title: 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.
authors.affiliation: Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
authors.forename: Małgorzata
authors.initials: M
authors.lastname: Wojtkowska
authors.forename: Marcin
authors.initials: M
authors.lastname: Jąkalski
authors.forename: Joanna R
authors.initials: JR
authors.lastname: Pieńkowska
authors.forename: Olgierd
authors.initials: O
authors.lastname: Stobienia
authors.forename: Andonis
authors.initials: A
authors.lastname: Karachitos
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Przytycka
authors.forename: January
authors.initials: J
authors.lastname: Weiner
authors.forename: Hanna
authors.initials: H
authors.lastname: Kmita
authors.forename: Wojciech
authors.initials: W
authors.lastname: Makałowski
mesh_terms: D000048:Acanthamoeba / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D004023:Dictyostelium / Q000378:metabolism; D019143:Evolution, Molecular; D005819:Genetic Markers; D016013:Likelihood Functions; D008565:Membrane Proteins / Q000235:genetics*; D051336:Mitochondrial Membranes / Q000378:metabolism*; D008969:Molecular Sequence Data; D010802:Phylogeny; D015800:Protozoan Proteins / Q000235:genetics*; D050994:Voltage-Dependent Anion Channels / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D008565:Membrane Proteins; D015800:Protozoan Proteins; D050994:Voltage-Dependent Anion Channels