Avoidance of antisense, antiterminator tRNA anticodons in vertebrate mitochondria

BioSystems

Volumn 101, Issue 1, 2010, Pages 42-50

  Seligmann, Hervé ^a  

^a UNIVERSITY OF OSLO   (Norway)

Author keywords

Codon anticodon interaction; Double strand coding; Genetic code; Nonsense tRNA; Suppressor tRNA; TRNA synthetase

Indexed keywords

GENOMIC RNA; TRANSFER RNA; ANTICODON; COMPLEMENTARY RNA; RNA; RNA, MITOCHONDRIAL; STOP CODON;

AVOIDANCE REACTION; CHEMOSYNTHESIS; ENZYME ACTIVITY; GENE EXPRESSION; GENOME; MITOCHONDRION; MOLECULAR ANALYSIS; MUTATION; PROTEIN; RNA-DNA RATIO;

AMINO ACID SEQUENCE; ANTICODON; ARTICLE; CODON USAGE; CONTROLLED STUDY; DNA REPLICATION; DNA STRAND; GENETIC CODE; MITOCHONDRIAL GENE; NONHUMAN; PHYLOGENETIC TREE; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; RNA STRUCTURE; RNA TRANSLATION; THERMODYNAMICS; ANIMAL; BIOLOGICAL MODEL; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE; STOP CODON; VERTEBRATE;

MAMMALIA; VERTEBRATA;

ANIMALS; ANTICODON; BASE SEQUENCE; CODON, TERMINATOR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; RNA; RNA, ANTISENSE; RNA, TRANSFER; SPECIES SPECIFICITY; VERTEBRATES;

EID: 77953615968     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.04.004     Document Type: Article

References (44)

1. Belshaw R., Pybus O.G., Rambaut A. The evolution of genome compression and genomic novelty in RNA viruses. Genome Res. 2007, 17:1496-1504.
2. Carter C.W., Duax W.L. Did tRNA synthetase classes arise on opposite strands of the same gene?. Mol. Cell 2002, 10:705-708.
3. Clayton D.A. Transcription of the mammalian mitochondrial genome. Annu. Rev. Biochem. 1984, 53:573-594.
4. de Magalhaes J.P., Costa J. A database of vertebrate longevity records and their relation to other life-history traits. J. Evol. Biol. 2009, 22:1770-1774.
5. Eddy S.R., Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994, 22:2079-2088.
6. Eigen M., Schuster P. The hypercycle. A principle of natural self-organization. Part A: emergence of the hypercycle. Naturwissenschaften 1977, 64:541-565.
7. Elzanowski A., Ostell J., Leipe D., Soussov V. The Genetic Codes 2000, National Center for Biotechnology Information (NCBI), Bethesda, MD. http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi%3Fmode=c%23SG2.
8. Florentz F., Sohm B., Tryoen-Tóth P., Pütz P., Sissler M. Human mitochondrial tRNAs in health and disease. Cell Mol. Life Sci. 2003, 60:1356-1375.
9. Giegié R. Toward a more complete view of tRNA biology. Nat. Struct. Mol. Biol. 2008, 15:1007-1014.
10. Grisanti P., Francisci S., Tataseo P., Palleschi C. Symmetrical transcription in the transfer-RNA region of the mitochondrial genome of Saccharomyces cerevisiae. Curr. Genet. 1993, 24:122-125.
11. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 1982, 18:199-209.
12. Hershberg R., Petrov D.A. General rules for optimal codon choice. PLoS Genet. 2009, 5:e1000556.
13. Hodgson J.A., Sterner K.N., Matthews L.J., Burrell A.S., Jani R.A., Raaum R.L., Stewart C.B., Disotell T.R. Successive radiations, not stasis, in the South American primate fauna. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:5534-5539.
14. Jameson D., Gibson A.O., Hudelot C., Higgs P.G. OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucleic Acids Res. 2003, 31:202-206.
15. Laslett D., Canbäck B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
16. LéJohn H.B., Cameron L.E., Yang B., Rennie S.L. Molecular characterization of an NAD-specific glutamate-dehydrogenase gene inducible by l-glutamine-antisense gene pair arrangement with L-glutamine-inducible heat-shock 70-like protein gene. J. Biol. Chem. 1994, 269:4523-4531.
17. Li D., Fan L., Zeng B., Yin H., Zou F., Wang H., Meng Y., King E., Yue B. The complete mitochondrial genome of Macaca thibetana and a novel nuclear mitochondrial pseudogene. Gene 2009, 429:31-36.
18. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
19. Matsui A., Rakotndraparany F., Munechika I., Hasegawa M., Horai S. Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs. Gene 2009, 441:53-66.
20. Michel U., Stringaris A.K., Nau R., Rieckmann P. Differential expression of sense and antisense transcripts of the mitochondrial DNA region coding for ATPase 6 in fetal and adult porcine brain: Identification of novel unusually assembled mitochondrial RNAs. Biochem. Biophys. Res. Commun. 2000, 271:170-180.
21. Nikolajewa S., Friedel M., Beyer A., Wilhelm T. The new classification scheme of the genetic code, its early evolution and tRNA usage. J. Bioinform. Comput. Biol. 2006, 4:609-620.
22. Ojala D., Merkel C., Gelfand R., Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 1980, 22:393-403.
23. Pheasant M., Mattick J.S. Raising the estimate of functional human sequences. Genome Res. 2007, 17:1245-1253.
24. Pütz J., Dupuis B., Sissler M., Florentz C. Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures. RNA 2007, 13:1184-1190.
25. Rodin A.S., Rodin S.N. Translation of both complementary strands might govern early evolution of the genetic code. In Silico Biol. 2007, 7:309-317.
26. Rodin S., Ohno S., Rodin A. Transfer-RNAs with complementary anticodons-could they reflect early evolution of discriminative genetic-code adapters. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:4723-4727.
27. Rodin S.N., Rodin A.S. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 2008, 100:341-355.
28. Rodin A.S., Rodin S.N., Carter C.W. On primordial sense-antisense coding. J. Mol. Evol. 2009, 69:555-567.
29. Rossmanith W., Tullo A., Potuschak T., Karwan R., Sbisà E. Human mitochondrial transfer-RNA processing. J. Biol. Chem. 1995, 270:12885-12891.
30. Ruiz-Pesini E., Lott M.T., Procaccio V., Poole J., Brandon M.C., Mishmar D., Yi C., Kreuziger J., Baldi P., Wallace D.C. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res. 2007, 35:D823-D828.
31. Sbisà E., Nardelli M., Tanzariello F., Tullo A., Saccone C. The complete and symmetric transcription of the main non coding region of rat mitochondrial genome: in vivo mapping of heavy and light transcripts. Curr. Genet. 1993, 17:247-253.
32. Sbisà E., Tullo A., Nardelli M., Tanzariello F., Saccone C. Transcription mapping of the Ori L region reveals novel precursors of mature RNA species and antisense RNAs in rat mitochondrial genome. FEBS Lett. 1992, 296:311-316.
33. Seligmann H. Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin. J. Mol. Biol. 2008, 379:188-199.
34. Seligmann H., Amzallag G.N. Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code. Naturwissenschaften 2002, 89:542-551.
35. Seligmann H., Krishnan N.M. Mitochondrial replication origin stability and propensity of adjacent tRNA genes to form putative replication origins increase developmental stability in lizards. J. Exp. Zool. B: Mol. Dev. Evol. 2006, 306:433-449.
36. Seligmann H., Krishnan N.M., Rao B.J. Possible multiple origins of replication in primate mitochondria: alternative role of tRNA sequences. J. Theor. Biol. 2006, 241:321-332.
37. Seligmann H., Krishnan N.M., Rao B.J. Mitochondrial tRNA sequences as unusual replication origins: pathogenic implications for Homo sapiens. J. Theor. Biol. 2006, 243:375-385.
38. Selkoe D.J. Cell biology of protein misfolding: the examples of Alzheimer's and Parkinsons's diseases. Nat. Cell Biol. 2004, 6:1054-1061.
39. Siemion I.Z., Stefanowicz P. Periodical changes of amino acid reactivity within the generic code. Biosystems 1992, 27:77-84.
40. Tabak H.F., Grivell L.A., Borst P., Attardi G. Transcription of mitochondrial DNA. Crit. Rev. Biochem. Mol. Biol. 1983, 14:297-317.
41. Trifonov E.N. Tracing life back to elements. Phys. Life Rev. 2008, 5:121-132.
42. Williams T.A., Wolfe K.H., Fares M.A. No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Mol. Biol. Evol. 2009, 26:445-450.
43. Yu C.H., Liao J.Y., Zhou H., Qu L.H. The rat mitochondrial Ori L encodes a novel small RNA resembling an ancestral tRNA. Biochem. Biophys. Res. 2008, 372:634-638.
44. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.