An amplified insect dihydrofolate reductase gene contains a single intron

We have used methotrexate-resistant mosquito (Aedes albopictus) cells as the source of DNA for cloning an 8.5-kb EcoRI fragment containing an amplified dihydrofolate reductase (DHRF) gene. An estimated 1200 copies of the DHFR gene were represented in nuclear DNA from Mtx-5011-256 cells, which were 3000-fold more resistant to methotrexate than wild-type cells. Southern blot analysis indicated that all of the amplified DHFR genes were contained within a 1.8-kb AccI fragment represented in the cloned DNA. In contrast to mammalian DHFR genes which span approximately 30 kb, the complete amino acid coding sequence of the mosquito DHFR gene spanned 614 nucleotides, including a single 56-nucleotide intron that interrupted a conserved Arg codon at amino acid position 27. Additional introns characteristic of mammalian DHFR genes were absent; conservation of the first intron in the mosquito DHFR gene supports a regulatory role for this intron. The mosquito DHFR gene coded for a 186-amino-acid protein with 43-48% similarity to vertebrate DHFR.     

Assembly of the mitochondrial membrane system: isolation of mitochondrial transfer ribonucleic acid mutants and characterization of transfer ribonucleic acid genes of Saccharomyces cerevisiae

A method is described for isolating cytoplasmic mutants of Saccharomyces cerevisiae with lesions in mitochondrial transfer ribonucleic acids (tRNA's). The mutants were selected for slow growth on glycerol and for restoration of wild-type growth by cytoplasmic "petite" testers that contain regions of mitochondrial deoxyribonucleic acid (DNA) with tRNA genes. The aminoacylated mitochondrial tRNA's of several presumptive tRNA mutants were analyzed by reverse-phase chromatography on RPC-5. Two mutant strains, G76-26 and G76-35, were determined to carry mutations in the cysteine and histidine tRNA genes, respectively. The cysteine tRNA mutant was used to isolate cytoplasmic petite mutants whose retained segments of mitochondrial DNA contain the cysteine tRNA gene. The segment of one such mutant (DS504) was sequenced and shown to have the cysteine, histidine, and threonine tRNA genes. The structures of the three mitochondrial tRNA's were deduced from the DNA sequence.     

Cytochrome oxidase subunit III gene in Neurospora crassa mitochondria. Location and sequence

We have located and sequenced the gene for cytochrome oxidase subunit III (CoIII) in Neurospora crassa mitochondria. The CoIII gene is located downstream from the small rRNA gene within a cluster of tRNA genes and is coded by the same strand as the tRNA and the rRNA genes. Like the tRNA and the rRNA genes, the CoIII gene is also flanked by the GC-rich palindromic DNA sequences which are highly conserved in N. crassa mitochondria. The CoIII coding sequence predicts a protein 269 amino acids long including 8 tryptophan residues. All 8 tryptophan residues are coded for by UGA. This supports our previous conclusion based on the anticodon sequence of N. crassa mitochondrial tryptophan tRNA and provides evidence for the notion that use of UGA as a codon for tryptophan rather than chain termination may be a feature common to most mitochondrial protein synthesis systems. The close correspondence between the amino acid composition of N. crassa CoIII and that of the protein predicted by the CoIII gene sequence suggests that unlike in mammalian mitochondria, AUA is a codon for isoleucine and not for methionine in N. crassa mitochondria. The N. crassa CoIII sequence shows strong homologies to the corresponding yeast and human proteins (53 and 47%, respectively). The overall hydrophobic character of the protein is consistent with suggestions that most of CoIII is embedded in the mitochondrial inner membrane.     

Assembly of the mitochondrial membrane system. Sequence of the oxi 2 gene of yeast mitochondrial DNA

The region of mitochondrial DNA (mtDNA) containing the oxi 2 locus has been sequenced in a rho- clone (DS40) derived from the respiratory competent strain D273-10B/A48 of Saccharomyces cerevisiae. The DS40 clone was established to have retained only genetic markers in the oxi 2 locus and to have a segment of mtDNA extending from 18.6 to 24.3 units of the wild type map. The mitochondrial genome of DS40 includes a sequence that has been tentatively identified as the structural gene of Subunit 3 of cytochrome oxidase. The coding sequence is 810 nucleotides long and generates a protein with a molecular weight of 30,340. The amino acid composition of the oxi 2 gene product deduced from the nucleotide sequence is in agreement with the composition of the purified Subunit 3 of yeast cytochrome oxidase. The orientation of the DS40 mtDNA segment relative to wild type mtDNA indicates that the oxi 2 gene is transcribed from the same DNA strand as the oxi 1 and several other mitochondrial genes.     

Direct sequencing of deleted mitochondrial DNA in myopathic patients

To investigate the mechanism of mitochondrial DNA deletion in human diseases, we amplified the deleted mitochondrial DNA of five patients with mitochondrial myopathy by using the polymerase chain reaction, and directly sequenced the crossover regions of the deleted mitochondrial DNA without cloning. In Patient 1, a 7-bp directly repeated sequence of 5'-ATCCCCA-3' was found at the boundaries of deleted segment spanning 7,039 bp between the ATPase 6 and the cytochrome b genes. In Patients 2, 3, and 4, a 13-bp sequence of 5'-ACCTCCCTCACCA-3' was found in the boundaries of deleted segment spanning 4,977 bp between the ATPase 8 and the ND5 genes. In Patient 5, a 3-bp sequence of 5'-CCT-3' was found in the boundaries of deleted segment spanning 3,717 bp between the ATPase 6 and the ND5 genes. Similar directly repeated sequences may contribute to mitochondrial DNA deletions in human degenerative diseases.     

The sequence of the gene for cytochrome c oxidase subunit I, a frameshift containing gene for cytochrome c oxidase subunit II and seven unassigned reading frames in Trypanosoma brucei mitochrondrial maxi-circle DNA.

A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the corresponding genes in fungal and mammalian mtDNA, the only striking point of divergence being an unusually high cysteine content (about 4.5%). The reading frame coding for cytochrome c oxidase subunit II is discontinuous: the C-terminal portion of about 40 aminoacids, is present in the DNA-sequence in a -1 reading frame with respect to the N-terminal moiety. URF5, 8 and 10, show a low but distinct homology (about 20%) to mammalian mitochondrial URF-1, 4 and 5, respectively. In URF5, the first AUG is found at codon 145, whereas extensive homology to mammalian URF-1 sequences occurs upstream of this position. The possibility exists that UUG can serve as an initiator codon. URF7 and URF9 have a highly unusual aminoacid composition and do not possess AUG or UUG initiator codons. These URFs probably do not have a protein-coding function. The segment does not contain conventional tRNA genes.     

A major lysine tRNA with a CUU anticodon in insect mitochondria

We have sequenced a lysine tRNA from mosquito mitochondria that has the anticodon CUU. The preponderance of AAA lysine codons in insect mitochondrial genes, the parsimonious organization of the genomes, and the fact that this tRNA is a major component of the mosquito mitochondrial tRNA complement, lead us to suggest that the CUU anticodon recognizes AAC and AAA codons.     

Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates

The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced. The avian genome encodes the same set of genes (13 proteins, 2 rRNAs and 22 tRNAs) as do other vertebrate mitochondrial DNAs and is organized in a very similar economical fashion. There are very few intergenic nucleotides and several instances of overlaps between protein or tRNA genes. The protein genes are highly similar to their mammalian and amphibian counterparts and are translated according to the same variant genetic code. Despite these highly conserved features, the chicken mitochondrial genome displays two distinctive characteristics. First, it exhibits a novel gene order, the contiguous tRNA(Glu) and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous tRNA(Pro), tRNA(Thr) and cytochrome b genes, which border the displacement loop region in other vertebrate mitochondrial genomes. This unusual gene order is conserved among the galliform birds. Second, a light-strand replication origin, equivalent to the conserved sequence found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far, is absent in the chicken genome. These observations indicate that galliform mitochondrial genomes departed from their mammalian and amphibian counterparts during the course of evolution of vertebrate species. These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level.     

The mitochondrial genome of the lizard Calotes versicolor and a novel gene inversion in South Asian draconine agamids

A complete mitochondrial DNA (mtDNA) sequence was determinedfor the lizard Calotes versicolor (Reptilia; Agamidae). The16,670-bp genome with notable shorter genes for some protein-codingand tRNA genes had the same gene content as that found in othervertebrates. However, a novel gene arrangement was found inwhich the proline tRNA (trnP) gene is located in the light strandinstead of its typical heavy-strand position, providing thefirst known example of gene inversion in vertebrate mtDNAs.A segment of mtDNA encompassing the trnP gene and its flankinggenes and the control region was amplified and sequenced forvarious agamid taxa to investigate timing and mechanism of thegene inversion. The inverted trnP gene organization was sharedby all South Asian draconine agamids examined but by none ofthe other Asian and African agamids. Phylogenetic analyses includingclock-free Bayesian analyses for divergence time estimationsuggested a single occurrence of the gene inversion on a lineageleading to the draconine agamids during the Paleogene period.This gene inversion could not be explained by the tandem duplication/randomloss model for mitochondrial gene rearrangements. Our availablesequence data did not provide evidence for remolding of thetrnP gene by an anticodon switch in a duplicated tRNA gene.Based on results of sequence comparisons and other circumstantialevidence, we hypothesize that inversion of the trnP gene wasoriginally mediated by a homologous DNA recombination and thatthe de novo gene organization that does not disrupt expressionof mitochondrial genes has been maintained in draconine mtDNAsfor such a long period of time.     

The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom)

In this study, the full mitochondrial genome of a basidiomycete fungus, Pleurotus ostreatus, was sequenced and analyzed. It is a circular DNA molecule of 73 242 bp and contains 44 known genes encoding 18 proteins and 26 RNA genes. The protein-coding genes include 14 common mitochondrial genes, one ribosomal small subunit protein 3 gene, one RNA polymerase gene and two DNA polymerase genes. In addition, one RNA and one DNA polymerase genes were identified in a mitochondrial plasmid. These two genes show relatively low similarities to their homologs in the mitochondrial genome but they are nearly identical to the known mitochondrial plasmid genes from another Pleurotus ostreatus strain. This suggests that the plasmid may mediate the horizontal gene transfer of the DNA and RNA polymerase genes into mitochondrial genome, and such a transfer may be an ancient event. Phylogenetic analysis based on the cox1 ORFs verified the traditional classification of Pleurotus ostreatus among fungi. However, the discordances were observed in the phylogenetic trees based on the six cox1 intronic ORFs of Pleurotus ostreatus and their homologs in other species, suggesting that these intronic ORFs are foreign DNA sequences obtained through HGT. In summary, this analysis provides valuable information towards the understanding of the evolution of fungal mtDNA.     

Nucleotide Sequence and Gene Organization of the Starfish Asterina Pectinifera Mitochondrial Genome

The 16,260-bp mitochondrial DNA (mtDNA) from the starfish Asterina pectinifera has been sequenced. The genes for 13 proteins, two rRNAs and 22 tRNAs are organized in an extremely economical fashion, similar to those of other animal mtDNAs, with some of the genes overlapping each other. The gene organization is the same as that for another echinoderm, sea urchin, except for the inversion of a 4.6-kb segment that contains genes for two proteins, 13 tRNAs and the 16S rRNA. Judging from the organization of the protein coding genes, mammalian mtDNAs resemble the sea urchin mtDNA more than that of the starfish. The region around the 3' end of the 12S rRNA gene of the starfish shows a high similarity with those for vertebrates. This region encodes a possible stem and loop structure; similar potential structures occur in this region of vertebrate mtDNAs and also in nonmitochondrial small subunit rRNA. A similar stem and loop structure is also found at the 3' end of the 16S rRNA genes in A. pectinifera, in another starfish Pisaster ochraceus, in vertebrates and in Drosophila, but not in sea urchins. The full sequence data confirm the presumption that AGA/AGG, AUA and AAA codons, respectively, code for serine, isoleucine, and asparagine in the starfish mitochondria, and that AGA/AGG codons are read by tRNA(GCU)(Ser), which possesses a truncated dihydrouridine arm, that was previously suggested from a partial mtDNA sequence. The structural characteristics of tRNAs and possible mechanisms for the change in the mitochondrial genetic code are also discussed.     

Genes encoding Xenopus laevis Ig L chains. Implications for the evolution of kappa and lambda chains.

Xenopus laevis Ig contain two distinct types of L chains, designated rho or L1 and sigma or L2. We have analyzed Xenopus genomic DNA by Southern blotting with cDNA probes specific for L1 V and C regions. Many fragments hybridized to the V probe, but only one or two fragments hybridized to the C probe. Corresponding C, J, and V gene segments were identified on clones isolated from a genomic library prepared from the same DNA. One clone contains a C gene segment separated from a J gene segment by an intron of 3.4 kb. The J and C gene segments are nearly identical in sequence to cDNA clones analyzed previously. The C segment is somewhat more similar and the J segment considerably more similar in sequence to the corresponding segments of mammalian kappa chains than to those of mammalian lambda chains. Upstream of the J segment is a typical recombination signal sequence with a spacer of 23 bp, as in J kappa. A second clone from the library contains four V gene segments, separated by 2.1 to 3.6 kb. Two of these, V1 and V3, have the expected structural and regulatory features of V genes, and are very similar in sequence to each other and to mammalian V kappa. A third gene segment, V2, resembles V1 and V3 in its coding region and nearby 5'-flanking region, but diverges in sequence 5' to position -95 with loss of the octamer promoter element. The fourth V-like segment is similar to the others at the 3'-end, but upstream of codon 64 bears no resemblance in sequence to any Ig V region. All four V segments have typical recombination signal sequences with 12-bp spacers at their 3'-ends, as in V kappa. Taken together, the data suggest that Xenopus L1 L chain genes are members of the kappa gene family.     

Mitochondrial gene expression in mammalian striated muscle. Evidence that variation in gene dosage is the major regulatory event

The oxidative capacity of mammalian striated muscles can vary markedly over a nearly 10-fold range, reflecting major differences in the expression of genes that encode enzymes of oxidative metabolism, including genes located exclusively within mitochondrial DNA. To clarify the regulatory events that govern expression of mitochondrial genes in striated muscle, nucleic acid hybridization procedures employing cloned segments of mitochondrial DNA as probes were utilized to determine the concentrations of mitochondrial DNA, mitochondrial ribosomal RNA, and cytochrome b mRNA (a mitochondrial gene product) in rabbit striated muscles of markedly different oxidative capacities. When cardiac muscle and Type I (red, oxidative) skeletal muscle were compared to Type II (white, glycolytic) skeletal muscle, mitochondrial DNA, mitochondrial ribosomal RNA, and cytochrome b mRNA, each increased in direct proportion to increases in oxidative capacity. Furthermore, when the phenotypic characteristics of Type II skeletal muscle were altered by electrical stimulation in vivo, mitochondrial DNA, mitochondrial rRNA, and cytochrome b mRNA also increased proportionately with increases in oxidative capacity. These results indicate that the expression of mitochondrial genes in mammalian striated muscle is proportionate to their copy number, and support the hypothesis that amplification of the mitochondrial genome relative to chromosomal DNA is an important feature underlying enhanced expression of mitochondrial genes in highly oxidative tissues.     

Molecular characterization of a cloned dolphin mitochondrial genome

Summary DNA clones have been isolated that span the complete mitochondrial (mt) genome of the dolphin,Cephalorhynchus commersonii. Hybridization experiments with purified primate mtDNA probes have established that there is close resemblance in the general organization of the dolphin mt genome and the terrestrial mammalian mt genomes. Sequences covering 2381 bp of the dolphin mt genome from the major noncoding region, three tRNA genes, and parts of the genes encoding cytochrome b, NADH dehydrogenase subunit 3 (ND3), and 16S rRNA have been compared with corresponding regions from other mammalian genomes. There is a general tendency throughout the sequenced regions for greater similarity between dolphin and bovine mt genomes than between dolphin and rodent or human mt genomes.