Fig 1.
Distribution of BAM domain proteins across the tree of life.
A. BAM domain distribution across the three domains of life. BAM domain proteins are present in all three domains of life, but only plants, animals, and a single fungus contain BAM proteins that are followed by a RING domain. Filled circles indicate many taxa contain at least one BAM protein. Open circles indicate only one or two species were identified with BAM proteins. B. Distribution of MAPL (BAM-RING) in holozoa (clade comprising animals and their closest single-celled relatives), with particular focus on non-vertebrates. Most species contain MAPL, but several instances of loss are recorded. C. Expansion of MAPL in the vertebrate lineage followed by loss in mammals. Multiple MAPL paralogues are present in non-mammalian vertebrates (MAPL2 and MAPL2-like). D. Expansion of MAPL in multicellular plants. Green algae contain a single MAPL whereas multicellular plants have gained a paralogue. The Capsella-Arabidopsis clade has further gained a paralogue that has lost the RING domain (MAPL-R).
Fig 2.
Phylogenetic reconstruction of BAM domain-containing proteins from opisthokonts, archaeplastida, and prokaryotes.
BAM domain-containing protein sequences were aligned using MUSCLE, Sites that could not be aligned with confidence (including the eukaryote-specific RING domains) were removed manually. The resulting alignment was subjected to phylogenetic analysis (see methods section for details). In this analysis, prokaryotic BAM proteins group together to the exclusion of all eukaryote proteins. Thus, the BAM domain-containing proteins present in various eukaryotes cannot be traced to independent HGT events. In this and all following phylogenetic analyses, numerical values represent Bayesian posterior probabilities and maximum-likelihood bootstrap values (Bayesian/PhyML/RAxML). Node values are given to highlight the clades of interest, denoted by coloured boxes and annotated by protein name. All other node support is iconized as inset.
Fig 3.
Phylogenetic analysis of Opisthokont MAPL proteins.
This analysis demonstrates that all vertebrate MAPL proteins group together to the exclusion of all other opisthokont MAPL proteins. MAPL has been retained in all major vertebrate clades. MAPL-like is an ancient vertebrate protein lost in the mammalian lineage. MAPL-like2 is specific to fishes. The RING domain was included in the alignment in this analysis as the vast majority of predicted proteins contained this domain. Node support as in Fig 2.
Fig 4.
Phylogenetic analysis of Archaeplastid MAPL proteins.
This analysis demonstrates that A. thaliana and C. rubella BAM proteins that lack the RING domain group within a weakly supported clade comprising sequences from multicellular plants that retain a RING domain. The RING domain was excluded from this analysis. Node support as in Fig 2.
Fig 5.
Phylogenetic analysis of SAR BAM proteins.
In this analysis the BAM proteins from E. siliculosis and B. natans group with prokaryotic sequences suggesting that these eukaryotic proteins have a different origin than other MAPL and might be derived from recent HGT events. The RING domain was excluded from this analysis. Analysis and node support as in Fig 2.