Sequence of Mammalian Mitochondrial DNA

Barrell, Bart; Anderson, Stephen; Bankier, Alan T.; Bruijn, M.H.L. de; Chen, E.; Coulson, Alan; Drouin, J.; Eperon, I C; Nierlich, Donald P.; Roe, Bruce A.; Sanger, F.; Schreier, Peter; Smith, Andrew J.H.; Staden, Rodger; Young, Ian G.

doi:10.1007/978-3-642-81557-7_2

Cited by 26 publications

(33 citation statements)

References 40 publications

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“…Furthermore, the alanine and proline tRNAs and the serine tRNA reading the UCN codons (where N stands for G, C, A, or U) also have an unsubstituted uridine in the wobble position. Along with the previous results (15), the emerging picture of the tRNA genes and their gene products in M. mycoides thus shows a striking resemblance to the situation in mitochondria, particularly yeast mitochondria (8)(9)(10)(11)(12). However, the resemblance to mitochondrial codon reading is not complete since our analysis of the threonine tRNAs has demonstrated an additional isoacceptor tRNA for threonine with adenosine in the wobble position.…”

supporting

confidence: 80%

“…In the second category of unconventional codon reading, the four codons of a family box are read without nucleotide discrimination in the third position, reminiscent of the twoout-of-three reading that we have observed in protein synthesis in vitro using the phage MS2 RNA as message (3)(4)(5)(6)(7). The analysis of mitochondrial tRNA genes and their gene products in the laboratories of Sanger (8), Tzagoloff (9), and RajBhandary (10) has established beyond doubt that in mammalian, Neurospora, and yeast mitochondria the family boxes are read by only one tRNA each. In all these cases the tRNA gene has a thymidine in the position corresponding to the wobble nucleotide, and, whenever the primary structure ofthe tRNA itselfis known, the wobble nucleotide has turned out to be an unsubstituted uridine (11).…”

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confidence: 99%

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Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

Samuelsson¹,

Guindy²,

Lustig³

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

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We report a cluster of four tRNA genes from Mycoplasma mycoides as well as the sequence of the alanine, proline, and valine tRNAs and the serine tRNA reading the UCN codons (where N stands for G, A, C, or U). This brings the total number of tRNA genes that we have so far characterized in this organism to 14, 6 of which code for tRNAs that read the codons of family boxes. In each of these latter cases, we found only one gene per family box, and the gene sequence contains a thymidine in the position corresponding to the wobble nucleotide, with the exception of the arginine tRNA gene that has an adenosine in this position. Furthermore, all of the tRNA structures reported here have an unsubstituted uridine in the wobble position. These rindings are similar to those reported for mitochondria, especially yeast mitochondria, that contain an arginine tRNA with the anticodon ACG. However, the resemblance is not complete since we have demonstrated the presence of two isoacceptor tRNAs for threonine having uridine and adenosine, respectively, in the wobble position. It is suggested that in the M. mycoides at least some ofthe family codon boxes are read by only one tRNA each, using an unconventional method without discrimination between the nucleotides in the third codon position.The genetic code can be thought of as being made up of sixteen boxes with four codons in each box. All codons in a box have the same nucleotides in the first two positions; the variation between the codons is in the third position. In half of the boxes all four codons specify the same amino acid, and in what follows we will refer to such boxes as family boxes (Fig. 1). Regarding the codon families it makes no difference, as far as translational fidelity is concerned, how the third codon nucleotide is read since the first two are enough to specify the amino acid. In the rest of the boxes the codons have been divided up between amino acids or between amino acids and stop words. When reading the codons of these boxes, it is obviously necessary to be able to discriminate among nucleotides in the third codon position to avoid translational errors. To explain such discrimination, Crick in his wobble rules (1) excludes a number of pairings between the third nucleotide of the codon and the wobble nucleotide of the anticodon on structural grounds.Most of the accumulated data concerning codon reading in vivo indicate that codons are read in the cell according to the wobble rules. Nevertheless, there is evidence in the literature for codon readings in vivo involving almost all of the forbidden base pairs. These exceptions to the rules are oftwo different types, (i) unconventional reading with discrimination among the nucleotides in the third codon position, albeit using principles other than those laid down in the wobble rules, and (ii) reading without discrimination in this position

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confidence: 80%

mentioning

confidence: 99%

Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

Samuelsson¹,

Guindy²,

Lustig³

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

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“…2). It appears that, as in fungal and mammalian mtDNAs (8,(27)(28)(29), TGA codons specify tryptophan in the Drosophila mitochondrial genetic code (1,(3)(4)(5). While two out of three of the TGAs of the D. yakuba URF3 sequence correspond to tryptophan-specifying codons (TGAs) in the mouse URF3 sequence, none of the three TGA codons of the D. yakuba URF5 sequence correspond to tryptophan-specifying codons in the mouse URF5 sequence.…”

Section: And Discussionmentioning

confidence: 99%

A cluster of six tRNA genes inDrosophilamitochondrial DNA that includes a gene for an unusual tRNA^ser_AGY

Clary

Wolstenholme

1984

Nucl Acids Res

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Genes for URF3, tRNAala, tRNAarg, tRNAasn, tRNASer, tRNA1u, tRNAphe, and the carboxyl terminal segment of the URF5 gene have een identified within a sequenced segment of the mtDNA molecule of Drosophila yakuba. The genes occur in the order given. The URF5 and tRNAPhe genes are transcribed in the same direction as replication while the URF3 and remaining five tRNA genes are transcribed in the opposite direction. Considerable differences exist in the relative arrangement of these genes in D. yakuba and mammalian mtDNA molecules. In the tRNAser gene an eleven nucleotide loop, within which secondary structure formation seems unlikely, replaces the dihydrouridine am, and both the variable loop (six nucleotides) and the TPC loop (nine nucleotides) are larger than in any other D. yakuba tRNA gene. As available evidence is consistent with AGA codons specifying serine rather than arginine in the Drosophila mitochondrial genetic code, the possibility is considered that the 5GU anticodon of the D. yakuba tRNAser gene can recognize AGA as well as AGY codons.

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“…The nucleotide sequence, predicted secondary structure and number of mammalian mitochondrial tRNAs are distinct from eubacterial or nuclear-encoded tRNAs. The limited number of tRNA genes in mitochondria results from an expanded codon usage in which some tRNAs are able to read additional codons (4). The mitochondrial genome of maize is considerably more complex than the mammalian mitochondrial genome and its organization is not well understood.…”

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Identification of Two Methionine Transfer RNA Genes in the Maize Mitochondrial Genome

Parks

Dougherty²,

Levings³

et al. 1984

Plant Physiol.

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Two methionine transfer RNA (tRNA) genes were identified in the maize mitochondrial genomne by nucleotide sequence analysis. One tRNA gene was similar in nucleotide sequence and secondary structure to the initiator methionine tRNA genes of eubacteria and higher plant chloroplast genomes. This tRNA gene also had extensive nucleotide homology (99%) with an initiator methionine tRNA gene described for the wheat mitochondrial genome. The other methionine tRNA gene sequence was distinct and more closely resembled an elongator methionine tRNA.

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Sequence of Mammalian Mitochondrial DNA

Cited by 26 publications

References 40 publications

Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

A cluster of six tRNA genes inDrosophilamitochondrial DNA that includes a gene for an unusual tRNA^ser_AGY

Identification of Two Methionine Transfer RNA Genes in the Maize Mitochondrial Genome

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Sequence of Mammalian Mitochondrial DNA

Cited by 26 publications

References 40 publications

Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides.

A cluster of six tRNA genes inDrosophilamitochondrial DNA that includes a gene for an unusual tRNAserAGY

Identification of Two Methionine Transfer RNA Genes in the Maize Mitochondrial Genome

Contact Info

Product

Resources

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A cluster of six tRNA genes inDrosophilamitochondrial DNA that includes a gene for an unusual tRNA^ser_AGY