Phage T4-like intermediates of DNA replication and recombination in the mitochondria of the higher plant Chenopodium album (L.)

Abstract

We have studied intermediates of the recombination and replication of chromosomal mitochondrial (mt) DNA prepared from suspension cultured cells of Chenopodium album (L.) by electron microscopy during the whole growth cycle. We identified several types of potential recombination and replication intermediates including rosette-like structures, as well as other branched and sigma-like molecules. The absolute and relative amounts of these structures changed dramatically during the growth cycle, indicating high dynamics in the structural organization of the mt genome. The rosette-like molecules had sizes of 2-5 genome units and were found to contain putative replication forks and 'Holliday'-junctions known from recombination intermediates. The high number of rosettes during the first days of culture, and their drastic reduction in the stationary growth stage, were found to be inversely related to changes in the quantity of linear molecules of 40-200 kb. This observation suggests that linear molecules participate in the formation of giant branched rosette-like structures. Most linear molecules were previously found to have at least one single-stranded end, which may allow recombinative invasion of other double-stranded molecules. Thus, recombination events may lead to the formation of more complex molecules and initiate replication similar to phage T4. We propose the coexistence of a recombination-dependent mode of replication with a presumably recombination-independent rolling-circle mode of replication in the mitochondria of C. album.

Characterization of the Structure and DNA Complexity of Mung Bean Mitochondrial Nucleoids

“…Although the size range of the mitochondrial nucleoid DNA molecules that we observed was less than optimal, nonetheless our finding of various irregular and complex DNA structures (Fig. 6) is consistent with other plant mtDNA molecules that have been visualized (Backert and Börner, 2000;Backert et al, 1996Backert et al, , 1997Bendich, 1996;Lilly and Havey, 2001;Oldenburg and Bendich, 1998). It is likely that these irregular and complex DNA structures are temporary intra-/inter-molecular pairings of short repetitive sequences and/or single-stranded regions abundant in plant mtDNA genomes.…”

“…Linear molecules contained in the 50-200 kb smear zone have also been observed (Backert and Börner, 2000;Backert et al, 1997;Oldenburg and Bendich, 1996;. Our finding that ethidium-UV treatment retarded a fraction of mung bean mtDNA molecules present in the 50-200 kb zone (Fig.…”

“…It was proposed that plant mtDNA may use a T4 phage-like recombination-dependent mechanism of replication and/or an alternative rolling-circle mode of replication (Backert and Börner, 2000;Oldenburg and Bendich, 2001). The predicted replication-intermediate structures from these two replication mechanisms have been proposed as the probable cause of the immobile wb form in PFGE fractionation analysis.…”

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

“…[This consideration is quite apart from the issue of whether any plant mitogenome assembly actually corresponds to the in vivo arrangement of the genome (64)(65)(66).] Instead, within an individual and possibly even at the level of a single mitochondrion, the Viscum genome almost certainly exists as an extremely complicated population of recombinationally interrelated, overlapping molecules of a broad range of sizes and stoichiometries.…”

Plant Mitochondrial Recombination Surveillance Requires Unusual RecA and MutS Homologs

“…These include the incorporation of foreign DNA sequences, a partially linearized genome, split gene sequences requiring RNA trans-splicing for proper expression, large, recombinationally active repeats, a stoichiometrically variable multipartite genome organization, and an unusually high incidence of illegitimate recombination leading to gene chimeras (Adams and Palmer, 2003;Knoop, 2004). The linear genome structure and T4 phage-like features (Backert and Borner, 2000) of the genome imply that components of the genome maintenance apparatus may have been acquired over plant evolution (Lang et al, 1999). Furthermore, the linear genome organization would be consistent with a recombinationmediated replication initiation system (Kreuzer, 2005).…”