The Mitochondrial DNA of the Amoeboid Protozoon, Acanthamoeba castellanii: Complete Sequence, Gene Content and Genome Organization

Abstract

In phylogenetic trees based on comparison of nuclear small subunit rRNA sequences, Acanthamoeba castellanii(an amoeboid protozoon) is positioned near the base of the radiation leading to the animals, fungi and plants. However, the specific affiliation of this protist with the major multicellular lineages of eukaryotes is currently uncertain. To further explore the evolutionary position of A. castellanii, we have determined the complete primary sequence of its mitochondrial genome. We find that the circular mtDNA (41,591 bp; 70.6% A+T) encodes two rRNAs (small subunit and large subunit), 16 tRNAs and 33 proteins (17 subunits of the respiratory chain and 16 ribosomal proteins). As well, this genome contains eight open reading frames (ORFs) larger than 60 codons and of undefined function. Two of these ORFs ( orf124and orf142) have homologs in other mtDNAs ( “orf25”and “orfB”,respectively), three are unique to A. castellaniimtDNA ( orf83, orf115and orf349), and three are intronic ORFs. Among notable features of A. castellaniimtDNA are the following: (1) Genes and ORFs are all encoded on the same strand and are tightly packed, with only 6.8% of the total sequence not having an evident coding function and intergenic spacer sequences ranging from only 1 to 616 bp (average 64 bp). Ten pairs of protein-coding genes overlap by up to 38 bp and two subunits of cytochrome oxidase (COX1 and COX2) are specified by a single continuous ORF. (2) Only three introns, all group I and each containing a free-standing ORF, are present; these are localixzed in the 3′-half of the large subunit rRNA gene. (3) The genome encodes fewer than the minimal number of tRNA species required to support mitochondrial protein synthesis, suggesting that additional tRNAs are imported from the cytosol into A. castellaniimitochondria. O f the 16 tRNAs specified by A. castellaniimtDNA (one with an 8-nucleotide anticodon loop), 13 have been shown or are predicted to undergo a novel form of RNA editing within the acceptor stem. (4) A modified genetic code is used in which UGA specifies tryptophan. (5) Repeated sequences and obvious small sequence motifs that might represent regulatory elements are ab sent. In overall size, gene content and organizational pattern, A. castellaniimtDNA most closely resembles the mtDNA of the chlorophycean alga Prototheca wickerhamii(55,326 bp; 74.2% A+T), but is quite different in these respects from the mtDNA of Chlamydomonas reinhardtii(15,758 bp; 54.8% A+T), another chlorophysean alga, as well from characterized animal and fungal mitochondrial genomes. The mtDNAs of A. castellaniiand P. wickerhamiishare with those of land plants a virtually identical set of respiratory and ribosomal protein genes, with a number of these being arranged in the same way. In contrast, C. reinhardtiimtDNA lacks several of the standard respiratory genes and does not encode any ribosomal proteins. In addition, the mitochondrial genomes of A. castellaniiand P. wicker hamii(but not that of C. reinhardtii) contain homologs of two genes ( orf25and orfB) that have previously been found only in land plant mtDNA. These new genomic data provide additional phylogenetic markers linking the mitochondrial genomes of land plants, P. wickerhamiiand A. castellanii, to the exclusion of C. reinhardtii, fungi and animals. We suggest that land plant, P. wickerhamiiand A. castelaniimtDNAs are relatively conservative, slowly evolving genomes that retain a number of ancestral features that were present in a common mitochondrial progenitor. These features have largely been lost in mtDNAs such as that of C. reinhardtii, which appear to have evolved relatively rapidly and radically away from the ancestral pattern.