Evolutionary analysis of sea urchin mitochondrial tRNAs: Folding of the molecules as suggested by the non-random occurrence of nucleotides

Current Genetics

Volumn 30, Issue 3, 1996, Pages 191-199

  De Giorgi, Carla ^a   Martiradonna, Antonia ^a   Saccone, Cecilia ^b  

^a UNIVERSITY OF BARI   (Italy)

^b CNR   (Italy)

Author keywords

Consensus diagram; Signature; Tertiary structures

Indexed keywords

MITOCHONDRIAL RNA; TRANSFER RNA;

ANIMAL CELL; ARTICLE; BIOGENESIS; CONSENSUS SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA CONFORMATION; RNA SEQUENCE; SEA URCHIN;

ANIMALS; BASE SEQUENCE; CONSENSUS SEQUENCE; DNA, MITOCHONDRIAL; EVOLUTION; MODELS, STRUCTURAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, TRANSFER, AMINO ACID-SPECIFIC; SEA URCHINS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ANIMALIA; ARBACIA LIXULA; ECHINOIDEA; METAZOA; PARACENTROTUS LIVIDUS; STRONGYLOCENTROTUS PURPURATUS;

EID: 0029811658     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050120     Document Type: Article

References (38)

1. Anderson S, de Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol 156:683-717
2. Asakawa S, Himeno H, Miura K, Watanabe K (1995) Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics 140:1047-1060.
3. Basavappa R, Sigler PB (1991) A crystal structure of yeast initiator tRNA: functional implication in initiator/elongator discrimination. EMBO J 10:3105-3111
4. Brennan T, Sundaralingam M (1976) Structure of tRNA molecules containing the long variable loop. Nucleic Acids Res 3:3235-3251
5. Bruijn MHL de, Klug A (1983) A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire dihydrouridine loop and stem. EMBO J 2:1309-1321
6. Cantatore P, Gadaleta MN, Roberti M, Saccone C, Wilson AC (1987) Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329:853-855
7. Cantatore P, Roberti M, Rainaldi G, Gadaleta MN, Saccone C (1989) The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J Biol Chem 264:10965-10975
8. De Giorgi C, Martiradonna A, Saccone C (1995) The mitochondrial genome in the sea urchin. In: Palmieri F, Papa S, Saccone C, Gadaleta MN (eds) Progress in cell research. Elsevier Science Publisher, BV, pp 155-159
9. De Giorgi C, Martiradonna A, Lanave C, Saccone C (1996) Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula. Conserved features of the echinoid mitochondrial genome. Mol Phylog Evol 5:323-332
10. Hou YM, Schimmel P (1992) Novel transfer RNAs that are active in Escherichia coli. Biochemistry 31:4157-4160
11. Jacobs HT, Elliot DJ, Math VB, Farquharson A (1988) Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol 202:185-217
12. Köchel HG, Lazarus CM, Basak N, Küntzel H (1981) Mitochondrial tRNA gene clusters in Aspergillus nidulans: organization and nucleotide sequence. Cell 23:625-633
13. Kumazawa Y, Nishida M (1993) Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 37:380-398
14. Kumazawa Y, Yokogawa T, Hasegawa E, Miura K, Watanabe K (1989) The aminoacylation of structurally variant phenylalanine tRNAs from mitochondrial sources by bovine mitochondrial phenylalanine-tRNA synthetase. J Biol Chem 264:13005-13011
15. Ladner JE, Jack A, Robertus JD, Brown RS, Rhodes D, Clark BFC, Klug A (1975) Structure of yeast phenylalanine transfer RNA at 2.5 Å resolution. Proc Natsl Acad Sci USA 72:4414-4418
16. Mattoccia P, Baldi IM, Gandini-Attardi D, Ciafré S, Tocchini Valentini G (1988) Site selection by the tRNA splicing endonuclease of Xenopus laevis. Cell 55:731-738
17. Moritz C, Dowling TE, Brown W (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst 18:269-292
18. f-Met and small- subunit ribosomal RNA, and standard genetic code specificity for AGR and ATA codons. J Mol Evol 39:387-399
19. Reyes VM, Abelson J (1988) Substrate recognition and splice site determination in yeast tRNA splicing. Cell 55:719-730
20. Rich A, Rajbhandary UL (1976) Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem 45:805-860
21. Rossmanith W, Potuschak T, Tullo A, Karwan R, Sbisà E (1995) Human mitochondrial tRNA processing. J Biol Chem 270:12885-12891
22. Gln and ATP at 2.8 Å resolution. Science 246:1135-1142
23. Saccone C, Attimonelli M, De Giorgi C, Lanave C, Sbisà E (1990) The role of tRNA genes in the evolution of animal mitochondrial DNA. In: Quagliariello E, Papa S, Palmieri F, Saccone C (eds) Structure, function and biogenesis of energy transfer system. Elsvier Science Publisher BV, pp 93-96
24. Sampson JR, Direnzo AB, Behlen LS, Uhlenbeck OC (1990) Role of the tertiary nucleotides in the interaction of yeast phenylalanine tRNA with its cognate synthetase. Biochemistry 29:2523-2532
25. Smith D, Yarus M (1989) Transfer RNA structure and coding specificity. J Mol Biol 206:489-501
26. Smith MJ, Banfield DK, Doteval K, Gorski S, Kowbel DJ (1990) Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus. J Mol Evol 31:195-204
27. Sprinzl M, Hartmann T, Weber J, Blank J, Zeidler R (1989) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 17:r1-r172
28. Staden R (1980) A computer program to search for tRNA genes. Nucleic Acids Res 8:817-826
29. Steinberg S, Misch A, Sprinzl M (1993) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 21:3011-3015
30. Ser to common three- dimensional constraints. J Mol Biol 236:982-989
31. Ser (AGY) is a main recognition site for homologous seryl-tRNA synthetase. Nucleic Acids Res 20:2217-2222
32. Phe lacking the "conserved" GG and TΨCG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res 22:347-353
33. Westhof E, Dumas P, Moras D (1985) Crystallographic refinement of yeast aspartic acid transfer RNA. J Mol Biol 184:119-145
34. Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173-216
35. Wolstenholme DR, Okimoto R, Macfarlane JL (1994) Nucleotide correlations that suggest tertiary interactions in theTV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Nucleic Acids Res 22:4300-4306
36. fmet. Nature 286:346-351
37. Yokogawa T, Kumazawa Y, Miura K, Watanabe K (1989) Purification and characterization of two serine isoacceptor tRNAs from bovine mitochondria by using a hybridization assay method. Nucleic Acids Res 17:2623-2638
38. Ser (UCN). Nucleic Acids Res 19:6101-6105