Protein binding to a single termination-associated sequence in the mitochondrial DNA D-loop region

Differences in crossover frequency and distribution among three sibling species of Drosophila

Comparisons of the genetic and cytogenetic maps of three sibling species of Drosophila reveal marked differences in the frequency and cumulative distribution of crossovers during meiosis. The maps for two of these species, Drosophila melanogaster and D. simulans, have previously been described, while this report presents new map data for D. mauritiana, obtained using a set of P element markers. A genetic map covering nearly the entire genome was constructed by estimating the recombination fraction for each pair of adjacent inserts. The P-based genetic map of mauritiana is approximately 1.8 times longer than the standard melanogaster map. It appears that mauritiana has higher recombination along the entire length of each chromosome, but the difference is greates in centromere-proximal regions of the autosomes. The mauritiana autosomes show little or no centromeric recombinational suppression, a characteristic that is prominent in melanogaster. D. simulans appears to be intermediate both in terms of total map length and intensity of the autosomal centromeric effect. These interspecific differences in recombination have important evolutionary implications for DNA sequence organization and variability. In particular, mauritiana is expected to differ from melanogaster in patterns and amounts of sequence variation and transposon insertions.

Precise sequence assignment of replication origin in the control region of chick mitochondrial DNA relative to 5' and 3' D-loop ends, secondary structure, DNA synthesis, and protein binding

The data reported identify for the first time the sequence of an avian mitochondrial heavy-strand replication origin, OH, located only about 12 nucleotides (nt) downstream from the conserved sequence block CSB-1, as well as the sequence of premature synthesis arrest of the 781 (+/-1) nt D-loop strand, only 6-7 nt downstream from a TAS-like (termination-associated) element. Both sites are associated with putative cruciform secondary structures. A major sequence-specific DNA-binding/cleavage site of a potential regulatory protein, the approximately 36-kDa aMDP1 (shown previously to stimulate mtDNA synthesis), is located about 90 nt upstream of OH. Correlated in vivo analysis of avian genome-length mtDNA replication provides missing evidence on the functional equivalence of D-loop origin with nascent initiation, and on the direction, asymmetry and temporal aspects of a full round of replication. The importance of the results to understanding the regulation of linked replication/transcription and the unusual sequence evolution of avian mtDNA is

A 67-kDa protein binding to the curved DNA in the main regulatory region of the rat mitochondrial genome

We have purified, by sequence-specific affinity chromatography, a mitochondrial (mt) matrix protein which binds to the curved DNA located between the replication origin (ori) of the leading strand (ori-H) and the two transcription promoters in the rat mt genome. The protein was characterized by gel electrophoresis as a 67-kDa polypeptide and seems to be involved in the DNA contact on the mt light strand. This protein differs (in the size and location of its DNA-binding site) from other DNA-binding proteins studied so far in animal mt systems. We suggest a role for the 67-kDa protein, assisted by other proteins, in regulating the initiation of leading-strand replication.

Identification of a stable RNA encoded by the H-strand of the mouse mitochondrial D-loop region and a conserved sequence motif immediately upstream of its polyadenylation site

By using a combination of Northern blot hybridization with strand-specific DNA probes, S1 nuclease protection, and sequencing of oligo-dT-primed cDNA clones, we have identified a 0.8 kb poly(A)-containing RNA encoded by the H-strand of the mouse mitochondrial D-loop region. The 5' end of the RNA maps to nucleotide 15417, a region complementary to the start of tRNA(Pro) gene and the 3' polyadenylated end maps to nucleotide 16295 of the genome, immediately upstream of tRNA(Phe) gene. The H-strand D-loop region encoded transcripts of similar size are also detected in other vertebrate systems. In the mouse, rat, and human systems, the 3' ends of the D-loop encoded RNA are preceded by conserved sequences AAUAAA, AAUUAA, or AACUAA, that resemble the polyadenylation signal. The steady-state level of the RNA is generally low in dividing or in vitro cultured cells, and markedly higher in differentiated tissues like liver, kidney, heart, and brain. Furthermore, an over 10-fold increase in the level of this RNA is observed during the induced differentiation of C2C12 mouse myoblast cells into myotubes. These results suggest that the D-loop H-strand encoded RNA may have yet unknown biological functions. A 20 base pair DNA sequence from the 3' terminal region containing the conserved sequence motif binds to a protein from the mitochondrial extracts in a sequence-specific manner. The binding specificity of this protein is distinctly different from the previously characterized H-strand DNA termination sequence in the D-loop or the H-strand transcription terminator immediately downstream of the 16S rRNA gene. Thus, we have characterized a novel poly(A)-containing RNA encoded by the H-strand of the mitochondrial D-loop region and also identified the putative ultimate termination site for the H-strand transcription.

When replication forks stop

DNA synthesis is an accurate and very processive phenomenon, yet chromosome replication does not proceed at a constant rate and progression of the replication fork can be impeded. Several structural and functional features of the template can modulate the rate of progress of the replication fork. These include DNA secondary structures, DNA damage and occupied protein-binding sites. In addition, prokaryotes contain sites where replication is specifically arrested. DNA regions at which the replication machinery is blocked or transiently slowed could be particularly susceptible to genome rearrangements. Illegitimate recombination, a ubiquitous phenomenon which may have dramatic consequences, occurs by a variety of mechanisms. The observation that some rearrangements might be facilitated by a pause in replication could provide a clue in elucidating these processes. In support of this, some homologous and illegitimate recombination events have already been correlated with replication pauses or arrest sites.

Purification and characterization of a mitochondrial DNA-binding protein that binds to double-stranded and single-stranded sequences of Paracentrotus lividus mitochondrial DNA

A mitochondrial protein, able to specifically bind two double-stranded homologous sequences of sea-urchin mitochondrial DNA, has been partially purified from Paracentrotus lividus eggs. This protein, present at a low concentration, is a polypeptide of 40 kDa. One of the binding sequences, located in the main non-coding region, contains the replication origin of the mitochondrial DNA H-strand. By a combination of band-shift, DNase footprinting, and modification interference analyses with homologous and heterologous probes we identified YCYYATCAN(A/T)RC as the minimum sequence required for the binding. The protein also shows a single-stranded DNA-binding activity, as it is able to specifically interact with one of the strands of the binding sites. These features are consistent with a function of the protein in the modulation of sea-urchin mitochondrial DNA replication during the development stages.

Conserved features of yeast and mammalian mitochondrial DNA replication

Mammalian mitochondrial DNA replication is initiated by the processing of RNA transcripts derived from an upstream promoter to create RNA primers for DNA replication. In the yeast Saccharomyces cerevisiae, mitochondrial ori/rep sequences contain a transcription promoter upstream of the site of transition from RNA to DNA synthesis, suggesting a common mode of replication initiation. Recent research has identified features in the mode and machinery of DNA replication conserved from yeast to mammals.