G.), Huashan Hospital, Fudan University, Shanghai, China; Department of Biochemistry and Molecular Pharmacology (M.L., K.D., Y.-M.H.), Thomas Jefferson University, Philadelphia, PA; Department of Human Genetics (S.N.O., A.A.), University of Michigan Medical School, Ann Arbor, MI; Department of Pediatrics and Department of Obstetrics and Gynecology (S.L.), University of Hawaii School of Medicine, Honolulu, HI; Department of Medical Oncology and Therapeutics Research (T.P.S.), Division of Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA; Department of Molecular and Human Genetics (P.L.M., A.L.M., L.E., S.R.L., Z.N., M.L.L., J.A.R., M.W., R.E.P., H.M., J.A.R., Y.Y., V.W.Z.), Baylor College of Medicine, Houston, TX; and AmCare Genomics Lab (V.W.Z.), Guangzhou, China.

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http://dx.doi.org/10.1212/NXG.0000000000000316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515944PMC
April 2019

Codon-Specific Translation by mG37 Methylation of tRNA.

Front Genet 2018 10;9:713. Epub 2019 Jan 10.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States.

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http://dx.doi.org/10.3389/fgene.2018.00713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335274PMC
January 2019

tRNA 3'-amino-tailing for stable amino acid attachment.

RNA 2018 12 14;24(12):1878-1885. Epub 2018 Sep 14.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.068015.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239183PMC
December 2018

Selective terminal methylation of a tRNA wobble base.

Nucleic Acids Res 2018 04;46(7):e37

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gky013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909439PMC
April 2018

Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel.

J Mol Biol 2017 06 5;429(12):1873-1888. Epub 2017 May 5.

Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2017.04.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5511029PMC
June 2017

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis.

Nucleic Acids Res 2017 04;45(7):4081-4093

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkw1229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397188PMC
April 2017

Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases.

Authors:
Ya-Ming Hou

Methods Mol Biol 2016 ;1421:79-96

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, BLSB 220, Philadelphia, PA, 19107-5719, USA.

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http://dx.doi.org/10.1007/978-1-4939-3591-8_8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864976PMC
December 2016

Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide.

Proc Natl Acad Sci U S A 2016 12 14;113(52):15096-15101. Epub 2016 Nov 14.

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;

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http://dx.doi.org/10.1073/pnas.1612268113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206563PMC
December 2016

Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria.

BMC Genomics 2016 12 8;17(1):1003. Epub 2016 Dec 8.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, BLSB 220, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1186/s12864-016-3314-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143459PMC
December 2016

Methyl transfer by substrate signaling from a knotted protein fold.

Nat Struct Mol Biol 2016 Oct 29;23(10):941-948. Epub 2016 Aug 29.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nsmb.3282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429141PMC
October 2016

Kinetic Analysis of tRNA Methyltransferases.

Methods Enzymol 2015 2;560:91-116. Epub 2015 Jun 2.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania USA.

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http://dx.doi.org/10.1016/bs.mie.2015.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860815PMC
May 2016

Molecular Basis and Consequences of the Cytochrome c-tRNA Interaction.

J Biol Chem 2016 May 9;291(19):10426-36. Epub 2016 Mar 9.

the Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and

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http://dx.doi.org/10.1074/jbc.M115.697789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858987PMC
May 2016

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.

Proc Natl Acad Sci U S A 2015 Aug 16;112(31):E4197-205. Epub 2015 Jul 16.

RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Structural Biology Laboratory, Tsurumi-ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1073/pnas.1422981112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534213PMC
August 2015

The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts.

Int J Mol Sci 2015 Jul 1;16(7):14866-83. Epub 2015 Jul 1.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.3390/ijms160714866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519876PMC
July 2015

Maintenance of protein synthesis reading frame by EF-P and m(1)G37-tRNA.

Nat Commun 2015 May 26;6:7226. Epub 2015 May 26.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1038/ncomms8226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445466PMC
May 2015

Post-transcriptional modifications to tRNA--a response to the genetic code degeneracy.

RNA 2015 Apr;21(4):642-4

Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA.

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http://dx.doi.org/10.1261/rna.049825.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371315PMC
April 2015

Loss-of-function alanyl-tRNA synthetase mutations cause an autosomal-recessive early-onset epileptic encephalopathy with persistent myelination defect.

Am J Hum Genet 2015 Apr 26;96(4):675-81. Epub 2015 Mar 26.

Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010, USA; Departments of Integrated Systems Biology and of Pediatrics, George Washington University, Washington, DC 20052, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385183PMC
April 2015

Impaired function is a common feature of neuropathy-associated glycyl-tRNA synthetase mutations.

Hum Mutat 2014 Nov;35(11):1363-71

Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan; Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan.

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http://dx.doi.org/10.1002/humu.22681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213347PMC
November 2014

Biochemical characterization of pathogenic mutations in human mitochondrial methionyl-tRNA formyltransferase.

J Biol Chem 2014 Nov 6;289(47):32729-41. Epub 2014 Oct 6.

From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,

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http://dx.doi.org/10.1074/jbc.M114.610626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239624PMC
November 2014

A divalent metal ion-dependent N(1)-methyl transfer to G37-tRNA.

Chem Biol 2014 Oct 11;21(10):1351-1360. Epub 2014 Sep 11.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10(th) Street, BLSB 220, Philadelphia, PA 19107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2014.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224600PMC
October 2014

Amino acid-dependent stability of the acyl linkage in aminoacyl-tRNA.

RNA 2014 Jun 21;20(6):758-64. Epub 2014 Apr 21.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.044123.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024630PMC
June 2014

The selective tRNA aminoacylation mechanism based on a single G•U pair.

Nature 2014 Jun 11;510(7506):507-11. Epub 2014 Jun 11.

1] RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [3] RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1038/nature13440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323281PMC
June 2014

A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys.

Biochem J 2014 Mar;458(3):513-23

*Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.

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http://dx.doi.org/10.1042/BJ20131451DOI Listing
March 2014

Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position.

J Mol Biol 2013 Oct 28;425(20):3888-906. Epub 2013 May 28.

Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA; Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521407PMC
October 2013

The temperature sensitivity of a mutation in the essential tRNA modification enzyme tRNA methyltransferase D (TrmD).

J Biol Chem 2013 Oct 28;288(40):28987-96. Epub 2013 Aug 28.

From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.

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http://dx.doi.org/10.1074/jbc.M113.485797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789996PMC
October 2013

Conservation of structure and mechanism by Trm5 enzymes.

RNA 2013 Sep 25;19(9):1192-9. Epub 2013 Jul 25.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.039503.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753926PMC
September 2013

Regulation of cell death by transfer RNA.

Antioxid Redox Signal 2013 Aug 28;19(6):583-94. Epub 2013 Mar 28.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1089/ars.2012.5171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717200PMC
August 2013

The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process.

J Biol Chem 2013 Aug 18;288(35):25562-74. Epub 2013 Jul 18.

Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan.

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http://dx.doi.org/10.1074/jbc.M113.485128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757217PMC
August 2013

High-purity enzymatic synthesis of site-specifically modified tRNA.

Authors:
Ya-Ming Hou

Methods Mol Biol 2012 ;941:195-212

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, BLSB, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/978-1-62703-113-4_15DOI Listing
March 2013

Recognition of guanosine by dissimilar tRNA methyltransferases.

RNA 2012 Sep 30;18(9):1687-701. Epub 2012 Jul 30.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1261/rna.032029.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425783PMC
September 2012

Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases.

RNA 2012 Feb 19;18(2):213-21. Epub 2011 Dec 19.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1261/rna.029983.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264908PMC
February 2012

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels.

Mol Syst Biol 2012 Feb 28;8:572. Epub 2012 Feb 28.

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/msb.2012.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293633PMC
February 2012

A role for SUMO in nucleotide excision repair.

DNA Repair (Amst) 2011 Dec 2;10(12):1243-51. Epub 2011 Oct 2.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.dnarep.2011.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220943PMC
December 2011

Pyrophosphorolysis of CCA addition: implication for fidelity.

J Mol Biol 2011 Nov 5;414(1):28-43. Epub 2011 Oct 5.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2011.09.036DOI Listing
November 2011

Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout.

J Biol Chem 2011 Oct 2;286(43):37721-31. Epub 2011 Sep 2.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

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http://dx.doi.org/10.1074/jbc.M111.246702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199515PMC
October 2011

Potential for interdependent development of tRNA determinants for aminoacylation and ribosome decoding.

Nat Commun 2011 ;2:329

Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1038/ncomms1331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799875PMC
September 2011

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.

RNA 2011 Jul 20;17(7):1236-46. Epub 2011 May 20.

Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.2706011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138561PMC
July 2011

Fluorophore labeling to monitor tRNA dynamics.

Methods Enzymol 2009 ;469:69-93

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1016/S0076-6879(09)69004-2DOI Listing
January 2011

Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5.

RNA 2010 Dec 27;16(12):2484-92. Epub 2010 Oct 27.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.2376210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995409PMC
December 2010

Biosynthesis: A new (old) way of hijacking tRNA.

Nat Chem Biol 2010 Nov;6(11):795-6

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http://dx.doi.org/10.1038/nchembio.459DOI Listing
November 2010

Apoptotic regulation and tRNA.

Protein Cell 2010 Sep;1(9):795-801

Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992325PMC
http://dx.doi.org/10.1007/s13238-010-0107-xDOI Listing
September 2010

Control of catalytic cycle by a pair of analogous tRNA modification enzymes.

J Mol Biol 2010 Jul 7;400(2):204-17. Epub 2010 May 7.

Thomas Jefferson University, Department of Biochemistry and Molecular Biology, 233 South 10th Street, BLSB 220, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892103PMC
July 2010

CCA addition to tRNA: implications for tRNA quality control.

Authors:
Ya-Ming Hou

IUBMB Life 2010 Apr;62(4):251-60

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, BLSB 220, Philadelphia 19107, PA, USA.

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http://dx.doi.org/10.1002/iub.301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848691PMC
April 2010

Stereochemical mechanisms of tRNA methyltransferases.

FEBS Lett 2010 Jan;584(2):278-86

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th St., Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.febslet.2009.11.075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797553PMC
January 2010

Distinct kinetic determinants for the stepwise CCA addition to tRNA.

RNA 2009 Oct 20;15(10):1827-36. Epub 2009 Aug 20.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.1669109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743048PMC
October 2009

Incorporation of tellurocysteine into glutathione transferase generates high glutathione peroxidase efficiency.

Angew Chem Int Ed Engl 2009 ;48(11):2020-3

State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Road, Changchun 130012, China.

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http://dx.doi.org/10.1002/anie.200805365DOI Listing
April 2009

The archetype gamma-class carbonic anhydrase (Cam) contains iron when synthesized in vivo.

Biochemistry 2009 Feb;48(5):817-9

Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA.

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http://dx.doi.org/10.1021/bi802246sDOI Listing
February 2009

RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine.

Nucleic Acids Res 2008 Dec 25;36(21):6806-15. Epub 2008 Oct 25.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkn755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588519PMC
December 2008

Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine.

Nucleic Acids Res 2008 Dec 5;36(22):6999-7008. Epub 2008 Nov 5.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkn797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602760PMC
December 2008

Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.

RNA 2008 Oct 28;14(10):2245-53. Epub 2008 Aug 28.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1261/rna.1158508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553749PMC
October 2008

The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.

J Biol Chem 2008 Aug 17;283(32):21997-2006. Epub 2008 Jun 17.

Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA.

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http://dx.doi.org/10.1074/jbc.M801838200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2494909PMC
August 2008

Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle.

J Biol Chem 2008 Jun 30;283(26):18431-40. Epub 2008 Apr 30.

Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

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http://dx.doi.org/10.1074/jbc.M801560200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2440604PMC
June 2008

Enzymatic synthesis of structure-free DNA with pseudo-complementary properties.

Nucleic Acids Res 2008 Jun 29;36(10):3409-19. Epub 2008 Apr 29.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkn209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2425472PMC
June 2008

tRNA integrity is a prerequisite for rapid CCA addition: implication for quality control.

J Mol Biol 2008 Jun 8;379(3):579-88. Epub 2008 Apr 8.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2008.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430420PMC
June 2008

Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys).

Nat Struct Mol Biol 2008 May 20;15(5):507-14. Epub 2008 Apr 20.

Department of Biochemistry and Molecular Biology, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1038/nsmb.1423DOI Listing
May 2008

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases.

Methods 2008 Feb;44(2):100-18

Department of Biochemistry, University of Vermont, Health Sciences Complex, 89 Beaumont Avenue, Burlington, VT 05405, USA.

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http://dx.doi.org/10.1016/j.ymeth.2007.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288706PMC
February 2008

Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases.

J Mol Biol 2007 Oct 21;373(3):623-32. Epub 2007 Aug 21.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2007.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064070PMC
October 2007

Fluorescent labeling of tRNAs for dynamics experiments.

RNA 2007 Sep 24;13(9):1594-601. Epub 2007 Jul 24.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://www.rnajournal.org/cgi/doi/10.1261/rna.475407
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http://dx.doi.org/10.1261/rna.475407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950756PMC
September 2007

Indirect readout of tRNA for aminoacylation.

Biochemistry 2007 Sep 24;46(37):10419-32. Epub 2007 Aug 24.

Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA.

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http://dx.doi.org/10.1021/bi7014647DOI Listing
September 2007

Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase.

J Mol Biol 2007 Apr 24;367(4):1063-78. Epub 2007 Jan 24.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2007.01.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041962PMC
April 2007

Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases.

J Mol Biol 2006 Aug 27;361(2):300-11. Epub 2006 Jun 27.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2006.06.015DOI Listing
August 2006

Acquisition of an insertion peptide for efficient aminoacylation by a halophile tRNA synthetase.

Biochemistry 2006 Jun;45(22):6835-45

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Suite 220, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi0521386DOI Listing
June 2006

Unrestricted hybridization of oligonucleotides to structure-free DNA.

Biochemistry 2006 Jun;45(22):6978-86

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi0600392DOI Listing
June 2006

Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline.

Biochemistry 2006 Jun;45(24):7463-73

Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi0602314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517134PMC
June 2006

Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA.

Nat Struct Mol Biol 2006 Apr 12;13(4):354-9. Epub 2006 Mar 12.

Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

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http://dx.doi.org/10.1038/nsmb1074DOI Listing
April 2006

Isolation of a site-specifically modified RNA from an unmodified transcript.

Nucleic Acids Res 2006 Feb 10;34(3):e21. Epub 2006 Feb 10.

Department of Biochemistry and Molecular Biology, Thomas Jefferson University 233 South 10th Street, BLSB 220, Philadelphia, PA 19107-5719, USA.

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http://dx.doi.org/10.1093/nar/gnj018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1363780PMC
February 2006

Unrestricted accessibility of short oligonucleotides to RNA.

RNA 2005 Sep;11(9):1441-7

Department of Biochemistry and Molecular Pharmacology, Room 222BLSB, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania, 19107, USA.

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http://dx.doi.org/10.1261/rna.2670705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370827PMC
September 2005

Metal-ion-dependent catalysis and specificity of CCA-adding enzymes: a comparison of two classes.

Biochemistry 2005 Sep;44(38):12849-59

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 1910, USA.

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http://dx.doi.org/10.1021/bi0509402DOI Listing
September 2005

Breaking the stereo barrier of amino acid attachment to tRNA by a single nucleotide.

J Mol Biol 2005 May;348(3):513-21

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2005.02.023DOI Listing
May 2005

Domain-domain communication for tRNA aminoacylation: the importance of covalent connectivity.

Biochemistry 2005 May;44(19):7240-9

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10 Street, BLSB 220, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi050285yDOI Listing
May 2005

Shape-selective RNA recognition by cysteinyl-tRNA synthetase.

Nat Struct Mol Biol 2004 Nov 17;11(11):1134-41. Epub 2004 Oct 17.

Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106-9510, USA.

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http://dx.doi.org/10.1038/nsmb849DOI Listing
November 2004

AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation.

Mol Cell 2004 Oct;16(1):107-16

Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet University Hospital, NO-0027 Oslo, Norway.

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http://dx.doi.org/10.1016/j.molcel.2004.09.002DOI Listing
October 2004

Modified bases in RNA reduce secondary structure and enhance hybridization.

Biochemistry 2004 Aug;43(31):10224-36

Division of Hematology/Oncology, University of Pennsylvania School of Medicine, BRB II/III Room 713, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1021/bi049196wDOI Listing
August 2004

Distinct origins of tRNA(m1G37) methyltransferase.

J Mol Biol 2004 Jun;339(4):707-19

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, BLSB 220, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.jmb.2004.04.025DOI Listing
June 2004

Synthesis of cysteinyl-tRNACys by a prolyl-tRNA synthetase.

RNA Biol 2004 May 5;1(1):35-41. Epub 2004 May 5.

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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May 2004

Amino acid discrimination by a highly differentiated metal center of an aminoacyl-tRNA synthetase.

Biochemistry 2003 Sep;42(37):10931-7

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi034812uDOI Listing
September 2003

Aminoacylation of an unusual tRNA(Cys) from an extreme halophile.

RNA 2003 Jul;9(7):794-801

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370446PMC
http://dx.doi.org/10.1261/rna.5320603DOI Listing
July 2003

Association of an aminoacyl-tRNA synthetase with a putative metabolic protein in archaea.

Biochemistry 2003 Jun;42(24):7487-96

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, BLSB 220, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi0344533DOI Listing
June 2003

Zinc-mediated amino acid discrimination in cysteinyl-tRNA synthetase.

J Mol Biol 2003 Apr;327(5):911-7

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 S 10th Street, BLSB 222, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/s0022-2836(03)00241-9DOI Listing
April 2003

Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.

RNA 2002 Nov;8(11):1363-72

Department of Biochemistry, University of Vermont, Burlington, Vermont 05405, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370343PMC
http://dx.doi.org/10.1017/s1355838202021180DOI Listing
November 2002

Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase.

EMBO J 2002 Jun;21(11):2778-87

Department of Chemistry and Biochemistry, Interdepartmental Program in Biomolecular Science and Engineering, University of California at Santa Barbara, Santa Barbara, CA 93106-9510, USA.

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http://dx.doi.org/10.1093/emboj/21.11.2778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126036PMC
June 2002

Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human.

J Mol Biol 2002 May;318(5):1207-20

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/s0022-2836(02)00232-2DOI Listing
May 2002

Poly(C) synthesis by class I and class II CCA-adding enzymes.

Biochemistry 2002 Apr;41(14):4521-32

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1021/bi0120953DOI Listing
April 2002

Prevention of mis-aminoacylation of a dual-specificity aminoacyl-tRNA synthetase.

J Mol Biol 2002 Feb;315(5):943-9

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1006/jmbi.2001.5297DOI Listing
February 2002

Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA.

J Mol Biol 2002 Feb;316(3):421-7

Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1006/jmbi.2001.5373DOI Listing
February 2002