An ancestral bacterial division system is widespread in eukaryotic mitochondria

Abstract

Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such as Saccharomyces cerevisiae, mammals, and Arabidopsis thaliana seem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoan Dictyostelium purpureum and the jakobid Andalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.

Keywords: Min proteins; MinCDE; mitochondria; mitochondrial division; mitochondrial fission.

Fig. 1.

Partial schematic overview of division machinery in E. coli. (A) Roles of Min proteins during FtsZ polymerization. (B) Subsequent recruitment of early and late stage proteins involved in Z-ring stabilization and attachment to the cell membrane. (C) Overview of septation initiation at the cell level. Dark-blue rectangles, FtsZ; dark-green circles, MinD; light-blue shapes, late-stage cell-division proteins; light-green circles, MinC; magenta circles, MinE; red shapes, early-stage cell-division proteins. For the sake of clarity, not all proteins known to localize to the mid-cell during division are shown. In particular, this schematic focuses on proteins known to localize to the cytoplasmic membrane and excludes most proteins localizing primarily to the peptidoglycan layer and the outer membrane. Based on reviews in refs. , , and .

Fig. 2.

Presence and absence of bacterial Min proteins and FtsZ in selected eukaryotic taxa. Blue, predicted mitochondrial proteins; gray, no protein found encoded in complete genome data; green, predicted plastid proteins; ?, no protein found encoded in transcriptome or incomplete genome data; *, chromatophore protein; †, predicted pseudogene; ‡, with the exception of Physcomitrella patens. Boxes shaded half blue and half green represent multiple paralogs, predicted to be mitochondrial and plastid, respectively. In cases where only a transcriptome or incomplete genome is available, it should be noted that the presence of a plastid protein does not exclude the possibility of one or more mitochondrial paralogs also being present, and vice versa. Eukaryotic taxa possessing predicted mitochondrial Min proteins are shaded in blue. Mitochondrial or plastid predictions are based on phylogenetic affinity with previously localized proteins, predicted subcellular localization, and localization in yeast (A. incarcerata, D. discoideum). Black circles indicate taxa in which reticulate mitochondria have previously been described; gray circles indicate groups for which reticulate mitochondria have been described in at least one member; black-bordered white circles indicate taxa in which only single or unbranched mitochondria have been described. The schematic phylogeny reflects the current understanding of relationships based on multiple phylogenomic analyses. For a more complete table, see Table S1.

Fig. 3.

Min proteins from D. purpureum (A) and A. incarcerata (B) expressed in S. cerevisiae to confirm predicted mitochondrial targeting. Differential interference contrast (DIC) images of S. cerevisiae cells expressing Min fusion proteins (Left); in green, MinC, MinD, or MinE expressed with the C-terminal GFP tag in S. cerevisiae; in red, mitochondria labeled with MitoTracker Red CMXRos (Mito); merged images (Merge) show mitochondrial localization of all Min proteins. (Scale bars: 5 µm.)

Fig. 4.

Unrooted maximum likelihood (ML) tree of MinD sequences. Phylogenetic analyses were performed on 328 sequences and 226 sites, using RAxML and PhyloBayes. Bootstrap support values greater than 50% and posterior probabilities greater than 0.5 are shown. Branches with 100% bootstrap support and posterior probability of 1.0 are indicated by black circles. Eukaryotes are shaded blue, cyanobacteria green, proteobacteria orange, and α-proteobacteria magenta.

Fig. 5.

Unrooted maximum likelihood (ML) tree of FtsZ sequences. Phylogenetic analyses were performed on 327 sequences and 257 sites, using RAxML and PhyloBayes. Bootstrap support values greater than 50% and posterior probabilities greater than 0.5 are shown. Branches with 100% bootstrap support and posterior probability of 1.0 are indicated by black circles. Eukaryotes are shaded blue, cyanobacteria green, proteobacteria orange, and α-proteobacteria magenta. Eukaryotic paralogs lacking the variable C-terminal spacer region are indicated by stars whereas those with incomplete sequence at the C-terminus are indicated by question marks. The exception to this pattern is a Corethron hystrix sequence that, despite branching with other stramenopiles in the MtFtsZ1 clade, possesses a C-terminal variable region (Fig. S3).