2024
Maharjan, S, Gamper, H, Yamaki, Y, Christian, T, Henley, RY, Li, NS, Suzuki, T, Suzuki, T, Piccirilli, JA, Wanunu, M, Seifert, E, Wallace, DC, Hou, YM. (2024) Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology. Nature Commun 15(1):9008, doi: 10.1038/s41467-024-53318-x; PMID: 39424798; PMCID:PMC11489592
Makhamreh, A, Tavakoli, S, Fallahi, A, Kang, X, Gamper, H, Nabizadehmashhadtoroghi, M, Jain, M, Hou, YM, Rouhanifard, SH, Wanunu, M. (2024) Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific; quantification requires dedicated synthetic controls. Sci Rep. 14(1): 22457. DOI: 10.1038/s41598-024-72994-9; PMID: 39341872; PMCID:PMC11438862.
Namani, S, Kavetsky, K, Lin, CY, Maharjan, S, Gamper, H, Li, NS, Piccirilli, J, Hou, YM, Drndic, M. (2024) Unraveling RNA conformation dynamics in MELAS syndrome with solid-state nanopores. ACS Nano, PMID: 38906834, DOI:10.1021/acsnano.4c04625
Masuda, I, Hou, YM. (2024) A tRNA modification pattern that facilitates interpretation of the genetic code. Submitted to Frontier in Microbiology, PMID: 38933027; PMCID: PMC11199890.
Avila, YI, Rebolledo, LP, Skelly, E, de Freitas Saito, R, Wei, H, Lilley, D, Stanley RE, Hou, YM, Yang, H, Sztuba-Solinska, J, Chen, SJ, Dokholyan, NV, Tan, C, Li, K, He, X, Zhang, X, Miles, W, Franco, E, Binzel, DW, Guo, P, Afonin, KA (2024) Cracking the code: Enhancing molecular tools for progress in nanotechnology. ACS Applied Bio Materials, PMID: 38833534; PMCID: PMC11190997.
Tubiana, L, Alexander, G, Barbensi, A, Buck, D, Cartwright, JHE, Chwastyk, M, Cieplak, M, Coluzza, I, Copar, S, Craik, DJ, Di Stefano, M, Everaers, R, Faisca, P, Ferrari, F, Giacometti, A, Goundaroulis, D, Haglund, E, Hou, YM, Ilieva, N, Jackson, S, Japaridze, A, Kaplan, N, Klotz, AR, Li, H. Likos, CN, Locatelli, E, Lopez-Leon, T, Machon, T, Micheletti, C, Michieletto, D, Niemi, A, Niemyska, W, Niewieczerzal, S, Nitti, F, Orlandini, E, Pasquali, S, Perlinska, AP, Podgornik, R, Potestio, R, Pugno, N, Ravnik, M, Ricca, R, Rohwer, CM, Rosa, A, Smrek, J, Souslov, A, Stasiak, A, Steer, D, Sulkowska, J, Sulkowski, P, Sumners, DL, Svaneborg, C, Szymczak, P, Tarenzi, T, Travasso, R, Virnau, P, Vlassopoulos, D, Ziherl, P, Zumer, S. (2024) Topology in soft and biological matter. Eutopia review. Physics Reports, https://doi.org/10.1016/j.physrep.2024.04.002. In press.
Hou, YM, Nakano, Y. (2024) Breaking the deadlock in genetic code expansion. Invited for an article in News & Views, commenting on the paper in Nature “Adding a,a-disubstituted and b-linked monomers to the genetic code of an organism. Nature Chem Biology, PMID: 38467845. https://www.nature.com/articles/s41589-024-01579-4
2023
Gamper, H, McCormick, C, Makhamreh, A, Wanunu, M, Rouhanifard, SH, Hou, YM. (2023) Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods in Enzymology, Academic Press, https://doi.org/10.1016/bs.mie.2023.04.024. PMID: 37925177
Jedrzejewski, M, Belza, B, Lewandowska, I, Sadlej, M, Perlinska, AP, Augustyniak, R, Christian, T, Hou, YM, Kalek, M, Sulkowska JI. (2023) Nucleolar essential protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by combined molecular dynamics simulation and quantum chemical calculations. Comput Struct Biotechnology J, 21: 3999-4008. PMID: 37649713; PMCID:PMC10462857
Li, Y, Majumdar, S, Treen, R., Manjari, S, Corro, J, Gamper, HB, Banavali, N, Sharma, M, Rhee, K, Stallings, C, Hou, YM, Agrawal, RK, Ojha, AK. (2023) Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation. Proc Natl Acad Sci, May 30; 120(22): e2302006120. PMID: 37216503; PMCID: PMC10235957
Avcilar-Kucukgoze, I, Gamper, H, Hou, YM, Kashina, A. (2023) Preparation of an enriched tRNAArg fraction for arginylation by expression in E. coli, Chapter 4 in “Protein Arginylation: Methods and Protocols”, 2nd edition, edited by Anna Kashina, Springer Nature series of “Methods in Molecular Biology” 2620:101-106. PMID: 37010754
Yamaki, Y, Gamper, H, Hou, YM. (2023) Synthesis of stably charged Arg-tRNAArg for structural analysis, Chapter 28 in “Protein Arginylation: Methods and Protocols”, 2nd edition, edited by Anna Kashina, Springer Nature series of “Methods in Molecular Biology” 2620: 263-271. PMID: 37010769
Masuda, I, Hou, YM. (2023) tRNA methylation resolves codon usage bias at the limit of cell viability. Yodosha company, Ltd, Jikken Igaku 41 (6): 955-956 (2023). https://www.yodosha.co.jp/jikkenigaku/articles/index.html?ci=40700. DOI: 10.18958/7223-00003-0000407-00
Masuda, I, Hou, YM. (2023) Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen. Star Protocols https://star-protocols.cell.com/protocols/2565; DOI: 10.1016/j.xpro.2023.102196
Tavakoli, S, Nabizadeh, M, Makhamreh, A, Gamper, H, Rezapour, NK, Hou, YM, Wanunu, M, Rouhanifard, SH. (2023) Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing. Nat Commun 14(1):334. PMID:36658122; PMCID:PMC9852470
2022
Masuda, I, Yamaki, Y, Detroja, R, Tagore, S, Moore, H, Maharjan, S, Nakano, Y, Christian, T, Matsubara, R, Lowe, T, Frenkel-Morgenstern, M, Hou, YM. (2022) tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Reports 41(4):111539. PMID: 36288695
Cui, Z, Li, X, Gamper, H, Hou, YM, Sacchettini, JC, Zhang, J. (2022) Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Nat Communications, PMID: 35064151.
Gamper, H, Masuda, I, Hou, YM. (2022) Genome expansion by tRNA +1 frameshifting at quadruplet codons. J. Mol Biol, in press. PMID: 34995554
2021
Carbone, C, Loveland, AB, Gamper, HB, Hou, YM, Demo, G, Korostelev, AA. (2021) Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Nat Communications, PMID: 34903725; PMCID:PMC8668904
Gamper, H, Mao, Y, Masuda, I, McGuigan, H, Blaha, G, Wang, Y, Xu, S, Hou, YM. (2021) Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis. Nucleic Acids Res, in press. PMID:34417618; PMCID:PMC8464047
Masuda, I, Hwang, JY, Christian, T, Maharjan, S, Mohammad, F, Gamper, H, Buskirk, AR, Hou, YM. (2021) Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife, 10:e70619. PMID: 34382933; PMCID: PMCID: PMC8384417
Demo, G, Gamper, H, Loveland, AB, Masuda, I, Svidritskiy, E, Hou*, YM, Korostelev*, AA. (2021) Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Communications, 12(1):4644. PMID:34330903. (*: co-corresponding author) PMCID: PMC8324841
Cai, J, Kropf, E, Hou, YM, Iacovitti, L. (2021) A stress-free strategy to correct point mutations in patient iPS cells. Stem Cell Res, https://doi.org/10.1016/j.scr.2021.102332, PMID: 33857832; PMCID:PMC8283763
Gamper, H, Li, H, Masuda, I, Robkis, DM, Christian, T, Conn, AB, Blaha, G, Petersson, EJ, Gonzalez, R, Hou, YM. (2021) Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat Communications, 12(1):328. PMID:33436566; PMCID:PMC7803779
2020
Avcilar-Kucukgoze, I, Gamper, H, Hou, YM, Kashina, A. (2020) Purification and use of tRNA for enzymatic addition of amino acids to proteins. Star Protocols (Cell press), https://doi.org/10.1016/j.xpro.2020.100207. PMID: 33377101; PMCID:PMC7757669
Gamper H, Hou YM. A Label-Free Assay for Aminoacylation of tRNA. Genes (Basel). 2020 Oct 7;11(10):E1173. doi: 10.3390/genes11101173. PMID: 33036365
Perlinska, AP, Kalek*, M, Christian T, Hou*, YM, Sulkowska*, JI. (2020) Mg2+-dependent methyl transfer by a knotted protein: a molecular dynamics simulation and quantum mechanics study (* denotes co-corresponding authors). ACS Catalysis. In press. Selected as the featured cover of vol. 10, issue 15, 2020. PMID: 32904895
Fay AJ, Garcia Y, Margeta M, Maharjan S, Jürgensen C, Briceño J, Garcia M, Yin S, Bassaganyas L, McMahon T, Hou YM, Fu YH, Ptáček LJ.Ann. A Mitochondrial tRNA Mutation Causes Axonal CMT in a Large Venezuelan Family. Neurol. 2020 Jul 26. doi: 10.1002/ana.25854. Online ahead of print. PMID: 32715519
Luo, J, Liu, L, Chen, S, Yu, M, Ge, C, Ren, M, Liu, B, Yang, X, Christian, T, Hou, YM, Zou, J, Zhu, W. (2020) Deacetylation of HSD17B10 by SIRT3 regulates cell growth and cell resistance under stress. Cell Death and Disease 11, 563. PMID: 32703935
Avcilar-Kucukgoze I, Gamper H, Polte C, Ignatova Z, Kraetzner R, Shtutman M, Hou YM, Dong DW, Kashina A. tRNAArg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation. Cell Chem Biol. 2020 Jun 11:S2451-9456(20)30190-2. doi: 10.1016/j.chembiol.2020.05.013. Online ahead of print. PMID: 32553119
Hou YM, Masuda I, Foster LJ. tRNA methylation: An unexpected link to bacterial resistance and persistence to antibiotics and beyond. Wiley Interdiscip Rev RNA. 2020 Jun 13:e1608. doi: 10.1002/wrna.1609. Online ahead of print. PMID: 32533808 Review.
2019
Morelli, KH, Griffin, LB, Pyne, NK, Wallace, LM, Fowler, AM, Oprescu, SN, Takase, R, Wei, N, Meyer-Schuman, R, Mellacheruvau, D, Kitzman, JO, Kocen, SG, Lupski, JR, Nesvizhskii, A, Mancias, P, Butler, I, Yang, XL, Hou, YM, Antonellis, A, Harper, SQ, Burgress, RW. (2019) Allele-specific RNA interference: Precision gene therapy for dominant inherited neuropathy. J. Clinical Investigation 129: 5568-5583. PMID: 31557132; PMCID:PMC6877339.
Yin S, Dhital B, Hou YM. How to Untie a Protein Knot. Structure, 2019.
Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet. 7 March 2019.
Isao Masuda, Ryuma Matsubara, Thomas Christian, Enrique R. Rojas, Srujana S. Yadavalli, Lisheng Zhang, Mark Goulian, Leonard Foster, Kerwyn Casey Huang, Ya-Ming Hou. tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance. Cell Systems 10 April 2019.
Chong Sun, Jie Song, Yanjun Jiang, Chongbo Zhao, Jiahong Lu, Yuxin Li, Yin Wang, Mingshi Gao, Jianying Xi, Sushan Luo, Meixia Li, Kevin Donaldson, Stephanie N. Oprescu, Thomas P. Slavin, Sansan Lee, Pilar L. Magoulas, Andrea M. Lewis, Lisa Emrick, Seema R. Lalani, Zhiyv Niu, Megan L. Landsverk, Magdalena Walkiewicz, Richard E. Person, Hui Mei, Jill A. Rosenfeld, Yaping Yang, Anthony Antonellis, Ya-Ming Hou, Jie Lin, Victor W. Zhang. Loss-of-function mutations in Lysyl-tRNA synthetase cause various leukoencephalopathy phenotypes. Neurology Genetics. April 2019.
Hou, YM, Masuda,I, Gamper, H (2019) Codon-Specific Translation by m1G37 Methylation of tRNA. Front. Genet. 10 January 2019
2018
Masuda, I, Takase, R, Matsubara, R, Paulines, MJ, Gamper, H, Limbach, PA, Hou, YM. (2018) Selective terminal methylation of a tRNA wobble base. Nucleic Acids Res, 46 (7):e37.
Weterman, MAJ, Kuo, M, Kenter, SB, Gordillo, S, Karjosukarso, D, Takase, R, Bronk, M, Oprescu, S, de Wissel, M, van Ruissen, F, Breuning, M, Hou, YM, de Visser, M, Antonellis, A, Baas, F. (2018) Hypermorphic and hypomorphic AARS alleles in patients with CMT2N expands clinical and molecular heterogeneities. Human Molecular Genetics, in press.
Gamper, H, Hou, YM. (2018) tRNA 3'-amino-tailing for stable amino acid attachment. RNA.
Kwon, NH, Lee, JY, Ryu, YL, Kim, C, Kong, J, Oh, S, Kim, SH, Ahn, SG, Jeong, J, Kim, HK, Kim, JH, Han, DY, Park, MC, Takase, R, Masuda, I, Hou, YM, Jang, SI, Chang, YS, Lee, DK, Guo, M, Kang, BS, Wang, MW, Basappa, B, Lee, JH, Kim, S. (2018) Stabilization of cyclin dependent kinase 4 by methionyl-tRNA synthetase in p16INK4a-negative cancer. ACS Pharmacology & Translational Science, 1, 21-31.
2017
Fan H, Conn AB, Williams PB, Diggs S, Hahm J, Gamper HB Jr, Hou YM, O'Leary SE, Wang Y, Blaha GM. Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res. 2017 Nov.
Oprescu SN, Chepa-Lotrea X, Takase R, Golas G, Markello TC, Adams DR, Toro C, Gropman AL, Hou YM, Malicdan MCV, Gahl WA, Tifft CJ, Antonellis A. Compound heterozygosity for loss-of-function GARS variants results in a multisystem developmental syndrome that includes severe growth retardation. Hum Mutat. 2017 Oct.
Hou YM, Matsubara R, Takase R, Masuda I, Sulkowska JI. TrmD: A Methyl Transferase for tRNA Methylation With m1G37. Enzymes. 41:89-115. 2017.
Po P, Delaney E, Gamper H, Szantai-Kis DM, Speight L, Tu L, Kosolapov A, Petersson EJ, Hou YM, Deutsch C. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. J Bol Miol. 429(12):1873-1888. Jun16 2017.
Masuda I, Igarashi T, Sakaguchi R, Nitharwal RG, Takase R, Han KY, Leslie BJ, Liu C, Gamper H, Ha T, Sanyal S, Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Res. Apr 20, 2017
2016
Gall AR, Datsenko KA, Figueroa-Bossi N, Bossi L, Masuda I, Hou YM, Csonka LN. Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide. Proc Natl Acad Sci USA. Dec 27 2016.
Ardell DH, Hou YM. Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria. BMC Genomics. 8 Dec 2016
Sakaguchi, R, Hou, YM. (2016) タンパク質の結び目構造からのシグナルによるtRNAのメチル化修飾. DOI:10.7875/first.author.2016.097.. First Author's
Christian T, Sakaguchi R, Perlinska AP, Lahoud G, Ito T, Taylor EA, Yokoyama S, Sulkowska JI, Hou YM. Methyl transfer by substrate signaling from a knotted protein fold.. Nat Struct Mol Biol. Aug 29, 2016
Liu C, Stonestrom AJ, Christian T, Yong J, Takase R, Hou YM, Yang X. Molecular Basis and Consequences of the Cytochrome c-tRNA Interaction.. J Biol Chem, 291, 10426-36. May 6, 2016
Falk MJ, Gai X, Shigematsu M, Vilardo E, Takase R, McCormick E, Christian T, Place E, Pierce EA, Consugar M, Gamper HB, Rossmanith W, Hou YM. A novel HSD17B10 mutation impairing the activities of the mitochondrial RNase P complex causes X-linked intractable epilepsy and neurodevelopmental regression.. RNA Biol, 13, 477-85 . May 3, 2016 Supplement
2015
Ito, T, Masuda, I, Yoshida, K, Goto-Ito, S, Suh, SW, Hou, YM, Yokoyama, S. Structural mechanism of site-specific RNA modification by the bacterial tRNA(m1G37)-methyltransferase TrmD. Proc Natl Acad Sci, 112, E4197-204. Aug 4 2015
Gamper, H, Masuda, I, Frenkel-Morgenstern, M, Hou, YM. The UGG isoacceptor of tRNAPro is naturally prone to frameshifts. Int J. Mol Sci. 16, 14866-14883. Jul 1, 2015
Hou, YM, Gamper, H, Yang, W. (2015) Post-transcriptional modifications of tRNA – A response to the genetic code degeneracy. RNA 21, 642-644. Apr 2015
Hou, YM, Masuda, I. (2015) Kinetic analysis of tRNA methyltransferases. Methods in Enzymology. Edited by Chuan He, 560, 91-116.
Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM, Maintenance of protein synthesis reading frame by EF-P and m1G37-tRNAAm J Human Benetics96(4):675-81. doi: 10.1016, April2, 2015
Ya-Ming Hou et al., Loss-of-Function Alanyl-tRNA Synthetase Mutations Cause an Autosomal-Recessive Early-Onset Epileptic Encephalopathy with Persistent Myelination DefectAm J Human Genetics96(4):675-81. doi: 10.1016, April2, 2015
2014
Akesh Sinha, Caroline Köhrer, Michael H. W. Weber, Isao Masuda, Vamsi K. Mootha, Ya-Ming Hou, and Uttam L. RajBhandary, Biochemical characterization of pathogenic mutations in human mitochondrial methionyl-tRNA formyltransferaseJ. Biol. Chem289(47):32729-41. doi: 10.10742
Griffin LB, Sakaguchi R, McGuigan D, Gonzalez MA, Searby C, Züchner S, Hou YM, Antonellis A., (November 2014) Impaired Function is a Common Feature of Neuropathy-Associated Glycyl-tRNA Synthetase MutationsHuman Mutation35(11):1363-71. doi: 10.1002
Sakaguchi R, Lahoud G, Christian T, Gamper H, Hou YM., (October 2014) A Divalent Metal Ion-Dependent N(1)-Methyl Transfer to G37-tRNA.J. Chem Biol.21(10):1351-60. doi: 10.1016
Oscar Vargas-Rodriguez and Karin Musier-Forsyth, (June 2014) Wobble puts RNA on targetNature News & Views. 480|Nature|Vol 510|26 June 2014.
Masahiro Naganuma, Shun-ichi Sekine1, Yeeting Esther Chong, Min Guo, Xiang-Lei Yang, Howard Gamper, Ya-Ming Hou, Paul Schimmel & Shigeyuki Yokoyama1, (June 2014) The selective tRNA aminoacylation mechanism based on a single G.U pairNature. doi:10.1038.
James S. PHAM, Reiko SAKAGUCHI, Lee M. YEOH, Nilushi S. DE SILVA, Geoffrey I. MCFADDEN‡, Ya-Ming HOU and Stuart A. RALPH (2014) A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys.Biochem J. 458: 512-523.
Jacob R. Peacock, Ryan R. Walvoord, Angela Y. Chang, et al. (2014) Amino acid-dependent stability of the acyl linkage in aminoacyl-tRNA.RNA 20: 758-764.
2013
Annia Rodriguez-Hernandez, Jessica L. Spears, Kirk W. Gaston, Patrick A. Limbach, Howard Gamper, Ya-Ming Hou, Rob Kaiser, Paul F. Agris, John J. Perona, (2013) Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position.J. Mol. Biol. 425(20):3888-3906.
Isao Masuda, Reiko Sakaguchi, Cuiping Liu, Howard Gamper, Ya-Ming Hou, (2013) The Temperature Sensitivity of a Mutation in the Essential tRNA Modification Enzyme tRNA Methyltransferase D (TrmD).JBC. 288(40):28987-28996
Thomas Christian, Howard Gamper, Ya-Ming Hou, (2013) Conservation of structure and mechanism by Trm5 enzymes.RNA. 19(9):1192-9. doi: 10.1261/rna.039503.113.
Anna Ochi, Koki Makabe, Ryota Yamagami, Akira Hirata, Reiko Sakaguchi, Ya-Ming Hou, Kazunori Watanabe, Osamu Nureki, Kunihiro Kuwajima, Hiroyuki Hori,(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. 288:25562-25574. doi: 10.1074/jbc.M113.485128
Ya-Ming Hou, Xiaolu Yang (2013) Regulation of Cell Death by Transfer RNA.Antioxidants & Redox Signaling. DOI: 10.1089/ars.2012.5171
2012
Reiko Sakaguchi, Anders Giessing, Qing Dai, Georges Lahoud, Zita Liutkeviciute, Saulius Klimasauskas, Joseph Piccirilli, Finn Kirpekar, Ya-Ming Hou (2012) Recognition of guanosine by dissimilar tRNA methyltransferases. RNA. 18: 1687-1701
Frenkel-Morgenstern M, Danon T, Christian T, Igarashi I, Cohen L, Hou YM, Jensen LJ. (2012) Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels.Molecular Systems Biology. 8:572.
Liu C, Sanders JM, Pascal JM, Hou YM. (2012) Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases.RNA. 18(2):213-21.
McLaughlin HM, Sakaguchi R, Giblin W; NIH Intramural Sequencing Center, Wilson TE, Biesecker L, Lupski JR, Talbot K, Vance JM, Züchner S, Lee YC, Kennerson M, Hou YM, Nicholson G, Antonellis A. (2012) A Recurrent loss-of-function alanyl-tRNA synthetase (AARS ) mutation in patients with charcot-marie-tooth disease type 2N (CMT2N).Human Mutation. 33(1):244-53.
2011
Silver HR., Nissley JA., Reed SH., Hou YM., Johnson ES. (2011) A role for SUMO in nucleotide excision repair. DNA Repair. 10(12):1243-51
Takao I., Liu C., Morinaga H., Kim S., Hou YM. (2011) Pyrophosphorolysis of CCA Additions: Implication for Fidelity. J. Mol. Bio. 414(1):28-43
Ghosh A., Sakaguchi R., Liu C., Vishveshwara S., Hou YM. (2011) Allosteric Communication in Cysteinyl tRNA Synthetase - A network of Direct and Indirect readout.J. Biol. Chem. 286(43):37721-31.
Lahoud G, Goto-Ito S, Yoshida KI, Ito T, Yokoyama S, Hou YM. (2011 July) Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.RNA. 17(7):1236-46.
Liu C, Gamper H, Liu H, Cooperman BS, Hou YM. (2011) Potential for interdependent development of tRNA determinants for aminoacylation and ribosome decodingNat. Commun.. 2:329 doi: 10.1038/ncomms1331 (supplementary )
2010
Christian, T, Lahoud, G, Liu, C, Hoffmann, K, Perona, JJ, Hou, YM. (2010) Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. RNA. 16, 2484-2492.
Lahouds, G, Hou, YM. (2010) Biosynthesis: A new (old) way of hijacking tRNA.Nature Chem Biol. 6, 795-796.
McLaughlin, HM, Sakaguchi, R, Liu, C, Igarashi, T, Chu, K, Lyer, R, Cruz, P, Cherukuri, PF, Hansen, NF, Mullikin, JC, NISC Comparative Sequencing Program, Biesecker, LG, Wilson, TE, Ionasescu, V, Nicholson, G, Searby, C, Talbot, K, Vance, JM, Zuchner, S, Szigeti, K, Lupski, JR, Hou, YM, Green, ED, Antonellis, A. (2010) Compound heterozygosity for loss-of-function lysyl-tRNA synthetase (KARS) mutations in a patient with peripheral neuropathy.J.Am Hum Genetics 87, 560-566.
Mei, Y, Stonestrom, A, Hou, YM, Yang, X. (2010) Apoptotic regulation and transfer RNA.Protein & Cell, 1, 795-801.
Christian, T, Lahoud, G, Liu, C, Hou, YM. (2010) Control of catalytic cycle by a pair of analogous tRNA modification enzymes.J. Mol. Biol. 400, 204-217.
Hou, YM. (2010) CCA addition to tRNA: Implications for tRNA quality control. IUBMB Life 62, 251-260.
Hou, YM, Perona, JJ. (2010) Stereochemical mechanisms of tRNA methyl transferases.FEBS Letters 584, 278-286.
2009
Liu, C, Betteridge, T, Hou, YM. (2009) Fluorophore labeling to monitor tRNA dynamics.Methods in Enzymology 469 (Editor Herschlag, D, academic press), 69-93.
Kim, S, Liu, CP, Halkidis, K, Gamper, H, Hou, YM. (2009) Distinct kinetic determinants for the stepwise CCA addition to tRNA.RNA 15, 1827-1836.
Liu, X, Silks, LA, Liu, C, Ollivault-Shiflett, M, Huang, X, Li, J, Wang, Y, Yu, H, Hou, YM, Liu, J, Shen, J. (2009) Incorporation of tellurocysteine into glutathione transferase installs high glutathione peroxidase efficiency. Angew Chem Int Ed Engl 48, 2020-2023.
Macauley, SR, Zimmerman, SA, Apolinario, EE, Evilia, C, Hou, YM, Ferry, JG, Sowers, KR. (2009) The archetype gamma-class carbonic anhydrase (Cam) contains iron when synthesized in vivo.Biochemistry 48, 817-819.
2008
Lahoud, G, Timoshchuk, V, Levedev, A, Arar, K, Hou, YM, Gamper, H. (2008) Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine.Nucleic Acids Res 36, 6999-7008.
Lahoud, G, Arar, K, Hou, YM, Gamper, H. (2008) RecA mediated DNA strand invasion by pseudo-complementary oligonucleotides.Nucleic Acids Res 36, 6806-6815.
Zhang, CM, Liu, C, Christian, T, Gamper, H, Rosenski, J, Pan, D, Randolph, JB, Wickstrom, E, Cooperman, BS, Hou, YM. (2008) Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.RNA 14, 2245-2253.
Hauenstein, SI, Hou, YM, Perona, JJ. (2008) The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.J. Biol. Chem. 283, 21997-22006.
Pan, D, Zhang, CM, Kirillov, S, Hou, YM, Cooperman, BS. (2008) Perturbation of the tRNA Tertiary Core Differentially Affects Specific Steps of the Elongation Cycle.J. Biol. Chem. 283, 18431-18440.
Lahoud, G, Timoshchuk, V, Lebedev, A, de Vega M, Salas, M, Arar, K, Hou, YM, Gamper, H. (2008) Enzymatic synthesis of structure-free DNA with pseudo-complementary properties.Nucleic Acids Res. 36, 3409-3419.
Dupasquier, M, Kim, S, Halkidis, K, Gamper, H, Hou, YM. (2008) tRNA integrity is a prerequisite for rapid CCA addition: Implication for quality control.J. Mol. Biol. 379, 579-588.
Zhang, CM, Liu, C, Slater, S, Hou, YM. (2008) Aminoacylation of tRNA with phosphoserine for synthesis of Cys-tRNACys.Nature Structural and Molecular Biology 15, 507-514.
Francklyn, C, Perona, JJ, First, E, Hou, YM. (2008) Methods for kinetics and thermodynamic analysis of aminoacyl-tRNA synthetases.Methods 44, 100-118.
2007
Perona, JJ, Hou, YM. (2007) Indirect readout of tRNA for aminoacylation.Biochemistry 46, 10419-10432. (Selected as an ACS hot article).
Christian, T, Hou, YM. (2007) Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases.J. Mol. Biol. 373, 623-632.
Betteridge, T, Liu, H, Gamper, H, Kirillov, S, Cooperman, BS, Hou, YM. (2007) Fluorescent labeling of tRNAs for dynamic experiments.RNA 13, 1594-1601.
Liu, CP, Gamper, H, Shtivelband, S, Hauenstein, S, Perona, JJ, Hou, YM. (2007) Kinetic quality control of anticodon recognition of a eukaryotic tRNA synthetase.J. Mol. Biol 367, 1063-1078.
2006
Zhang, CM, Perona, JJ, Ryu, K, Francklyn, C, Hou, YM. (2006) Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases.J. Molecular Biology 361, 300-311.
Christian T, Evilia, C, Hou, YM. (2006) Catalysis by the second class of tRNA (m1G37) methyl transferase requires a conserved proline.Biochemistry 45, 7463-7473.
Gamper, HB, Arar, K, Gewirtz, A, Hou, YM. (2006) Unrestricted hybridization of oligonucleotides to structure-free DNA.Biochemistry 45, 6978-6986.
Evilia, C, Hou, YM. (2006) Acquisition of an insertion peptide for efficient aminoacylation by a halophile tRNA synthetase.Biochemistry 45, 6835-6845.
Pan, D, Kirillov, S, Zhang, CM, Hou, YM, Cooperman, BS. (2006) Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA.Nature Structural and Molecular Biology 13, 354-359.
Hou, YM, Li, Z, Gamper, H. (2006) Isolation of a site-specifically modified RNA from an unmodified transcript.Nucleic Acids Res. 34, e21.
2005
Shitivelband, S, Hou, YM. (2005) Breaking the stereo barrier of amino acid attachment to tRNA by a single nucleotide.J. Mol. Biol, 348, 513-521.
Zhang, CM, Hou, YM. (2005) Domain-domain communication for tRNA aminoacylation: The importance of covalent connectivity.Biochemistry 44, 7240-7249.
Gamper, HB, Arar, K, Gewirtz, A, Hou, YM. (2005) Unrestricted accessibility of short oligonucleotides to RNA.RNA 11, 1441-1447.
Hou, YM, Gu, SQ, Ingerman, L, Zhou, HP. (2005) Metal-ion dependent catalysis and specificity of CCA enzymes: A comparison of two classes.Biochemistry 44, 12849-12859.
2004
Hauenstein, S, Zhang, CM, Hou, YM, Perona, JJ. (2004) Shape-selective RNA recognition by cysteinyl-tRNA synthetase.Nature Structural and Molecular Biology 11, 1134-1141. Biochemistry 44, 12849-12859.
Ougland, R, Zhang, CM, Liiv, A, Johansen, RF, Seeberg, E, Hou, YM, Remme, J, Falnes, PO. (2004) AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation.Mol Cell 16, 107-116. Biochemistry 44, 12849-12859.
Gamper, HB, Gewirtz, A, Edwards, J, Hou, YM. (2004) Modified bases in RNA reduce secondary structure and enhance hybridization.Biochemistry 43, 10224-10236. Biochemistry 44, 12849-12859.
Christian, T, Evilia, C, Williams, S, Hou, YM. (2004) Distinct origins of tRNA(m1G37) methyl transferase.J. Mol. Biol. 339, 707-719.
Zhang, CM, Hou, YM. (2004) Synthesis of cysteinyl-tRNACys by a prolyl-tRNA synthetase.RNA Biology 1, 35-41. Biochemistry 44, 12849-12859.
2003
Zhang, CM, Perona, JJ, Hou, YM. (2003) Amino acid discrimination by a highly differentiated metal center of an aminoacyl-tRNA synthetase.Biochemistry 42, 10931-10937.
Rajanna, C, Wang, J, Zhang, D, Xu, Z, Ali, A, Hou, YM, Karaolis, DKR. (2003) The Vibrio pathogenicity island forms precise extrachromosomal circular excision products. J. Bacteriology 185, 6893-6901.
Lipman, RSA, Chen, J, Evilia, C, Vitseva, O, Hou, YM. (2003) Association of an aminoacyl-tRNA synthetase with a metabolic protein in archaea.Biochemistry 42, 7487-96.
Evilia, C, Ming, XT, DasSarma, S, Hou, YM. (2003) Aminoacylation of an unusual tRNA from an extreme halophile.RNA 9, 794-801.
Zhang, CM, Christian, T, Newberry, KJ, Perona, JJ, Hou, YM. (2003) Zinc mediated amino acid discrimination in cysteinyl-tRNA synthetase.J. Mol. Biol., 327, 911-917.
2002
Francklyn, C, Perona, JJ, Putz, J, Hou, YM. (2002) Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.RNA 8, 1363-1372.
Ming, XT, Smith, K, Suga, H, Hou, YM. (2002) Recognition of tRNA backbone for aminoacylation with cysteine: Evolution from E. coli to human.J. Mol. Biol. 318, 1207-1220.
Hou, YM. (2002) Base pairing in RNA: Unusual patterns.Encyclopedia of Life Sciences, http://www.els.net. London: Nature Publishing Group.
Newberry, KJ, Hou, YM, Perona, JJ. (2002) Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase. EMBO J. 21, 2778-2787.
Seth, M, Thurlow, DL, Hou, YM. (2002) Poly(C) synthesis by class I and class II CCA-adding enzymes.Biochemistry 41, 4521-4532.
Lipman, RSA, Beuning, PJ, Musier-Forsyth, Hou, YM. (2002) Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA.J. Mol. Biol. 316, 421-427.
Lipman, RSA, Wang, JL, Sowers, KR, Hou, YM. (2002) Prevention of mis-aminoacylation of a dual-specificity aminoacyl-tRNA synthetase.J. Mol. Biol. 315, 943-949.
2001
Tardif, K, Liu, MS, Vitseva, O, Hou, YM, and Horowitz, J. (2001) Misacylation by E. coli valyl-tRNA synthetase: Evidence for two tRNA binding sites.Biochemistry 40, 8118-8125.
Burke, B, Lipman, RSA, Shiba, K, Musier-Forsyth, K, Hou, YM. (2001) Divergent adaptation of recognition of tRNAPro by Methanococcus jannaschii prolyl-tRNA synthetase.J. Biol. Chem. 276, 20286-20291.
Davidson, E, Caffarella, J, Vitseva, O, Hou, YM, King, MP. (2001) Isolation of two cDNAs encoding functional human cytoplasmic cysteinyl-tRNA synthetase. Biological Chemistry 382, 399-406.
Hou, YM, Zhang, XL, Holland, JA, Davis, DR. (2001) An important 2’-OH group for an RNA-protein interaction.Nucleic Acids Res 29, 976-985.
2000
Gamper, HB, Hou, YM, Kmiec. (2000) Evidence for a four-strand exchange catalyzed by the recA protein.Biochemistry 39, 15272-15281.
Christian, T, Lipman, RSA, Evilia, C, Hou, YM. (2000) Alternative design of a tRNA core for aminoacylation.J. Mol. Biol. 303, 503-514.
Hou, YM. (2000) Unusual synthesis by the E. coli CCA-adding enzyme.RNA 6, 1031-1043.
Hou, YM, Sundaram, M, Zhang, XL, Holland, JA, Davis, DR. (2000) Recognition of functional groups in an RNA helix by a class I tRNA synthetase.RNA 6, 922-927.
Lipman, RSA, Sowers, KR, Hou, YM. (2000) Synthesis of cysteinyl-tRNACys by a genome that lacks the normal cysteine-tRNA synthetase.Biochemistry 39, 7792-7798.
Madore, E, Lipman, RSA, Hou, YM, Lapointe J. (2000) Evidence for unfolding of the single-stranded GCCA 3’-end of a tRNA on its aminoacyl-tRNA synthetase from a stacked helical to a fold-back conformation.Biochemistry 39, 6791-6798.
Sherlin, LD, Bullock, TL, Newberry, KJ, Lipman, RSA, Hou, YM, Beijer, B, Sproat, BS, Perona, JJ. (2000) Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.J. Mol. Biol. 299, 431-446.
Hamann, CS, Hou, YM. (2000) Probing a tRNA core that contributes to aminoacylation.J. Mol. Biol. 295, 777-789.
1999
Hou, YM, Motegi, H, Lipman, RS, Hamann, CS, Shiba, K. (1999) Conservation of a tRNA core for aminoacylation. Nucleic Acids Res 27, 4743-4750. PMID: 10572174; PMCID: PMC148774
Hou, YM. (1999) Contribution of a tRNA core to aminoacylation: the role of a proposed adenosine base triple in aminoacylation with cysteine. Nucleic Acids Sym.Series 41, 208-210.
Holland, JA, Hou, YM, Davis, DR. (1999) NMR structural studies of the tRNACys amino acceptor stem of Mycoplasma pneumonia. Nucleic Acids Sym Series 41, 101-103.
Hamann, CS, Sowers, KR, Lipman, RSA, Hou, YM. (1999) An archaeal aminoacyl-tRNA synthetase missing from genomic analysis. J. Bacteriology 181, 5880-5884. PMID: 10482537; PMCID: PMC94116
Hou, YM. (1999) Transfer RNAs and pathogenicity islands. Trends in Biochemical Sciences 24, 295-298. PMID: 10431171
Newberry, KJ, Kohn, J, Hou, YM, Perona, JJ. (1999) Crystallization and preliminary diffraction analysis of Escherichia coli cysteinyl-tRNA synthetase. Acta Cryst. D. D55, 1046-1047. PMID: 10216301
1998
Lipman, RSA, Hou, YM. (1998) Aminoacylation of tRNA in the evolution of an aminoacyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA. 95, 13495-13500. PMID: 9811828; PMCID: PMC24847
Hou, YM, Lipman, RSA, Zarutskie, JA. (1998) A tRNA circularization assay: Evidence for the variation of the conformation of the CCA end. RNA 4, 733-738. PMID: 9671047; PMCID: PMC1369654
1997
Hamann, CS, Hou, YM. (1997) A strategy of tRNA recognition that includes determinants of RNA structure. Bioorganic & Medicinal Chemistry 5, 1011-1019. PMID: 9222494
Hamann, CS, Hou, YM. (1997) An RNA structural determinant for tRNA recognition. Biochemistry, 36, 7967-7972. PMID: 9201943
Hou, YM. (1997) Discriminating among the discriminator bases of tRNAs. Chem& Biol 4, 93-96. PMID: 9190291
1996
Hou, YM, Gamper, H. (1996) Inhibition of tRNA aminoacylation by 2'-O-methyl oligonucleotides. Biochemistry 35, 15340-15348. PMID: 8952485
Ohannesian, DW, Oh, J, Hou, YM. (1996) Mutational analysis of a leucine heptad repeat motif in a class I tRNA synthetase. Biochemistry 35, 14405-14412. PMID: 8916927
1995
Sterner, T, Jansen, M, Hou, YM. (1995) Structural and functional accommodation of nucleotide variations at a conserved tRNA tertiary base pair. RNA 1, 841-851. PMID: 7493329; PMCID: PMC1369324
Hou, YM, Sterner, T, Bhalla, R. (1995) Evidence for a conserved relationship between an acceptor stem and a tRNA in aminoacylation. RNA 1, 707-713. PMID: 7585255; PMCID: PMC1369312
Hou, YM. (1995) RNA recognition based on a pair of tertiary hydrogen interaction. Nucleic Acids Research Symposia Series 33, 172-175. PMID: 8643362
Hamann, CS, Hou, YM. (1995) Enzymatic aminoacylation of tRNA acceptor stem helices with cysteine is dependent on a single nucleotide. Biochemistry 34, 6527-6532. PMID: 7756283
Hou, YM, Sterner, T, Jansen, M. (1995) Permutation of a pair of tertiary nucleotides in a transfer RNA. Biochemistry 34, 2978-2984. PMID: 7534478
1994
Hou, YM. (1994) Structural elements that contribute to an unusual tertiary interaction in a transfer RNA. Biochemistry 33, 4677-4683. PMID: 8161525
1993
Hou, YM. (1993) The tertiary structure of tRNA and the development of the genetic code. Trends In Biochemistry Sciences. 18, 362-364. PMID: 8256282
Hou, YM, Westhof, E, Giegé, R. (1993) An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA. Proc. Natl. Acad. Sci. USA. 90, 6776-6780. PMID: 8341698; PMCID: PMC47015
1992
Hou, YM, Schimmel, P. (1992) Functional compensation of a recognition-defective transfer RNA by a distal base pair substitution. Biochemistry 31, 10310-10314. PMID: 1420150
Hou, YM. (1992) “The second genetic code”, in Fundamentals of Medical Cell Biology, vol. 4, Chemistry of the Living Cell, JAI press Inc, p105-165.
Hou, YM, Schimmel, P. (1992) Novel tRNAs that are active in E. coli. Biochemistry 31, 4157-4160. PMID: 1567861
1991
Miller, WT, Hou, YM, Schimmel, P. (1991) Mutant aminoacyl tRNA synthetase that compensates for a mutation in the major identity determinant of its tRNA. Biochemistry 30, 2635-2641. PMID: 2001352
Hou, YM, Shiba, K, Mottes, C, Schimmel, P. (1991) Sequence determination and modeling of structural motifs for the smallest aminoacyl tRNA synthetase. Proc. Natl. Acad. Sci. USA. 88, 976-980. PMID: 1992490; PMCID: PMC50937
1989
Hou, YM, Francklyn, C, Schimmel, P. (1989) Molecular dissection of a transfer RNA and the basis for its identity. Trends In Biochemistry 14, 233-237. PMID: 2669241
Hou, YM, Schimmel, P. (1989) Evidence that a major determinant for the identity of a transfer RNA is conserved in evolution. Biochemistry 28, 6800-6804. PMID: 2684266
Hou, YM, Schimmel, P. (1989) Modeling of in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry 28, 4942-4947. PMID: 2548595
Park, SJ, Hou, YM, Schimmel, P. (1989) A single base pair affects binding and catalytic parameters in the molecular recognition of a transfer RNA. Biochemistry 28 , 2740-2746. PMID: 2659081
1988
Hou, YM, Kim, R, Kim, SH. (1988) Expression of the mouse metallothionein-I gene in Escherichia coli: increased tolerance to heavy metals. Biochimica et Biophysica Acta, 951, 230-234. PMID: 3056525
Hou, YM, Schimmel, P. (1988) A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333, 140-145. PMID: 3285220 **Featured in Nature News and Views: de Duve, C. (1988) The second genetic code. Nature 333, 117-118. PMID: 3367984