Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination

Abstract

The currently accepted model of recombination-dependent replication (RDR) in plant mitochondrial DNA (mtDNA) does not clearly explain how RDR progresses and how highly complex mtDNA develops. This study aimed to investigate the correlation between RDR and mtDNA complexity during mitochondrial development in mung bean (Vigna radiata) seed, and the initiation and processing of RDR in plant mitochondria. Flow cytometry, pulsed-field gel electrophoresis, electron microscopy, real-time PCR and biochemical studies were used in this study. The highly dynamic changes in mtDNA complexity correspond to mtDNA RDR activity throughout mitochondrial development. With in vitro freeze-thaw treatment or prolonged in vivo cold incubation, the mtDNA rosette core disappeared and the rosette structure converted to a much longer linear DNA structure. D-loops, Holliday junctions and putative RDR forks often appeared near the rosette cores. We hypothesize that the rosette core may consist of condensed mtDNA and a replication starting sequence, and play an initial and central role in RDR. The satellite cores in the rosette structure may represent the re-initiation sites of mtDNA RDR in the same parental molecule, thereby forming highly complex and giant mitochondrial molecules, representing the RDR intermediates, in vivo.

Fission and Fusion of Plant Mitochondria, and Genome Maintenance

“…Similar changes in mitochondrial DNA structures have been observed in the growth cycles (but not cell cycles) of cultured tobacco cells in pioneering studies by Oldenburg and Bendich (1996; for review, see Oldenburg and Bendich, 2015) and Chenopodium album cells (Backert and Börner, 2000). Rapid amplification of organellar DNAs has been observed around meristems Fujie et al, 1994) and at specific stages, such as during germination (Cheng et al, 2017) and at the start of cell culture (Satoh et al, 1993). The rapid amplification of organellar DNA independent of the host cell cycle also seems to be like that in phages that use RDR for DNA synthesis.…”

“…If they do not exist, replication might occur only by RDR. Cheng et al (2017) recently observed the physical structures of DNA molecules isolated from mitochondria during the early germination of mung bean (Vigna radiata) seeds. At first, the DNA was in the form of simple linear molecules with sizes shorter than the genome size.…”

“…various sizes, some even longer than the genome size (Oldenburg and Bendich, 1996;Backert and Börner, 2000;Sloan, 2013;Cheng et al, 2017). Such linear structures are thought to have random fragments of a long head-to-tail concatemer sequence of the mitochondrial genomes ( Fig.…”

Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity

“…It has been proposed that this protein is involved in mismatch recognition , however a formal biochemical demonstration of this protein in mismatch repair or DNA processing has not been addressed to date. An alternative mechanism to explain the low mutation rates in plant organellar DNA, is the premise that organellar DNA replication is based on a recombination‐dependent replication mechanism . In this mechanism, double‐strand breaks generate regions of long homologies that are used for homologous recombination with one of the multiple copies of mitochondrial or plastid DNA as a template .…”

“…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.…”