The complete DNA sequence of the mitochondrial genome of Physarum polycephalum

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.

New Protein Pmn34 with an Exonuclease Motif Localizes in the Mitochondrial Nucleoid Periphery of Physarum polycephalum

“…Therefore, the first 43 amino acids were assumed to be a mitochondrial transit peptide resulting in a mature protein of 283 amino acids. This is consistent with Pmn34 being encoded by the nuclear genome, as the mitochondrial genome does not contain the Pmn34 gene (Takano et al 2001). A BLAST search against the Pfam database revealed that Pmn34 was predicted to encode a putative DEDD (DnaQlike) exonuclease superfamily protein that catalyzes the excision of nucleoside monophosphates at DNA or RNA termini in the 3Ј to 5Ј direction (Pfam, cd06127, E-value 7e-11) (Fig.…”

“…By contrast, the true slime mold Physarum polycephalum has an extraordinarily large amount of mtDNA in its rod-shaped mtnucleoids, with a long axis of ϳ1.5 mm (Kuroiwa 1974, making it a good model organism to study the function of mt-nucleoid. The mtDNA of P. polycephalum is composed of a circular molecule of 62,862 bp (Takano et al 2001), and at least 40 and 80 copies of mtDNA molecules are contained in each mt-nucleoid at the mitochondrial G1 and G2 phases, respectively (Kuroiwa and Kuroiwa 1980). A method for obtaining highly purified mt-nucleoids from P. polycephalum, without the contamination of cell nuclei, has been established (Sasaki et al 1998).…”

Unexpectedly Complex Editing Patterns at Dinucleotide Insertion Sites in Physarum Mitochondria

“…Six different types of dinucleotide insertions have been reported in Physarum mitochondrial RNAs: CU, GU, GC, UA, UU, and AA (7,(10)(11)(12)(13)16). As can be seen in Fig.…”

“…These data argue that at least a portion of the nascent RNA synthesized in vivo has CA rather than UA inserted at es31/32. There are six known cases in which two identical nucleotides are added at adjacent sites: two sites of AA insertion in both the small-subunit (SSU) rRNAs (10) and large-subunit rRNAs (11) and 2 UU nucleotides in the nd7 mRNA (12). Each of these insertions occurs in an ambiguous context (Fig.…”

“…Extensive insertional editing occurs during transcription in Physarum mitochondria, adding hundreds of single C residues, at an average spacing of approximately 25 nucleotides in mRNAs and 40 nucleotides in tRNAs and rRNAs, and a much smaller number of single U residues (6, 11). In addition, there are 19 reported instances of pairs of RNA residues known or likely to be inserted adjacent to each other (6,12). Physarum mitochondria are distinctive in also performing substitutional editing on a transcript that is insertionally edited: C-to-U conversion occurs at four known sites in the coI mRNA, apparently at a later stage in RNA production (7,8,13).…”