A mammalian mitochondrial serine transfer RNA lacking the “dihydrouridine” loop and stem

Bruijn, M.H.L. de; Schreier, Peter; Eperon, Ian C.; Barrell, Bart; Chen, E.Y.; Armstrong, Paul W.; Wong, Jeffrey A.; Roe, Bruce A.

doi:10.1093/nar/8.22.5213

Cited by 138 publications

(78 citation statements)

References 36 publications

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“…The structural features of the dog mitochondrial tRNA molecules, such as the anticodon (AC) stem and loops, T-⌿-C, and amino acid-acceptor (A-A) arms, showed an L-shaped tertiary structure identical to those found in other mammalian mitochondrial tRNA molecules (Cedegren et al, 1981;Kumazawa and Nishida, 1993). The tRNA-Ser-AGY, which was smallest in size, lacked the entire dihydrouridine (DHU) arm as in other mammalian tRNAs (Arcari and Brownlee, 1980;de Bruijn et al, 1980;Udea et al, 1985).…”

Section: Trna and Rrna Genesmentioning

confidence: 89%

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

Kim

Lee

Jeong

et al. 1998

Molecular Phylogenetics and Evolution

200

163

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The complete nucleotide sequence of the mitochondrial genome of the domestic dog, Canis familiaris, was determined. The length of the sequence was 16,728 bp; however, the length was not absolute due to the variation (heteroplasmy) caused by differing numbers of the repetitive motif, 5Ј-GTACACGT(A/G)C-3Ј, in the control region. The genome organization, gene contents, and codon usage conformed to those of other mammalian mitochondrial genomes. Although its features were unknown, the ''CTAGA'' duplication event which followed the translational stop codon of the COII gene was not observed in other mammalian mitochondrial genomes. In order to determine the possible differences between mtDNAs in carnivores, two rRNA and 13 protein-coding genes from the cat, dog, and seal were compared. The combined molecular differences, in two rRNA genes as well as in the inferred amino acid sequences of the mitochondrial 13 protein-coding genes, suggested that there is a closer relationship between the dog and the seal than there is between either of these species and the cat. Based on the molecular differences of the mtDNA, the evolutionary divergence between the cat, the dog, and the seal was dated to approximately 50 ؎ 4 million years ago. The degree of difference between carnivore mtDNAs varied according to the individual protein-coding gene applied, showing that the evolutionary relationships of distantly related species should be presented in an extended study based on ample sequence data like complete mtDNA molecules. 1998 Academic Press

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Section: Trna and Rrna Genesmentioning

confidence: 89%

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

Kim

Lee

Jeong

et al. 1998

Molecular Phylogenetics and Evolution

200

163

View full text Add to dashboard Cite

show abstract

“…Eleven nucleotides occur between the last nucleotide of the amino-acyl stem (nucleotide 7, numbering system shown in Fig. 3) and the first nucleotide of the anticodon stem (nucleotide 19), but these nucleotides cannot be arranged to form a structure resembling the usual dihydrouridine arm of other tRNAs. Nucleotides T10, G1l and A12 are complementary to T13, C14 and A15, as might be expected if they were the conserved dihydrouridine stem; however, if this is the case then two of the A16, G17 and T18 nucleotides must have been added during the evolution of this gene from a vene coding a tRNA with a standard cloverleaf configuration.…”

Section: And Discussionmentioning

confidence: 99%

“…In each of the mt-tRNAser genes of nine different mammals (hamster (17), bovine (18,19), human (19), mouse (8,20), rat (21), gorilla, chimpanzee, orangutan and gibbon (22) (23) have derived a structural model for bovine tRNAser. This model is similar in overall shape to the crystal structure of yeast tRNAphe (24)(25)(26) but is smaller, and involves a unique set of tertiary interactions.…”

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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“…Mitochondrial tRNAs are also smaller (59-75 nt) than their cytoplasmic or prokaryotic counterparts and have some structural differences. Most mitochondrial tRNAs lack the so-called constant nucleotide positions and the size of the 'DHU' loop is very variable or even absent in the case of tRNA Ser AGY (Arcari & Brownlee, 1980;Bruijn et al 1980). With this one exception, all mitochondrial tRNAs can fold adopting the typical cloverleaf structure, but their stabilization requires less tertiary interactions than cytoplasmic tRNAs.…”

Section: Mtdna Transcription and Rna Processingmentioning

confidence: 99%

Replication and Transcription of Mammalian Mitochondrial Dna

Fernández‐Silva¹,

Enrı́quez

Montoya

2003

Experimental Physiology

349

267

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Mitochondria are subcellular organelles, devoted mainly to energy production in the form of ATP, that contain their own genetic system. Mitochondrial DNA codifies a small, but essential number of polypeptides of the oxidative phosphorylation system. The mammalian mitochondrial genome is an example of extreme economy showing a compact gene organization. The coding sequences for two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 13 polypeptides are contiguous and without introns. The tRNAs are regularly interspersed between the rRNA and protein‐coding genes, playing a crucial role in RNA maturation from the polycistronic transcripts. A single major non‐coding region, called the D‐loop region, contains the main regulatory sequences for transcription and replication initiation. This genetic organization has its precise correspondence in the mode of expression and distinctive structural features of the RNAs. The basic mechanisms of mitochondrial DNA transcription and replication and the main cis‐acting elements playing a role in both processes have been determined. Many trans‐acting factors involved in mitochondrial gene expression, including the RNA and DNA polymerases, have been cloned or identified. However, the regulatory mechanisms participating in mitochondrial gene expression are still poorly understood. The interest to complete this knowledge is increased by the involvement of mitochondria in human diseases, in basic processes such as heat production, Ca2+ homeostasis and apoptosis, and by their potential role in ageing and carcinogenesis.

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A mammalian mitochondrial serine transfer RNA lacking the “dihydrouridine” loop and stem

Cited by 138 publications

References 36 publications

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

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

Replication and Transcription of Mammalian Mitochondrial Dna

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A mammalian mitochondrial serine transfer RNA lacking the “dihydrouridine” loop and stem

Cited by 138 publications

References 36 publications

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

The Complete Nucleotide Sequence of the Domestic Dog (Canis familiaris) Mitochondrial Genome

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

Replication and Transcription of Mammalian Mitochondrial Dna

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Product

Resources

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