Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants

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Journal titleJournal of Proteomics
Pages400416; # of pages: 17
Subjectglyoxylic acid; hybrid protein; iron; isocitrate lyase; malate synthase; mitochondrial protein; pyruvic acid; sulfur; tricarboxylic acid; ferrous sulfide; isocitrate lyase; malate synthase; mitochondrial DNA; proteome; ribosome protein; amino acid metabolism; amino acid sequence; bioinformatics; biosynthesis; cell nucleus; cell respiration; chemical composition; computer model; data mining; DNA metabolism; DNA replication; DNA transcription; mass spectrometry; mitochondrial targeting signal; molecular evolution; phylogeny; protein analysis; protein degradation; protein domain; protein metabolism; protein targeting; protein transport; RNA metabolism; citric acid cycle; nucleotide metabolism; protist; tandem mass spectrometry; Acanthamoeba castellanii; Amoebozoa; Fungi
AbstractWe present a combined proteomic and bioinformatic investigation of mitochondrial proteins from the amoeboid protist Acanthamoeba castellanii, the first such comprehensive investigation in a free-living member of the supergroup Amoebozoa. This protist was chosen both for its phylogenetic position (as a sister to animals and fungi) and its ecological ubiquity and physiological flexibility. We report 1033 A. castellanii mitochondrial protein sequences, 709 supported by mass spectrometry data (676 nucleus-encoded and 33 mitochondrion-encoded), including two previously unannotated mtDNA-encoded proteins, which we identify as highly divergent mitochondrial ribosomal proteins. Other notable findings include duplicate proteins for all of the enzymes of the tricarboxylic acid (TCA) cycle-which, along with the identification of a mitochondrial malate synthase-isocitrate lyase fusion protein, suggests the interesting possibility that the glyoxylate cycle operates in A. castellanii mitochondria. Additionally, the A. castellanii genome encodes an unusually high number (at least 29) of mitochondrion-targeted pentatricopeptide repeat (PPR) proteins, organellar RNA metabolism factors in other organisms. We discuss several key mitochondrial pathways, including DNA replication, transcription and translation, protein degradation, protein import and Fe-S cluster biosynthesis, highlighting similarities and differences in these pathways in other eukaryotes. In compositional and functional complexity, the mitochondrial proteome of A. castellanii rivals that of multicellular eukaryotes. Biological significance: Comprehensive proteomic surveys of mitochondria have been undertaken in a limited number of predominantly multicellular eukaryotes. This phylogenetically narrow perspective constrains and biases our insights into mitochondrial function and evolution, as it neglects protists, which account for most of the evolutionary and functional diversity within eukaryotes. We report here the first comprehensive investigation of the mitochondrial proteome in a member (A. castellanii) of the eukaryotic supergroup Amoebozoa. Through a combination of tandem mass spectrometry (MS/MS) and in silico data mining, we have retrieved 1033 candidate mitochondrial protein sequences, 709 having MS support. These data were used to reconstruct the metabolic pathways and protein complexes of A. castellanii mitochondria, and were integrated with data from other characterized mitochondrial proteomes to augment our understanding of mitochondrial proteome evolution. Our results demonstrate the power of combining direct proteomic and bioinformatic approaches in the discovery of novel mitochondrial proteins, both nucleus-encoded and mitochondrion-encoded, and highlight the compositional complexity of the A. castellanii mitochondrial proteome, which rivals that of animals, fungi and plants.
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AffiliationNational Research Council Canada; Human Health Therapeutics
Peer reviewedYes
NPARC number21275451
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Record identifierd47df9aa-60b7-4050-827e-0313554dc565
Record created2015-07-14
Record modified2016-05-09
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