Connecting tRNA Charging and Decoding through the Axis of Nucleotide Modifications at Position 37

Authors: Masuda, Isao ¹, McGuigan, Henri ¹, Maharjan, Sunita, Yamaki, Yuka, Hou, Ya-Ming ^⁎

Source: In Journal of Molecular Biology March 2025

A kinetic model for compound heterozygous pathogenic variants in Tyrosyl-tRNA synthetase gene YARS2-Associated neonatal phenotype

Authors: Christian, Thomas ^{1, ‡}, Maharjan, Sunita ^{1, ‡}, Yin, Sitao ¹, Yamaki, Yuka ¹, Masuda, Isao ¹, Li, Fenglin ², Muraresku, Colleen ³, Clever, Sheila ³, Ganetzky, Rebecca D. ^{3, 4, ∗}, Hou, Ya-Ming ^{1, ∗}

Source: In Journal of Biological Chemistry January 2025 301(1)

Preparation of an Enriched tRNA^A^r^g Fraction for Arginylation by Expression in E. coli

Authors: Avcilar-Kucukgoze, Irem, Gamper, Howard, Hou, Ya-Ming, Kashina, Anna S.

Source: Methods in molecular biology. 2620:101-106

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN633170652&indx=1&recIds=ETOCRN633170652

Synthesis of Stably Charged Arg-tRNA^A^r^g for Structural Analysis

Authors: Yamaki, Yuka, Gamper, Howard, Hou, Ya-Ming

Source: Methods in molecular biology. 2620:263-272

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN633170804&indx=1&recIds=ETOCRN633170804

Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study

Authors: Jedrzejewski, Mateusz, Belza, Barbara, Lewandowska, Iwona, Sadlej, Marta, Perlinska, Agata P., Augustyniak, Rafal, Christian, Thomas, Hou, Ya-Ming, Kalek, Marcin, Sulkowska, Joanna I.

Source: In Computational and Structural Biotechnology Journal 2023 21:3999-4008

tRNA methylation resolves codon usage bias at the limit of cell viability

Authors: Masuda, Isao, Yamaki, Yuka, Detroja, Rajesh, Tagore, Somnath, Moore, Henry, Maharjan, Sunita, Nakano, Yuko, Christian, Thomas, Matsubara, Ryuma, Lowe, Todd M., Frenkel-Morgenstern, Milana, Hou, Ya-Ming

Source: In Cell Reports 25 October 2022 41(4)

Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons

Authors: Gamper, Howard, Masuda, Isao, Hou, Ya-Ming

Source: In Journal of Molecular Biology 30 April 2022 434(8)

Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.

Authors: Nakano, Yuko, Gamper, Howard, McGuigan, Henri, Maharjan, Sunita, Li, Jiatong, Sun, Zhiyi, Yigit, Erbay, Grünberg, Sebastian, Krishnan, Keerthana, Li, Nan-Sheng, Piccirilli, Joseph A., Kleiner, Ralph, Nichols, Nicole, Gregory, Brian D., Hou, Ya-Ming

Source: Nature Communications; 1/26/2025, Vol. 16 Issue 1, p1-19, 19p

Subject Terms: GENETIC code, LIFE sciences, GENE expression, CELL lines, TRANSFER RNA, HOMEOSTASIS

A Mitochondrial tRNA Mutation Causes Axonal CMT in a Large Venezuelan Family

Authors: Fay, Alexander, Garcia, Yngo, Margeta, Marta, Maharjan, Sunita, Jürgensen, Claudia, Briceño, Jose, Garcia, Mariaelena, Yin, Sitao, Bassaganyas, Laia, McMahon, Thomas, Hou, Ya‐Ming, Fu, Ying‐Hui, Ptáček, Louis J.

Source: Annals of neurology. 88(4):830-842

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100108497619.0x000001&indx=1&recIds=ETOCvdc_100108497619.0x000001

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

Authors: Masuda, Isao, Matsubara, Ryuma, Christian, Thomas, Rojas, Enrique R., Yadavalli, Srujana S., Zhang, Lisheng, Goulian, Mark, Foster, Leonard J., Huang, Kerwyn Casey, Hou, Ya-Ming

Source: In Cell Systems 24 April 2019 8(4):302-314

Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology.

Authors: Maharjan, Sunita, Gamper, Howard, Yamaki, Yuka, Christian, Thomas, Henley, Robert Y., Li, Nan-Sheng, Suzuki, Takeo, Suzuki, Tsutomu, Piccirilli, Joseph A., Wanunu, Meni, Seifert, Erin, Wallace, Douglas C., Hou, Ya-Ming

Source: Nature Communications; 10/18/2024, Vol. 15 Issue 1, p1-17, 17p

Subject Terms: MITOCHONDRIAL pathology, LACTIC acidosis, GUANOSINE, METHYLATION, MITOCHONDRIA, TRANSFER RNA

Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls.

Authors: Makhamreh, Amr, Tavakoli, Sepideh, Fallahi, Ali, Kang, Xinqi, Gamper, Howard, Nabizadehmashhadtoroghi, Mohammad, Jain, Miten, Hou, Ya-Ming, Rouhanifard, Sara H., Wanunu, Meni

Source: Scientific Reports; 10/10/2024, Vol. 14 Issue 1, p1-13, 13p

Subject Terms: RNA modification & restriction, MACHINE learning, SUPERVISED learning, GENE expression, RNA sequencing

Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails

Authors: Kuo, Molly E., Theil, Arjan F., Kievit, Anneke, Malicdan, May Christine, Introne, Wendy J., Christian, Thomas, Verheijen, Frans W., Smith, Desiree E.C., Mendes, Marisa I., Hussaarts-Odijk, Lidia, van der Meijden, Eric, van Slegtenhorst, Marjon, Wilke, Martina, Vermeulen, Wim, Raams, Anja, Groden, Catherine, Shimada, Shino, Meyer-Schuman, Rebecca, Hou, Ya Ming, Gahl, William A., Antonellis, Anthony, Salomons, Gajja S., Mancini, Grazia M.S.

Source: American journal of human genetics. 104(3):520-529

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100081180840.0x000001&indx=1&recIds=ETOCvdc_100081180840.0x000001

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

Authors: Po, Pengse, Delaney, Erin, Gamper, Howard, Szantai-Kis, D. Miklos, Speight, Lee, Tu, LiWei, Kosolapov, Andrey, Petersson, E. James, Hou, Ya-Ming, Deutsch, Carol

Source: In Journal of Molecular Biology 16 June 2017 429(12):1873-1888

Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores.

Authors: Namani, Srilahari, Kavetsky, Kyril, Lin, Chih-Yuan, Maharjan, Sunita, Gamper, Howard B., Li, Nan-Sheng, Piccirilli, Joseph A., Hou, Ya-Ming, Drndic, Marija

Source: ACS Nano; 7/2/2024, Vol. 18 Issue 26, p17240-17250, 11p

Aminoacylation of tRNA in the Evolution of an Aminoacyl-tRNA Synthetase

Authors: Hou, Ya-Ming

Source: Proceedings of the National Academy of Sciences of the United States of America, 1998 Nov 01. 95(23), 13495-13500.

Access URL: https://www.jstor.org/stable/46714

TRNA 3′-amino-tailing for stable amino acid attachment

Authors: Gamper, Howard, Hou, Ya-Ming

Source: RNA. 24(12):1878-1885

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN618239104&indx=1&recIds=ETOCRN618239104

Molecular Basis and Consequences of the Cytochrome c-tRNA Interaction

Authors: Liu, Cuiping, Stonestrom, Aaron J., Christian, Thomas, Yong, Jeongsik, Takase, Ryuichi, Hou, Ya-Ming, Yang, Xiaolu

Source: In Journal of Biological Chemistry 6 May 2016 291(19):10426-10436

Mg 2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide

Authors: Gall, Aaron R., Datsenko, Kirill A., Figueroa-Bossi, Nara, Bossi, Lionello, Masuda, Isao, Hou, Ya-Ming, Csonka, Laszlo N.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Dec . 113(52), 15096-15101.

Access URL: https://www.jstor.org/stable/26473034

Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA

Authors: Gamper, Howard, Li, Haixing, Masuda, Isao, Miklos Robkis, D., Christian, Thomas, Conn, Adam B., Blaha, Gregor, Petersson, E. James, Gonzalez, Ruben L., Hou, Ya-Ming

Source: Nature communications. 12(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191414169.0x000001&indx=1&recIds=ETOCvdc_100191414169.0x000001