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The complete DNA sequence of the mitochondrial genome of Physarum polycephalum
1Department of Biological Science, Faculty of Science, Kumamoto University, Japan. takano@kumamoto-u.ac.jp
Abstract:
The complete sequence of the mitochondrial DNA (mtDNA) of the true slime mold Physarun polycephalum has been determined. The mtDNA is a circular 62,862-bp molecule with an A+T content of 74.1%. A search with the program BLAST X identified the protein-coding regions. The mitochondrial genome of P. polycephalum was predicted to contain genes coding for 12 known proteins [for three cytochrome c oxidase subunits, apocytochrome b, two F1Fo-ATPase subunits, five NADH dehydrogenase (nad) subunits, and one ribosomal protein], two rRNA genes, and five tRNA genes. However, the predicted ORFs are not all in the same frame, because mitochondrial RNA in P. polycephalum undergoes RNA editing to produce functional RNAs. The nucleotide sequence of an nad7 cDNA showed that 51 nucleotides were inserted at 46 sites in the mRNA. No guide RNA-like sequences were observed in the mtDNA of P. polycephalum. Comparison with reported Physarum mtDNA sequences suggested that sites of RNA editing vary among strains. In the Physarum mtDNA, 20 ORFs of over 300 nucleotides were found and ORFs 14 19 are transcribed.
Insights
The complete mitochondrial DNA (mtDNA) sequence of the slime mold Physarum polycephalum was determined, revealing genes for 12 proteins and 5 tRNAs. RNA editing is crucial for functional gene expression in this organism.
Area of Science:
- Molecular Biology
- Genomics
- Mycology
Background:
- The mitochondrial genome of the true slime mold Physarum polycephalum is a key area of study for understanding eukaryotic gene expression.
- Previous studies have hinted at unique features within its mitochondrial DNA (mtDNA).
Purpose of the Study:
- To determine the complete nucleotide sequence of the Physarum polycephalum mtDNA.
- To identify protein-coding genes, rRNA, and tRNA genes within the mtDNA.
- To investigate the phenomenon of RNA editing in Physarum polycephalum.
Main Methods:
- Whole mitochondrial genome sequencing.
- BLAST X analysis for protein-coding region identification.
- cDNA sequencing to analyze RNA editing in specific genes (e.g., nad7).
Main Results:
- The Physarum polycephalum mtDNA is a circular 62,862-bp molecule with high A+T content (74.1%).
- The genome contains genes for 12 proteins, 2 rRNAs, and 5 tRNAs, but predicted ORFs require RNA editing for functional expression.
- RNA editing involves nucleotide insertions, as demonstrated in the nad7 mRNA, with variations observed across strains.
Conclusions:
- The complete mtDNA sequence provides a foundational resource for Physarum polycephalum research.
- RNA editing is a significant post-transcriptional modification mechanism essential for producing functional mitochondrial RNAs in this slime mold.
- Strain-specific variations in RNA editing sites highlight the dynamic nature of mitochondrial genome expression.