Rearranged mitochondrial genes in the yeast nuclear genome

Two major sequence classes of ribosomal RNA genes in Plasmodium berghei

Primary sequence differences have been found between two different ribosomal DNA (rDNA) units of the rodent malaria parasite, Plasmodium berghei, within the coding areas of both the small and large ribosomal RNAs (rRNA). The coding regions of rDNA unit A are protected from nuclease S1 digestion by rRNA isolated from asexual blood stage parasites. Under the same conditions of analysis, the comparable coding regions from unit C are cut into small pieces by nuclease S1, the largest being 1.1 kb. Analysis of heteroduplexes of the respective DNA clones from units A and C by electron microscopy reveals that the two units differ in the 5' flanking and internal transcribed sequences and that there are extensive sequence differences in the DNA coding for the mature large rRNA. No introns were detected in either rDNA unit. The data shows that unit A is transcribed in blood stage parasites and that unit C is not.

Interruption of a human nuclear sequence homologous to mitochondrial DNA by a member of the KpnI 1.8 kb family

We reported that several DNA sequences homologous to mitochondrial DNA (mtDNA) are present in the human nuclear genome (Tsuzuki et al. (1983) Gene 25, 223-229). Detailed Southern blot analyses revealed that one of such sequences is interrupted by a repetitive sequence about 1.8 kb long, and that the insert is one member of the dispersed repeated DNA sequences of the KpnI 1.8 kb family. Nucleotide sequence analysis showed that the KpnI 1.8 kb DNA is flanked with imperfect 15-base pair (bp) direct repeats of mtDNA. This KpnI 1.8 kb DNA has an A-rich sequence at its 3'-end, and has a considerable homology with one of the published cDNA sequences homologous to one of the human KpnI families and also to one of the African green monkey KpnI families, KpnI-LS1. These structural features suggest that the KpnI 1.8 kb DNA is a movable element and is inserted within the mtDNA-like sequence by an RNA-mediated process.

Methylation pattern of mouse mitochondrial DNA

The pattern of methylation of mouse mitochondrial DNA (mtDNA) was studied using several techniques. By employing a sensitive analytical procedure it was possible to show that this DNA contains the modified base 5-methylcytosine (m5Cyt). This residue occurred exclusively at the dinucleotide sequence CpG at a frequency of 3 to 5%. The pattern of methylation was further investigated by determining the state of methylation of several MspI (HpaII) sites. Different sites were found to be methylated to a different extent, implying that methylation of mtDNA is nonrandom. Based on the known base composition and nucleotide sequence of mouse mtDNA, the dinucleotide sequence CpG was found to be underrepresented in this DNA. The features of mtDNA methylation (CpG methylation, partial methylation of specific sites and CpG underrepresentation) are also characteristic of vertebrate nuclear DNA. This resemblance may reflect functional relationship between the mitochondrial and nuclear genomes.

Genetic mapping of Ty elements in Saccharomyces cerevisiae

We used transformation to insert a selectable marker at various sites in the Saccharomyces cerevisiae genome occupied by the transposable element Ty. The vector CV9 contains the LEU2+ gene and a portion of the repeated element Ty1-17. Transformation with this plasmid resulted in integration of the vector via a reciprocal exchange using homology at the LEU2 locus or at the various Ty elements that are dispersed throughout the S. cerevisiae genome. These transformants were used to map genetically sites of several Ty elements. The 24 transformants recovered at Ty sites define 19 distinct loci. Seven of these were placed on the genetic map. Two classes of Ty elements were identified in these experiments: a Ty1-17 class and Ty elements different from Ty1-17. Statistical analysis of the number of transformants at each class of Ty elements shows that there is preferential integration of the CV9 plasmid into the Ty1-17 class.

Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery

Evolutionary constraints operating on animal mitochondrial tRNA were estimated to be reduced to about 1/30 of those that apply to cytoplasmic tRNA. In the nuclear-cytoplasmic system, an effect of a mutation in tRNA is likely to be amplified through positive feedback loops consisting of DNA polymerases, RNA polymerases, ribosomal proteins, aminoacyl-tRNA synthetases, tRNA processing enzymes, and others. This amplification phenomenon is called an "error cascade" and the loops that cause it are called "error loops." The freedom of evolutionary change of cytoplasmic tRNA is expected to be severely restricted to avoid the error cascade. In fact, cytoplasmic tRNA is highly conserved during evolution. On the other hand, in the animal mitochondrial system, all of the proteins involved in error loops are coded for in the nuclear genome and imported from the cytoplasm, and accordingly the system is free from the error cascade. The difference in constraints operating on animal tRNA between cytoplasm and mitochondria is attributed to the presence or absence of error loops. It is shown that the constraints on mitochondrial tRNA in fungi are not as relaxed as those in animals. This observation is attributed to the presence of an error loop in fungal mitochondria, since at least one protein of the mitochondrial ribosome is coded for in the mitochondrial genome of fungi. The evolutionary rates of proteins involved in the processing of genetic information are discussed in relation to the error cascade.

Genetic mapping of Ty elements in Saccharomyces cerevisiae

We used transformation to insert a selectable marker at various sites in the Saccharomyces cerevisiae genome occupied by the transposable element Ty. The vector CV9 contains the LEU2+ gene and a portion of the repeated element Ty1-17. Transformation with this plasmid resulted in integration of the vector via a reciprocal exchange using homology at the LEU2 locus or at the various Ty elements that are dispersed throughout the S. cerevisiae genome. These transformants were used to map genetically sites of several Ty elements. The 24 transformants recovered at Ty sites define 19 distinct loci. Seven of these were placed on the genetic map. Two classes of Ty elements were identified in these experiments: a Ty1-17 class and Ty elements different from Ty1-17. Statistical analysis of the number of transformants at each class of Ty elements shows that there is preferential integration of the CV9 plasmid into the Ty1-17 class.

tRNA-rRNA sequence homologies: a model for the origin of a common ancestral molecule, and prospects for its reconstruction

A model is proposed for the early evolution of the coding mechanism. A primordial RNA embodies the functions of today's nucleic acids in a single molecule. The molecule is generated by successive rounds of self-priming and -templating. After proximity is assured by enclosure in a cell, the functions can be partitioned among more efficient specialized molecules. The prediction of sequence homologies in later forms prompted a search for matches between t- and r-RNAs. These are described. Their distributions offer clues to their origins. The existance of overlapping homologies indicates an approach to the reconstruction of an ancestral molecule.

An approach to oncological genetics

Oncological genetics is defined as a branch of clinical cancer research dealing with the identification, description, analysis, and prevention of those human neoplasias and their related/associated syndromes in which a vertical (hereditary) transmission is assumed. The present clinical basis of this field is constituted by the 240 inherited preneoplasias and neoplasias that have been detected so far. The main hypothesis in oncological genetics might be the existence of an inherited cancer proneness phenotype (CPP), in whose determination the processes involved in the activation of cellular proto-oncogenes would presumably play a role. It is conjectured that CPP is a quantitative (random) variable with extreme values. Such indicators can be identified in small populations having a structure (i.e., tree) so that the collection of comprehensive pedigree data is indispensable.

Homologies between nuclear and plastid DNA in spinach

Homologies between spinach nuclear (n) DNA and Chloroplast (pt) DNA, have been detected with a clone bank of spinach ptDNA as hybridization probes to restriction fragments of nDNA prepared from purified root nuclei. Every cloned fragment of ptDNA showed homologies to discrete restriction fragments of nDNA, different from those of ptDNA, indicating integration of these homologies into nDNA. While most ptDNA clones were relatively large and probably contained several genes, sequence homologies were also found to the cloned plastid gene for RuBP carboxylase and the β subunit of ptATPase. Many of the homologies in nDNA occur in regions of the genome that are highly methylated and are not digested by the methylation sensitive restriction endonucleases HpaII and MspI. In contrast these enzymes cleave ptDNA into small fragments which allows the nDNA homologies to be distinguished in total root DNA. The sequence homologies observed were not due to contaminating non nuclear sequences as shown by hybridization to mitochondrial (mt) and bacterial DNAs. The total amount of homology to ptDNA in nDNA is equivalent to about five copies of the plastome per haploid nuclear genome. The homologies generally appear to be in individual segments of less than 2 kbp in length, integrated into several different places in the genome.

Presence of mitochondrial-DNA-like sequences in the human nuclear DNA

Two lambda phage clones carrying contiguous human nuclear DNA sequences with extensive homology to non-contiguous human mitochondrial 16S ribosomal RNA sequences were isolated from a human gene library. The one clone carried mitochondrial-DNA(mtDNA)-like sequences flanked with two kinds of repetitive nuclear DNA sequences and the other carried mtDNA-like sequences, between unique nuclear DNA sequences and repetitive DNA sequences of Alu-family. These results demonstrate that mtDNA-like sequences are present in human nuclear DNA.

Intracellular location of small circular DNA complexes in mammalian cell lines

For determination of the cellular location of small polydisperse circular DNA complexes, rat myoblastic L6 cells, HeLa cells, and mouse L cells were enucleated and processed by the micapress-adsorption method for electron microscopy (H. Yamagishi, T. Kunisada, and T. Tsuda, 1982, Plasmid 8, 299-306). Small circular DNA complexes from intact cells showed a heterogeneous size distribution of from 0.1 to more than 2 micron with a mean contour length of 0.6 to 0.8 micron, like that of covalently closed circular DNAs. Cells contained 400 to 1200 copies. The size distribution in the cytoplasts was narrow and the number-average length was 0.3 to 0.4 micron, whereas that in L6 karyoplasts was wide and the average length was 0.9 micron. The longer circular complexes appeared to be absent from the cytoplasts. The origin and biological functions of these complexes are discussed in relation to the cellular locations of the complexes.

tRNA-rRNA sequence homologies: evidence for a common evolutionary origin?

Many tRNAs of E. coli and yeast contain stretches whose base sequences are similar to those found in their respective rRNAs. The matches are too frequent and extensive to be attributed to coincidence. They are distributed without discernible pattern along and among the RNAs and between the two species. They occur in loops as well as in stems, among both conserved and non-conserved regions. Their distributions suggest that they reflect common ancestral origins rather than common functions, and that they represent true homologies.

Mitochondrial DNA and nuclear DNA from normal rat liver have a common sequence

Although Pst I does not cut the circular mitochondrial genome of the rat, BamHI generates from this genome two unequal fragments of DNA. Each of these fragments was cloned in pBR322. Nuclear DNA was digested from rat liver singly or doubly with Pst I and BamHI, and it was demonstrated that nuclear DNA shared a common sequence with the larger mitochondrial DNA BamHI fragment. The cloned larger mitochondrial DNA fragment was further subdivided with HindIII into four pieces that were labeled and then used to probe the double-digested nuclear DNA. The hybridization data showed that the common sequence is less than 3 kilobase pairs long and lies within the part of the mitochondrial genome containing the D-loop and a portion of the rRNA genes. It therefore appears that, as in lower eukaryotes, there are shared sequences between the nuclear and mitochondrial genomes in mammals.

The gene for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase is located close to the gene for the large subunit in the cyanobacterium Anacystis nidulans 6301

The gene for the small subunit (SS) of ribulose-1,5-bisphosphate carboxylase/oxygenase from a cyanobacterium, Anacystis nidulans 6301, has been cloned and subjected to sequence analysis. The SS coding region is located close to and downstream from the large subunit (LS) coding region on the same DNA strand. The spacer region between the LS and the SS coding regions contains 93 base pairs (bp), and has no promoter-like sequences. The coding region of A. nidulans SS gene contains 333 bp (111 codons). The deduced amino acid sequence of the A. nidulans SS protein shows 40% homology with those of higher plants.

Maize mitochondrial DNA contains a sequence homologous to the ribulose-1,5-bisphosphate carboxylase large subunit gene of chloroplast DNA

The mitochondrial genome of maize contains a DNA sequence homologous to the chloroplast gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (LS gene). The presence in mitochondrial DNA of both coding and flanking sequences of this gene has been demonstrated first, by cross hybridization between the purified organelle DNAs and between cloned mitochondrial and chloroplast DNA sequences and second, by in vitro transcription-translation of cloned mitochondrial DNA in an E. coli cell free system where a 21,000 dalton polypeptide is synthesized that can be precipitated with antibodies to wheat ribulose-1,5-bisphosphate carboxylase. In contrast to the 12 kb chloroplast homologous sequence found in the mitochondrial genome (Stern and Lonsdale, 1982), the sequence homologous to the LS gene is unaltered in mitochondrial DNA isolated from the male sterile cytoplasms of maize. The LS gene homologous sequence in the mitochondrial genome is located some 65 kb from the 18S mitochondrial rRNA gene and approximately 20 kb from the mitochondrial DNA sequence having homology to the chloroplast 16S rRNA gene.

Comparison of sea urchin and human mtDNA: evolutionary rearrangement

Clones of full-length mtDNA have been isolated from a Strongylocentrotus franciscanus recombinant DNA library by screening a cDNA clone of cytochrome oxidase subunit 1 mRNA. Restriction fragment cross-hybridization analysis shows the following difference in gene arrangement between sea urchin and human mtDNA. The 16S rRNA and cytochrome oxidase subunit 1 genes are directly adjacent in sea urchin mtDNA. These two genes are separated in human and other mammalian mtDNAs by the region containing unidentified reading frames 1 and 2. In spite of the difference in gene order, gene polarity appears to have been conserved. We conclude that the difference in gene order reflects a rearrangement that took place in the sea urchin lineage since sea urchins and mammals last shared a common ancestor.

Mitochondrial inheritance in a mitochondrially mediated disease

Mendelian inheritance involves the transmission to successive generations of DNA contained in genes in the nucleus, but DNA is also contained in mitochondria, where it is believed to be responsible for the encoding of certain mitochondrial enzymes. Since nearly all mitochondrial DNA is maternally transmitted, one might expect a nonmendelian pattern of inheritance in mitochondrial cytopathy, a syndrome in which there are abnormalities in mitochondrial structure and deficiencies in a variety of mitochondrial enzymes. We studied the pedigrees of 6 affected families whose members we had examined personally and of 24 families described in the literature. In 27 families, exclusively maternal transmission occurred; in 3 there was also paternal transmission in one generation. Altogether, 51 mothers but only 3 fathers had transmitted the condition. These results are consistent with mitochondrial transmission of mitochondrial cytopathy; the inheritance and enzyme defects of mitochondrial cytopathy can be considered in the light of recent evidence that subunits of respiratory-enzyme complexes are encoded solely by mitochondrial DNA. The occasional paternal transmission may be explained if certain enzyme subunits that are encoded by nuclear DNA are affected.

Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences

Splicing of the ribosomal RNA precursor of Tetrahymena is an autocatalytic reaction, requiring no enzyme or other protein in vitro. The structure of the intervening sequence (IVS) appears to direct the cleavage/ligation reactions involved in pre-rRNA splicing and IVS cyclization. We have probed this structure by treating the linear excised IVS RNA under nondenaturing conditions with various single- and double-strand-specific nucleases and then mapping the cleavage sites by using sequencing gel electrophoresis. A computer program was then used to predict the lowest-free-energy secondary structure consistent with the nuclease cleavage data. The resulting structure is appealing in that the ends of the IVS are in proximity; thus, the IVS can help align the adjacent coding regions (exons) for ligation, and IVS cyclization can occur. The Tetrahymena IVS has several sequences in common with those of fungal mitochondrial mRNA and rRNA IVSs, sequences that by genetic analysis are known to be important cis-acting elements for splicing of the mitochondrial RNAs. In the predicted structure of the Tetrahymena IVS, these sequences interact in a pairwise manner similar to that postulated for the mitochondrial IVSs. These findings suggest a common origin of some nuclear and mitochondrial introns and common elements in the mechanism of their splicing.