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Complex terminal structure of a linear mitochondrial plasmid from Physarum polycephalum: three terminal inverted
H Takano1, S Kawano, T Kuroiwa
1Department of Biology, Faculty of Science, University of Tokyo, Japan.
Abstract:
The mitochondria of Physarum polycephalum have a linear plasmid (mF) which promotes mitochondrial fusion. To determine the terminal structure of the mF plasmid, restriction fragments derived from its ends were cloned and sequenced. The sequences showed that the mF plasmid has three kinds of terminal inverted repeats (TIRs). The most characteristic feature is a 144-bp repeating unit which exists between a 205-bp TIR at the extreme ends of the plasmid and another 591-bp TIR. All of the clones showed at least one of these 144-bp repeating units. The GC content of the 205-bp TIR (49%) was higher than those of the other TIRs and of another sequenced region (23%). This TIR can form three thermodynamically-stable hairpin structures based on complex internal palindromic components. Moreover, in the right terminal region of the mF plasmid, there is an open reading frame (ORF) which covers the entire 591-bp TIR and most of one of the 144-bp repeating units. This ORF encodes a 547-amino-acid polypeptide, ORF-547, and shows extensive homology with the polymerization domain of the putative DNA polymerases of linear mitochondrial plasmids from other sources.
Insights
The Physarum polycephalum mitochondrial plasmid (mF) has unique terminal structures, including repeating units and hairpin-forming sequences, which may regulate mitochondrial fusion.
Area of Science:
- Mitochondrial genetics
- Molecular biology
- Eukaryotic cell biology
Background:
- Mitochondria in Physarum polycephalum contain a linear plasmid (mF).
- The mF plasmid is implicated in promoting mitochondrial fusion.
- Understanding the terminal structure of linear plasmids is crucial for their replication and function.
Purpose of the Study:
- To elucidate the terminal structure of the Physarum polycephalum mitochondrial plasmid (mF).
- To identify repetitive elements and potential regulatory sequences at the plasmid ends.
- To investigate the genetic elements potentially involved in mitochondrial fusion.
Main Methods:
- Cloning and sequencing of restriction fragments from the mF plasmid ends.
- Bioinformatic analysis of DNA sequences to identify repeats and open reading frames.
- Thermodynamic analysis of potential secondary structures within terminal regions.
Main Results:
- The mF plasmid possesses three types of terminal inverted repeats (TIRs).
- A 144-bp repeating unit is a characteristic feature, located between a 205-bp TIR and a 591-bp TIR.
- The 205-bp TIR exhibits a high GC content and can form stable hairpin structures.
- An open reading frame (ORF-547) encoding a 547-amino-acid polypeptide was identified in the right terminal region, showing homology to DNA polymerases.
Conclusions:
- The mF plasmid exhibits complex terminal structures with repetitive elements and potential regulatory sequences.
- The identified ORF-547 suggests a role in DNA replication or maintenance of the mitochondrial plasmid.
- These findings provide insights into the molecular mechanisms of linear mitochondrial plasmid biology and mitochondrial fusion in Physarum polycephalum.