Phylogenetic Analysis of Mitochondrial Outer Membrane β-Barrel Channels

Abstract

Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have β-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial β-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane β-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta.

Novel TPR-containing subunit of TOM complex functions as cytosolic receptor for Entamoeba mitosomal transport

“…These data indicate that a common ancestor of amoebozoan species also contained Tom40, Tom22, and Tom7 in its TOM complex. This presumption is also supported by the existence of Tom40 homologs in the genome of other amoebozoan species including Polysphondylium 45, and Acanthamoeba 45, and the transcriptome of Mastigamoeba (Stairs, C. and Roger, A., personal communication), and Tom7 homologs in Polysphondylium (EFA78398) and Acanthamoeba (Contig6955 in the Acanthamoeba genome database). However, we did not detect Tom22 homologs in these amoebozoa.…”

Voltage-dependent anion channels: the wizard of the mitochondrial outer membrane

“…The N-terminus itself is currently thought to affect the conductance of ions and metabolites across the membrane as well as the interactions with some effector proteins. The α-β 19 architecture is apparently preserved in other structurally not-yet-characterized mitochondrial OM proteins like the TOM40 component of the pre-protein translocase, the SAM50 subunit of the sorting and assembly machinery and Mdm10 of the endoplasmic reticulum-mitochondria encounter structure (Wojtkowska et al, 2012). Interestingly, the SAM50 and TOM40 transport machineries are not only ubiquitous in eukaryotes like VDAC, but also crucial for its proper biogenesis in the outer mitochondrial membrane.…”

The The TOB/SAM complex composition in mitochondria of Dictyostelium discoideum during progression from unicellularity to multicellularity

“…As a result, additional proteins were identified. In the 600 kDa complex, Tom40 (Wojtkowska et al, 2012) and mitofilin/Mic60 were found (Table 2), the latter for the first time in this study (Table S2 at https://ojs.ptbioch.edu.pl/). Importantly, mitofilin/Mic60 was detected only at the U stage.…”

“…As we had previously predicted the main subunits of the D. discoideum TOB/SAM complex using available genomic and transcriptomic sequences (Wojtkowska et al, 2012;Buczek et al, 2016), we decided to confirm the presence of the Tob55/Sam50 and metaxin subunits at a protein level. The designed polyclonal antibody against Tob55/Sam50 (Materials and Methods) was used to confirm the presence of Tob55/Sam50 in mitochondria of intact cells at the studied stages (Fig.…”