Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms.

Wolstenholme, David R.; Macfarlane, Jane L.; Okimoto, Ronald; Clary, Douglas O.; Wahleithner, Jill A.

doi:10.1073/pnas.84.5.1324

Cited by 249 publications

(153 citation statements)

References 31 publications

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“…Already at the time of sequencing the first complete mitochondrial genome, that of bovine (Anderson et al 1981), it appeared that, despite a cloverleaf-like secondary structure, the mitochondrial tRNAs markedly deviate from classical tRNAs. These unexpected features have been confirmed for mitochondrial tRNAs from other organisms (e.g., Wolstenholme et al 1987) and especially from mammals. Compilation and comparison of tRNAs from 31 fully sequenced mammalian mitochondrial genomes within 22 groups (one per amino acid specificity, two for leucine, and two for serine according to the anticodon triplet) demonstrated that these tRNAs distinguish from classical tRNAs in regard of the size of D-and T-domains (especially loops) and the absence of expected conserved and semi-conserved nucleotides, leaving the understanding of three-dimensional (3D) folding of these tRNAs mainly open (Helm et al 2000), despite efforts in this direction (Steinberg et al 1997).…”

Section: Introductionsupporting

confidence: 53%

Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures

Pütz¹,

Dupuis²,

Sissler³

et al. 2007

RNA

143

144

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Mamit-tRNA (http://mamit-tRNA.u-strasbg.fr), a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes. To accommodate the rapid growing availability of fully sequenced mammalian mitochondrial genomes, Mamit-tRNA has implemented a relational database, and all annotated tRNA genes have been curated and aligned manually. System administrative tools have been integrated to improve efficiency and to allow real-time update (from GenBank Database at NCBI) of available mammalian mitochondrial genomes. More than 3000 tRNA gene sequences from 150 organisms are classified into 22 families according to the amino acid specificity as defined by the anticodon triplets and organized according to phylogeny. Each sequence is displayed linearly with color codes indicating secondary structural domains and can be converted into a printable two-dimensional (2D) cloverleaf structure. Consensus and typical 2D structures can be extracted for any combination of primary sequences within a given tRNA specificity on the basis of phylogenetic relationships or on the basis of structural peculiarities. Mamit-tRNA further displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. The site offers also a table allowing for an easy conversion of human mitochondrial genome nucleotide numbering into conventional tRNA numbering. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments.

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Section: Introductionsupporting

confidence: 53%

Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures

Pütz¹,

Dupuis²,

Sissler³

et al. 2007

RNA

143

144

View full text Add to dashboard Cite

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“…As in other mammals, 22 tRNA genes were found in the dog mtDNA, and had a similar organization. The small number of tRNA genes in the mammalian mtDNA is thought to be the result of strong pressure for the economization of the genome size (Anderson et al, 1981(Anderson et al, , 1982Bibb et al, 1981;Clary and Wolstenholme, 1985;Wolstenholme et al, 1987;Gadaleta et al, 1989;Desjardins and Morais, 1990;Okimoto et al, 1992). 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).…”

Section: Trna and Rrna Genesmentioning

confidence: 99%

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

Kim

Lee

Jeong

et al. 1998

Molecular Phylogenetics and Evolution

204

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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“…The nematode mtDNA genetic code (Wolstenholme et al, 1987;Okimoto et al, 1992) was used to predict amino acid sequences from the 582 nt obtained for all taxa. Predicted polypeptide sequences were aligned using CLUSTAL V (Higgins et al, 1992); alignment of the coding nucleotide sequences was straightforward.…”

Section: Sequence Analysismentioning

confidence: 99%

Phylogeny of the Ascaridoidea (Nematoda: Ascaridida) Based on Three Genes and Morphology: Hypotheses of Structural and Sequence Evolution

Nadler¹,

Hudspeth²

2000

The Journal of Parasitology

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Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms.

Cited by 249 publications

References 31 publications

Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures

Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures

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

Phylogeny of the Ascaridoidea (Nematoda: Ascaridida) Based on Three Genes and Morphology: Hypotheses of Structural and Sequence Evolution

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