Mitochondrial tRNA-lookalikes in nuclear chromosomes: Could they be functional?

RNA Biology

Volumn 12, Issue 4, 2015, Pages 375-380

  Telonis, Aristeidis G ^a   Kirino, Yohei ^a   Rigoutsos, Isidore ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

Mitochondrion; tRF; tRNA; tRNA fragment; tRNA half; tRNA lookalike

Indexed keywords

MITOCHONDRIAL RNA; TRANSFER RNA;

ARTICLE; CHROMOSOME; GENE EXPRESSION; HUMAN; INVERTEBRATE; MARSUPIAL; MITOCHONDRION; NONHUMAN; RNA ANALYSIS; RNA SEQUENCE; RNA TRANSCRIPTION; RODENT; SIMIAN; ANIMAL; CELL NUCLEUS; EVOLUTION; GENETICS; METABOLISM; PRIMATE; REGULATORY SEQUENCE;

DIDELPHIDAE; INVERTEBRATA; METATHERIA; PRIMATES; RATTUS; RODENTIA; SAIMIRI;

ANIMALS; BIOLOGICAL EVOLUTION; CELL NUCLEUS; CHROMOSOMES; HUMANS; INVERTEBRATES; MITOCHONDRIA; PRIMATES; REGULATORY SEQUENCES, NUCLEIC ACID; RNA, TRANSFER; RODENTIA;

EID: 84929328804     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.1080/15476286.2015.1017239     Document Type: Article

References (40)

1. Giege R. Toward a more complete view of tRNA biology. Nat Struct Mol Biol 2008; 15:1007-14; PMID:18836497; http://dx.doi.org/10.1038/nsmb.1498
2. Phizicky EM, Hopper AK. tRNA biology charges to the front. Genes Dev 2010; 24:1832-60; PMID:20810645; http://dx.doi.org/10.1101/gad.1956510
3. Raina M, Ibba M. tRNAs as regulators of biological processes. Front Genet 2014; 5:171; PMID:24966867; http://dx.doi.org/10.3389/fgene.2014.00171
4. Abbott JA, Francklyn CS, Robey-Bond SM. Transfer RNA and human disease. Front Genet 2014; 5:158; PMID:24917879; http://dx.doi.org/10.3389/fgene.2014.00158
5. Shigematsu M, Honda S, Kirino Y. Tranfer RNA as a source of small functional RNA. J Mol Biol Mol Imaging 2014; 1(2):8.
6. Sobala A, Hutvagner G. Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA 2011; 2:853-62; PMID:21976287; http://dx.doi.org/10.1002/wrna.96
7. Telonis AG, Loher P, Kirino Y, Rigoutsos I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet 2014; 5:344; PMID:25339973; http://dx.doi.org/10.3389/fgene.2014.00344
8. Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009; 37:D93-7; PMID:18984615; http://dx.doi.org/10.1093/nar/gkn787
9. Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57- 74; PMID:22955616
10. Bensasson D, Feldman MW, Petrov DA. Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol 2003; 57:343-54; PMID:14629044; http://dx.doi.org/10.1007/s00239- 003-2485-7
11. Yao YG, Kong QP, Salas A, Bandelt HJ. Pseudomitochondrial genome haunts disease studies. J Med Genet 2008; 45:769-72; PMID:18611982; http://dx.doi.org/10.1136/jmg.2008.059782
12. Leister D. Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 2005; 21:655-63; PMID:16216380
13. Ramos A, Barbena E, Mateiu L, del Mar Gonzalez M, Mairal Q, Lima M, Montiel R, Aluja MP, Santos C. Nuclear insertions of mitochondrial origin: Database updating and usefulness in cancer studies. Mitochondrion 2011; 11:946-53; PMID:21907832; http://dx.doi.org/10.1016/j.mito.2011.08.009
14. Tsuji J, Frith MC, Tomii K, Horton P. Mammalian NUMT insertion is non-random. Nucleic Acids Res 2012; 40:9073-88; PMID:22761406; http://dx.doi.org/10.1093/nar/gks424
15. Woodson JD, Chory J. Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 2008; 9:383-95; PMID:18368053; http://dx.doi.org/10.1038/nrg2348
16. Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981; 290:470-4; PMID:7219536; http://dx.doi.org/10.1038/290470a0
17. Orioli A, Pascali C, Pagano A, Teichmann M, Dieci G. RNA polymerase III transcription control elements: themes and variations. Gene 2012; 493:185-94; PMID:21712079; http://dx.doi.org/10.1016/j. gene.2011.06.015
18. Watanabe Y, Suematsu T, Ohtsuki T. Losing the stemloop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet 2014; 5:109; PMID:24822055; http://dx.doi.org/10.3389/fgene.2014.00109
19. Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, et al. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Sstruct Mol Biol 2010; 17:620-8; PMID:20418882; http://dx.doi.org/10.1038/nsmb.1801
20. Lai LB, Vioque A, Kirsebom LA, Gopalan V. Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Letters 2010; 584:287-96; PMID:19931535; http://dx.doi.org/10.1016/j.febslet.2009.11.048
21. Rossmanith W. Of P and Z: mitochondrial tRNA processing enzymes. Biochimi Biophy Acta 2012; 1819:1017-26; PMID:22137969; http://dx.doi.org/10.1016/j.bbagrm.2011.11.003
22. Craig LC, Wang LP, Lee MM, Pirtle IL, Pirtle RM. A human tRNA gene cluster encoding the major and minor valine tRNAs and a lysine tRNA. DNA 1989; 8:457-71; PMID:2766931; http://dx.doi.org/10.1089/dna.1.1989.8.457
23. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, et al. The DNA sequence and analysis of human chromosome 6. Nature 2003; 425:805-11; PMID:14574404; http://dx.doi.org/10.1038/nature02055
24. Michalak P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 2008; 91:243-8; PMID:18082363
25. Van Bortle K, Corces VG. tDNA insulators and the emerging role of TFIIIC in genome organization. Transcription 2012; 3:277-84; PMID:22889843; http://dx.doi.org/10.4161/trns.21579
26. Donze D. Extra-transcriptional functions of RNA Polymerase III complexes: TFIIIC as a potential global chromatin bookmark. Gene 2012; 493:169-75; PMID:21986035; http://dx.doi.org/10.1016/j. gene.2011.09.018
27. Suzuki T, Nagao A, Suzuki T. Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu Rev Genet 2011; 45:299-329; PMID:21910628; http://dx.doi.org/10.1146/annurevgenet- 110410-132531
28. Betat H, Rammelt C, Morl M. tRNA nucleotidyltransferases: ancient catalysts with an unusual mechanism of polymerization. Cell Mol Life Sci 2010; 67:1447-63; PMID:20155482; http://dx.doi.org/10.1007/s00018- 010-0271-4
29. Suzuki T, Suzuki T. A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs. Nucleic Acids Res 2014; 42:7346-57; PMID:24831542; http://dx.doi.org/10.1093/nar/gku390
30. Gebetsberger J, Polacek N. Slicing tRNAs to boost functional ncRNA diversity. RNA biology 2013; 10:1798-806; PMID:24351723; http://dx.doi.org/10.4161/rna.27177
31. Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. Rna 2008; 14:2095-103; PMID:18719243; http://dx.doi.org/10.1261/rna.1232808
32. Brown WM, George M, Jr., Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A 1979; 76:1967-71.
33. Helm M, Brule H, Friede D, Giege R, Putz D, Florentz C. Search for characteristic structural features of mammalian mitochondrial tRNAs. Rna 2000; 6:1356-79; PMID:11073213; http://dx.doi.org/10.1017/S1355838200001047
34. Ohtsuki T, Watanabe Y. T-armless tRNAs and elongated elongation factor Tu. IUBMB life 2007; 59:68- 75; PMID:17454297; http://dx.doi.org/10.1080/15216540701218722
35. Rubio MA, Hopper AK. Transfer RNA travels from the cytoplasm to organelles. Wiley Interdiscip Reviews RNA 2011; 2:802-17; PMID:21976284; http://dx.doi.org/10.1002/wrna.93
36. Schneider A. Mitochondrial tRNA import and its consequences for mitochondrial translation. Annu Review Biochem 2011; 80:1033-53; PMID:21417719; http://dx.doi.org/10.1146/annurev-biochem-060109-092838
37. Dorner M, Altmann M, Paabo S, Morl M. Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 2001; 12:2688-98; PMID:11553708; http://dx.doi.org/10.1091/mbc.12.9.2688
38. Kaminska M, Shalak V, Francin M, Mirande M. Viral hijacking of mitochondrial lysyl-tRNA synthetase. J Virol 2007; 81:68-73; PMID:17050605; http://dx.doi.org/10.1128/JVI.01267-06
39. Kleiman L, Jones CP, Musier-Forsyth K. Formation of the tRNALys packaging complex in HIV-1. FEBS Letters 2010; 584:359-65; PMID:19914238; http://dx.doi.org/10.1016/j.febslet.2009.11.038
40. Pavon-Eternod M, Wei M, Pan T, Kleiman L. Profiling non-lysyl tRNAs in HIV-1. Rna 2010; 16:267-73; PMID:20007329; http://dx.doi.org/10.1261/rna.1928110