The Dual Origin of the Yeast Mitochondrial Proteome

Abstract

<jats:p>We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.</jats:p>

Genome‐wide analysis of mRNAs targeted to yeast mitochondria

“…We investigated the relationships between the subcellular location of mRNA species and the two phylogenetic classes of mitochondrial proteins described by Karlberg et al (2000). We observed a clear correlation between the MLR value and the origin of the corresponding gene ( Figure 5).…”

Proteomic Approach to Identify Novel Mitochondrial Proteins in Arabidopsis

“…Slightly smaller values were predicted by a different study of the Arabidopsis chloroplast proteome that was based on evolutionary considerations (1,900-2,500 different proteins, Abdallah et al, 2000). In yeast, the size of the mitochondrial proteome is estimated to be in the range of 400 to 500 different proteins (Karlberg et al, 2000;Lithgow et al, 2000), which represents 6.6% to 8.3% of the 6,000 postulated proteins of this organism. Hence, plants seem to have significantly more mitochondrial proteins than yeast, which should be due to the presence of isoforms of several mitochondrial enzymes and to the occurrence of additional mitochondrial functions in plants.…”

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

“…The present genome sequence extends this evidence: phylogenetic analyses of putative genes for seryltRNA synthetase, transcription initiation factor IIB, subunit A of vacuolar ATPase, and a GTP-binding protein place microsporidia as a sister group of fungi with bootstrap supports ranging from 70% to 92% (see Supplementary Information; a systematic phylogenetic analysis of the genome will be presented elsewhere). Genes of putative mitochondrial evolutionary origin in the E. cuniculi genome were systematically sought by comparison with the 423 recently surveyed yeast mitochondrial proteins encoded by the nuclear and the mitochondrial genomes 22 . Twenty-two genes with signi®cant similarity to the yeast genes were identi®ed and phylogenetic analysis showed that six of them are closely related to homologues from a-proteobacteria, the bacterial group from which mitochondria are believed to derive 23 .…”