Two potential Petunia hybrida mitochondrial DNA replication origins show structural and in vitro functional homology with the animal mitochondrial DNA heavy and light strand replication origins

Haas, Jan M. de; Hille, Jacques; Kors, Frank; Meer, Bert van der; Kool, A. J.; Folkerts, Otto; Nijkamp, H. J. J.

doi:10.1007/bf00334779

Cited by 29 publications

(8 citation statements)

References 37 publications

(39 reference statements)

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“…D. teissieri also has a similar secondary structure with conserved flanking sequences (data not shown) in its A + T-rich region (Monnerot et al 1990); please refer to Monforte et al (1993). a stem-and-loop secondary structure in plant mtDNA (de Haas et al 1991) and the mammalian L-strand-replication origin even shares primary sequence homologies with some nonmitochondrial systems (Clayton 1982). Thus it is interesting to know whether the conserved hairpin-forming sequences identified in S. gregaria and C. parallelus are equivalent to that found in Drosophila species (Fig.…”

Section: Conserved Secondary Structure In S Gregaria and C Parallelmentioning

confidence: 99%

Evolution and structural conservation of the control region of insect mitochondrial DNA

1995

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The control regions of mitochondrial DNA of two insects, Schistocerca gregaria and Chorthippus parallelus, have been isolated and sequenced. Their sizes are 752 bp and 1,512 bp, respectively, with the presence of a tandem repeat in C. parallelus. (The sequences of the two repeats are highly conserved, having a homology of 97.5%.) Comparison of their nucleotide sequences revealed the presence of several conserved sequence blocks dispersed through the whole control region, showing a different evolutionary pattern of this region in these insects as compared to that in Drosophila. A highly conserved secondary structure, located in the 3' region near the small rRNA gene, has been identified. Sequences immediately flanking this hairpin structure rather than the sequences of this structure themselves are conserved between S. gregaria/C. parallelus and Drosophila, having a sequence consensus of "TATA" at 5' and "GAA(A)T" at 3'. The motif "G(A)nT" is also present in the 3' flanking sequences of mammalian, amphibian, and fish mitochondrial L-strand replication origins and a potential plant mitochondrial second-strand-replication origin, indicating its universal conservation and functional importance related to replication origins. The stem-and-loop structure in S. gregaria/C. parallelus appears to be closely related to that found in Drosophila despite occupying a different position, and may be potentially associated with a second-strand-replication origin. This in turn suggests that such a secondary structure might be widely conserved across invertebrates while their location in the control region may be variable. We have looked for such a conserved structure in the control regions of two other insects, G. firmus and A. mellifera, whose DNA sequences have been published, and their possible presence is discussed. Mitochondrial control regions characterized to date in five different insect taxa (Drosophila, G. firmus, A. mellifera, S. gregaria, and C. parallelus) may be classed into two distinct groups having different evolutionary patterns. It is observed that tandem repetition of regions containing a probable replication origin occurred in some species from disjunct lineages in both groups, which would be the result of convergent evolution. We also discuss the possibility of a mechanism of "parahomologous recombination by unequal crossing-over" in mitochondria, which can explain the generation of such tandemly repeated sequences (especially the first critical repetition) in the control region of mtDNA, and also their convergent evolution in disjunct biological lineages during evolution.

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Section: Conserved Secondary Structure In S Gregaria and C Parallelmentioning

confidence: 99%

Evolution and structural conservation of the control region of insect mitochondrial DNA

1995

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“…The mechanisms that mediate DNA replication in plant organelles are largely unknown. Several mechanisms like D‐loop, theta‐like, rolling circle, and recombination‐dependent DNA replication are proposed to account for DNA replication in mitochondrial and chloroplast genomes . Animal and plant mitochondrial genomes code for approximately the same number of essential genes.…”

Section: Introductionmentioning

confidence: 99%

Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity

et al. 2018

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The coding sequences of plant mitochondrial and chloroplast genomes present a lower mutation rate than the coding sequences of animal mitochondria. However, plant mitochondrial genomes frequently rearrange and present high mutation rates in their noncoding sequences. DNA replication in plant organelles is carried out by two DNA polymerases (DNAP) paralogs. In Arabidopsis thaliana at least one DNAP paralog (AtPolIA or AtPolIB) is necessary for plant viability, suggesting that both genes are partially redundant. To understand how AtPolIs replicate genomes that present low and high mutation rates, we measured their nucleotide incorporation for all 16-base pair combinations in vitro. AtPolIA presents an error rate of 7.26 × 10 , whereas AtPolIB has an error rate of 5.45 × 10 . Thus, AtPolIA and AtPolIB are 3.5 and 26-times less accurate than human mitochondrial DNAP γ. The 8-fold difference in fidelity between both AtPolIs results from a higher catalytic efficiency in AtPolIA. Both AtPolIs extend from mismatches and the fidelity of AtPolIs ranks between high fidelity and lesion bypass DNAPs. The different nucleotide incorporation fidelity between AtPolIs predicts a prevalent role of AtPolIA in DNA replication and AtPolIB in DNA repair. We hypothesize that in plant organelles, DNA mismatches generated during DNA replication are repaired via recombination-mediated or DNA mismatch repair mechanisms that selectively target the coding region and that the mismatches generated by AtPolIs may result in the frequent expansion and rearrangements present in plant mitochondrial genomes.

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“…The results were consistent with unidirectional theta replication. Two short stretches of chromosomal mtDNA harboring putative replication origins have been identified by an in vitro assay (10). These sequences showed a certain degree of homology with the H-and L-strand origins of mammalian mtDNA, but it remains to be shown if they function as origins of replication in organello.…”

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Rolling-Circle Replication of Mitochondrial DNA in the Higher Plant Chenopodium album (L.)

Backert

Dörfel

Lurz

et al. 1996

Molecular and Cellular Biology

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The mitochondrial genomes of higher plants are larger and more complex than those of all other groups of organisms. We have studied the in vivo replication of chromosomal and plasmid mitochondrial DNAs prepared from a suspension culture and whole plants of the dicotyledonous higher plant Chenopodium album (L.). Electron microscopic studies revealed sigma-shaped, linear, and open circular molecules (subgenomic circles) of variable size as well as a minicircular plasmid of 1.3 kb (mp1). The distribution of single-stranded mitochondrial DNA in the sigma structures and the detection of entirely single-stranded molecules indicate a rolling-circle type of replication of plasmid mp1 and subgenomic circles. About half of the sigma-like molecules had tails exceeding the lengths of the corresponding circle, suggesting the formation of concatemers. Two replication origins (nicking sites) could be identified on mp1 by electron microscopy and by a new approach based on the mapping of restriction fragments representing the identical 5 ends of the tails of sigma-like molecules. These data provide, for the first time, evidence for a rolling-circle mode of replication in the mitochondria of higher plants.

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Two potential Petunia hybrida mitochondrial DNA replication origins show structural and in vitro functional homology with the animal mitochondrial DNA heavy and light strand replication origins

Cited by 29 publications

References 37 publications

Evolution and structural conservation of the control region of insect mitochondrial DNA

Evolution and structural conservation of the control region of insect mitochondrial DNA

Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity

Rolling-Circle Replication of Mitochondrial DNA in the Higher Plant Chenopodium album (L.)

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