Structural probing of a pathogenic tRNA dimer
Open accessAbstract
The A3243G mutation within the human mitochondrial (hs mt) tRNALeuUUR gene is associated with maternally inherited deafness and diabetes (MIDD) and other mitochondrial encephalopathies. One of the most pronounced structural effects of this mutation is the disruption of the native structure through stabilization of a high-affinity dimeric complex. We conducted a series of studies that address the structural properties of this tRNA dimer, and we assessed its formation under physiological conditions. Enzymatic probing was used to directly define the dimeric interface for the complex, and a discrete region of the D-stem and loop of hs mt tRNALeuUUR was identified. The dependence of dimerization on magnesium ions and temperature was also tested. The formation of the tRNA dimer is influenced by temperature, with dimerization becoming more efficient at physiological temperature. Complexation of the mutant tRNA is also affected by the amount of magnesium present, and occurs at concentrations present intracellularly. Terbium probing experiments revealed a specific metal ion-binding site localized at the site of the A3243G mutation that is unique to the dimer structure. This metal ion-binding site presents a striking parallel to dimeric complexes of viral RNAs, which use the same hexanucleotide sequence for complexation and feature a similarly positioned metal ion-binding site within the dimeric structure. Taken together, these results indicate that the unique dimeric complex formed by the hs mt tRNALeuUUR A3243G mutant exhibits interesting similarities to biological RNA dimers, and may play a role in the loss of function caused by this mutation in vivo.
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m.3243A N G disrupts the L-shaped tertiary fold of mt-tRNA Leu(UUR) by preventing A14/U8 interaction.
“whereas m.3243A N G, in the DHU stem, is responsible for a dramatic structural change, which disrupts both the L-shaped tertiary fold of mt-tRNA Leu(UUR) by preventing np A14/U8 interaction [200]”
From Mitochondrial DNA mutations and human disease (2010) · cites this paper as [200]
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Cites
Goto, Y.-I., Nonaka, I., & Horai, S. (1990) · Nature · doi:10.1038/348651a0 · Cited by 2,070 · see citing works
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki012 · Cited by 1,916 · see citing works
van den Ouweland, J. M. W., Lemkes, H. H. P. J., Ruitenbeek, W., Sandkuijl, L. A., de Vijlder, M. F., Struyvenberg, P. A. A., van de Kamp, J. J. P., & Maassen, J. A. (1992) · Nature Genetics · doi:10.1038/ng0892-368 · Cited by 1,127 · see citing works
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.148 · Cited by 750 · see citing works
A subtype of diabetes mellitus associated with a mutation of mitochondrial DNA.
Kadowaki, T., Kadowaki, H., Mori, Y., Tobe, K., Sakuta, R., Suzuki, Y., Tanabe, Y., Sakura, H., Awata, T., Goto, Y.-I., et al. (1994) · New England Journal of Medicine · doi:10.1056/nejm199404073301403 · Cited by 551 · see citing works
Mitochondrial function in normal and diabetic β-cells
Maechler, P., & Wollheim, C. B. (2001) · Nature · doi:10.1038/414807a · Cited by 519 · see citing works
Chomyn, A., Martinuzzi, A., Yoneda, M., Daga, A., Hurko, O., Johns, D. R., Lai, S. T., Nonaka, I., Angelini, C. I., & Attardi, G. M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.10.4221 · Cited by 491 · see citing works
King, M. P., Koga, Y., Davidson, M., & Schon, E. A. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.2.480 · Cited by 458 · see citing works
Mitochondrial DNA Mutations and Pathogenesis
Schon, E. A., Bonilla, E., & DiMauro, S. (1997) · Journal of Bioenergetics and Biomembranes · doi:10.1023/a:1022685929755 · Cited by 421 · see citing works
Skripkin, E., Paillart, J. C., Marquet, R., Ehresmann, B., & Ehresmann, C. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.11.4945 · Cited by 401 · see citing works
Search for characteristic structural features of mammalian mitochondrial tRNAs
Helm, M., Brulé, H., FRIEDE, D., et al. (2000) · RNA · doi:10.1017/s1355838200001047 · Cited by 284 · see citing works
Yasukawa, T., Suzuki, T., Suzuki, T., Ueda, T., Ohta, S., & Watanabe, K. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.6.4251 · Cited by 268 · see citing works
Ordered Interstrand and Intrastrand DNA Transfer During Reverse Transcription
Panganiban, A. T., & Fiore, D. (1988) · Science · doi:10.1126/science.2457948 · Cited by 221 · see citing works
Paillart, J. C., Marquet, R., Skripkin, E., Ehresmann, B., & Ehresmann, C. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)47011-1 · Cited by 201 · see citing works
Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C., & Dumas, P. (2001) · Nature Structural Biology · doi:10.1038/nsb727 · Cited by 199 · see citing works
Chomyn, A., Enriquez, J. A., Micol, V., Fernandez-Silva, P., & Attardi, G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m908734199 · Cited by 197 · see citing works
Marquet, R., Baudin, F., Gabus, C., Darlix, J., Mougel, M., Ehresmann, C., & Ehresmann, B. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.9.2349 · Cited by 180 · see citing works
Laughrea, M., & Jetté, L. (1996) · Biochemistry · doi:10.1021/bi951838f · Cited by 175 · see citing works
Lead-catalyzed cleavage of yeast tRNAPhe mutants
Behlen, L. S., Sampson, J. R., DiRenzo, A. B., & Uhlenbeck, O. C. (1990) · Biochemistry · doi:10.1021/bi00462a013 · Cited by 155 · see citing works
Muriaux, D. M., Fossé, P., & Paoletti, J. (1996) · Biochemistry · doi:10.1021/bi952822s · Cited by 152 · see citing works
Stabilization of RNA Structure by Mg Ions
Laing, L. G., Gluick, T. C., & Draper, D. E. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1256 · Cited by 151 · see citing works
Impact of disease-related mitochondrial mutations on tRNA structure and function
Wittenhagen, L. M. (2003) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2003.09.006 · Cited by 102 · see citing works
Self-citationHelm, M., Florentz, C., Chomyn, A., & Attardi, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.3.756 · Cited by 99 · see citing works
Towards Understanding Human Mitochondrial Leucine Aminoacylation Identity
Sohm, B., Frugier, M., Brulé, H., Olszak, K., Przykorska, A., & Florentz, C. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00373-5 · Cited by 92 · see citing works
Decreased aminoacylation of mutant tRNAs in MELAS but not in MERRF patients
Börner, G. V. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.4.467 · Cited by 92 · see citing works
Pathophysiology of the MELAS 3243 Transition Mutation
Flierl, A., Reichmann, H., & Seibel, P. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.43.27189 · Cited by 90 · see citing works
Dimerization of a pathogenic human mitochondrial tRNA
Wittenhagen, L. M., & Kelley, S. O. (2002) · Nature Structural Biology · doi:10.1038/nsb820 · Cited by 90 · see citing works
Self-citationJanssen, G. M. C., Maassen, J. A., & van den Ouweland, J. M. W. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.42.29744 · Cited by 86 · see citing works
Park, H. J., Davidson, E., & King, M. P. (2002) · Biochemistry · doi:10.1021/bi026882r · Cited by 79 · see citing works
The mitochondrial tRNALeu(UUR) mutation in MELAS: a model for pathogenesis
Schon, E. A., Koga, Y., Davidson, M. M., Moraes, C. T., & King, M. P. (1992) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/0005-2728(92)90226-r · Cited by 74 · see citing works
Rossmanith, W., & Karwan, R. M. (1998) · FEBS Letters · doi:10.1016/s0014-5793(98)00928-4 · Cited by 73 · see citing works
Matsumura, K., & Komiyama, M. (1997) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021765 · Cited by 65 · see citing works
Mitochondrial diabetes: Pathophysiology, clinical presentation, and genetic analysis
Maassen, J. A. (2002) · American Journal of Medical Genetics · doi:10.1002/ajmg.10346 · Cited by 65 · see citing works
Fossé, P., Motté, N., Roumier, A., Gabus, C., Muriaux, D. M., Darlix, J., & Paoletti, J. (1996) · Biochemistry · doi:10.1021/bi9613786 · Cited by 57 · see citing works
The np 3243 MELAS mutation: damned if you aminoacylate, damned if you don't
Jacobs, H. T. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.4.463 · Cited by 45 · see citing works
Use of terbium as a probe of tRNA tertiary structure and folding
Hargittai, M. R. S., & Musier‐Forsyth, K. (2000) · RNA · doi:10.1017/s135583820000128x · Cited by 42 · see citing works
Madore, É., Florentz, C., Giegé, R., & Lapointe, J. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.17.3583 · Cited by 39 · see citing works
Dimers of alanine transfer RNA with acceptor activity.
Loehr, J. S., & Keller, E. B. (1968) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.61.3.1115 · Cited by 38 · see citing works
Zachau, H. G. (1968) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1968.tb00406.x · Cited by 36 · see citing works
Mitochondrial tRNALeu isoforms in lung carcinoma cybrid cells containing the np 3243 mtDNA mutation
Meziane, A. E. (1998) · Human Molecular Genetics · doi:10.1093/hmg/7.13.2141 · Cited by 36 · see citing works
Properties of a dimer of tRNATyr (Escherichia coli)
Yang, S. K., Soell, D., & Crothers, D. M. (1972) · Biochemistry · doi:10.1021/bi00762a016 · Cited by 33 · see citing works
Molecular Investigations on tRNAs Involved in Human Mitochondrial Disorders
Florentz, C. (2002) · Bioscience Reports · doi:10.1023/a:1016065107165 · Cited by 32 · see citing works
GEL FILTRATION PROPERTIES OF CCD-PREPARED E. COLI B sRNA
Schleich, T., & Goldstein, J. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.52.3.744 · Cited by 31 · see citing works
The pathogenic U3271C human mitochondrial tRNALeu(UUR) mutation disrupts a fragile anticodon stem
Wittenhagen, L. M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg131 · Cited by 26 · see citing works
Self-citationIncreased mitochondrial processing intermediates associated with three tRNALeu(UUR) gene mutations
Koga, A., Koga, Y., Akita, Y., Fukiyama, R., Ueki, I., Yatsuga, S., & Matsuishi, T. (2003) · Neuromuscular Disorders · doi:10.1016/s0960-8966(02)00267-5 · Cited by 24 · see citing works
Kholod, N. (1999) · PubMed · Cited by 15 · see citing works
Specific aggregation of yeast glycine tRNA
HAMPEL, A. E., Cherayil, J. D., & Bock, R. M. (1971) · Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis · doi:10.1016/0005-2787(71)90053-0 · Cited by 14 · see citing works
tRNA processing in human mitochondrial disorders
Masucci, J. P., & Schon, E. A. (1996) · Molecular Biology Reports · doi:10.1007/bf00988727 · Cited by 10 · see citing works
Interdomain Communication between Weak Structural Elements within a Disease-Related Human tRNA
Roy, M. D., Wittenhagen, L. M., Vozzella, B. E., et al. (2003) · Biochemistry · doi:10.1021/bi035711z · Cited by 8 · see citing works
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Mitochondrial DNA mutations and human disease
Tuppen, H. A. L., Blakely, E. L., Turnbull, D. M., & Taylor, R. W. (2010) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2009.09.005 · Cited by 676 · see citing works
“3243ANG, in the DHU stem, is responsible for a dramatic structural change, which disrupts both the L-shaped tertiary fold of mt-tRNA by preventing np A14/U8 interaction [200] and its quaternary structure by promoting the formation of a dimeric complex by intermolecular D-loop base pairing [201].”
Background
- Authors
- ROY, M. D., WITTENHAGEN, L. M., & KELLEY, S. O.
- Affiliations
- Boston College (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2005-02-08
- Volume
- 11
- Issue
- 3
- Pages
- 254-260
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC1370715
- OpenAlex
- W2145657918
- Cited by
- 31
- References
- 49
- Citations by year
- 2025: 1 · 2022: 2 · 2021: 1 · 2020: 1 · 2017: 2 · 2016: 2 · 2015: 1 · 2013: 4 · 2012: 4
- FWCI
- 0.63
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health (1r01gm063890-01a2)
- National Institute of General Medical Sciences (R01 GM063890, GM063980-01A2)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- mitochondrial tRNA, A3243G mutation, mitochondrial encephalopathy, D-stem, magnesium binding, metal binding sites, RNA dimerization, temperature dependence, RNA structure
- MeSH terms
- Base Sequence, Electrophoresis, Polyacrylamide Gel, Humans, Magnesium, Nucleic Acid Conformation, RNA, Transfer, Leu, Temperature, Terbium, Molecular Probes, Dimerization
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